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  • 1995-1999  (5,372)
  • 1960-1964  (228)
  • 1955-1959  (39)
  • Biochemistry and Biotechnology  (5,554)
  • Phosphorus
  • 1
    Electronic Resource
    Electronic Resource
    Mycorrhizal influence on protein and lipid of durum wheat grown at different soil phosphorus levels (1999)
    Springer
    Mycorrhiza 9 (1999), S. 97-101 
    Details
    ISSN: 1432-1890
    Keywords: Key words Glomus mosseae ; Lipid ; Phosphorus ; Protein ; Seed ; Triticum durum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Root colonization by arbuscular mycorrhizal fungi (AMF) may affect protein and lipid composition of plants by altering P nutrition or by eliciting other metabolic responses in the host plant. This study was conducted to determine the effects of an AMF and soil P on seed protein and lipid contents and yield of two genotypes of durum wheat (Triticum durum L.). Plants were grown in a greenhouse using soil: sand mixes with different levels of P, and with or without the AMF Glomus mosseae [(Nicol. and Gerd.) Gerd. and Trappe]. Percentage AMF root colonization decreased as P added to soil increased. The wheat genotype CR057 had higher AMF root colonization but lower seed P and protein concentrations than CR006. Without added soil P, protein concentration was significantly lower and lipid concentration and seed dry weight higher in arbuscular mycorrhizal (AM) than in nonAM plants. Seed lipid and protein contents were highly correlated with P content of plants. In nonAM plants, seed lipid and protein contents were low with no added soil P and did not differ with added soil P. Seed protein/lipid (Pro/L) concentration ratios of AM plants were higher than those of nonAM plants only when no P was added to the soil. The data indicate different patterns of seed P accumulation and different relationships between seed P and protein and lipid in AM and nonAM plants. Thus, both the presence and degree of AMF root colonization affected seed lipid metabolism in these durum wheat genotypes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050006
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  • 2
    Electronic Resource
    Electronic Resource
    The mycorrhizal status of an emergent aquatic, Lythrum salicaria L., at different levels of phosphorus availability (1999)
    Springer
    Mycorrhiza 9 (1999), S. 191-197 
    Details
    ISSN: 1432-1890
    Keywords: Key words Arbuscular mycorrhizae ; Lythrumsalicaria ; Phosphorus ; Wetland ; Emergent aquatic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The relationship between nutrient availability and mycorrhizal status has been well studied for terrestrial plant species, but has been examined rarely in aquatic and emergent aquatic species. The purpose of this study was to determine the effect of phosphorus availability on the arbuscular mycorrhizal (AM) status of an emergent aquatic, Lythrum salicaria L. L. salicaria was grown in hydroponic sand culture at five phosphorus concentrations (0, 100, 1000, 10 000, and 47 500 μg PO4/l nutrient solution) for 49 days with or without mycorrhizal inoculum obtained from wetland soil. Inoculated plants at the lowest three phosphorus concentrations were colonized by AM, whereas there was no colonization of plants grown at the highest two phosphorus concentrations. Colonization by AM fungi occurred in conjunction with symptoms of phosphorus deficiency in L. salicaria under experimental conditions: plants at the lowest three phosphorus concentrations had lower biomass and higher root: shoot weight ratios than plants at the highest two concentrations. However, total biomass and internal phosphorus concentration did not differ between inoculated and control plants. Further studies are needed under conditions more closely mimicking natural dynamics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050266
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  • 3
    Electronic Resource
    Electronic Resource
    Pisolithus arhizus ectomycorrhiza affects plant competition for phosphorus between Pinus elliottii and Panicum chamaelonche (1999)
    Springer
    Mycorrhiza 9 (1999), S. 199-204 
    Details
    ISSN: 1432-1890
    Keywords: Key words Competition ; Ectomycorrhiza ; External hyphae ; Phosphorus ; Pisolithus arhizus ; Uptake kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Our objective was to evaluate the ability of an ectomycorrhizal fungus to alter the competitive interaction of pine seedlings growing with grass, and to determine whether the interaction was modified by soil-phosphorus (P) concentration. Slash pine (Pinus elliottii), inoculated with the ectomycorrhizal fungus Pisolithus arhizus or fortuitously colonized by Thelephora terrestris, and a native grass (Panicum chamaelonche) were grown in a greenhouse at three P levels (0.32, 3.22, 32.26 μM H3PO4). Pine inoculated with P. arhizus took up more P when competing with the nonmycorrhizal grass than when competing with another pine (irrespective of pine mycorrhizal status). Phosphorus uptake kinetics (Cmin, the minimum concentration at which P can be absorbed from a solution; Imax, the maximum uptake rate) for pine and grass were also determined under hydroponic conditions. Pine had a higher Imax than grass but grass had a lower Cmin, suggesting that pine is more competitive at higher nutrient concentrations while grass is more competitive at lower nutrient concentrations. The controlled conditions used in these experiments allowed us to evaluate specific parameters (P uptake and absorbing surface area) affecting plant competition.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050267
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  • 4
    Electronic Resource
    Electronic Resource
    Nitrogen and phosphorus uptake in two Idaho (USA) headwater wilderness streams (1999)
    Springer
    Oecologia 119 (1999), S. 247-255 
    Details
    ISSN: 1432-1939
    Keywords: Key words Nitrogen ; Phosphorus ; Nutrient spiraling ; Uptake rate and length ; Stream nutrient cycling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nitrate and phosphate solutions were released into two reaches of two central Idaho streams to determine within- and between-stream variability in uptake lengths, uptake rates, and mass transfer coefficients. Physical and biotic stream characteristics and periphyton nitrate-uptake rates in recirculating chambers were measured to determine their influence on nutrient dynamics. Phosphate uptake length did not differ among the four reaches. There were no within-stream differences in nitrate uptake lengths but they did differ between the two streams. Long nitrate uptake lengths likely were due to instream concentrations above saturation but also may have been influenced by differences in active surface area and algal abundance. Nitrate and phosphate uptake lengths were longer, and uptake rates higher, than most other published values. However, mass transfer coefficients were comparable to measurements in other streams. Mass transfer coefficients may be a better parameter for temporal and spatial comparisons of instream nutrient dynamics, and for determining the underlying causes of variability in uptake length.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004420050783
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  • 5
    Electronic Resource
    Electronic Resource
    Importance of epiphytic cyanobacteria as food sources for heterotrophs in a tropical seagrass bed (1999)
    Springer
    Coral reefs 18 (1999), S. 263-271 
    Details
    ISSN: 1432-0975
    Keywords: Key words Syringodium isoetifolium ; Cyanobacteria ; Stable isotopes ; Nitrogen ; Phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences
    Notes: Abstract  The natural carbon and nitrogen stable isotope ratios (δ13C, δ15N) of various autotrophs and heterotrophs were measured in a Syringodium isoetifolium-dominated seagrass bed at Dravuni Island, Fiji to define carbon and nitrogen sources for heterotrophic organisms in a system where few animals graze directly on seagrass leaves. The organic carbon, nitrogen, and phosphorus content of organisms was also determined. The δ13C and δ15N data suggest that herbivorous heterotrophs in this seagrass bed depend significantly on epiphytic cyanobacteria rather than seagrass leaves and its detritus. This can be attributed to relative differences in nitrogen content of those organic materials. The cyanobacteria nitrogen content (3.6–4.8% of DW) is nearly half that of heterotrophs (7.0–8.6% N of DW) while that of S. isoetifolium origin (0.6–1.1% N of DW) is less than one third of the cyanobacteria nitrogen content. Phosphorus content was similar among cyanobacteria (0.8–1.1 mg g-1) and S. isoetifolium (0.4–1.4 mg g-1). These results suggest that cyanobacteria are important food sources for heterotrophs at the study site, and that inorganic nitrogen released through breakdown of cyanobacteria by heterotrophs may support the continued production of S. isoetifolium.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003380050191
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  • 6
    Electronic Resource
    Electronic Resource
    Leucaena hedgerow intercropping and cattle manure application in the Ethiopian highlands I. Decomposition and nutrient release (1999)
    Springer
    Biology and fertility of soils 28 (1999), S. 182-195 
    Details
    ISSN: 1432-0789
    Keywords: Key words Alley cropping ; Calcium ; Magnesium ; Nitrogen ; Phosphorus ; Intercropping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  A litter bag technique was used to study the decomposition and release of N, P, K, Ca, and Mg from Leucaena leucocephala and L. pallida prunings and cattle manure in a hedgerow intercropping trial conducted in the Ethiopian highlands. Hedgerow intercropping (also called alley cropping or alley farming) is an agroforestry system in which trees are grown in dense hedges between alleys where short-cycle crops are grown. The hedges are pruned periodically during the cropping period and the prunings are added to the soil as green manure. Manure was the most resistant to decomposition, losing only 15% of its dry matter (DM) in 15 weeks, compared to 41–57% lost by leucaena prunings. Large quantities of K (up to 104 kg ha–1) were mineralized from prunings and manure, but Ca and Mg were mostly immobilized. More N and P were released from prunings than from manure, which resulted in net immobilization of these nutrients in the initial stages of decomposition and net mineralization in later stages. Between the leucaenas more N was mineralized and less Ca and Mg were immobilized when L. leucocephala prunings were applied than when L. pallida prunings were applied. Fertilizer N increased DM decomposition and N mineralization. Mineralization of the nutrients was constrained by lignin and polyphenol contents. It is concluded that leucaena mulch and cattle manure may be significant sources of N and K for crop growth, but external sources of P, Ca and Mg may be required, particularly in acid soils which have low contents of these nutrients. However, this fertility effect has to be evaluated against the competition effect of trees to predict crop response.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003740050482
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  • 7
    Electronic Resource
    Electronic Resource
    Leucaena hedgerow intercropping and cattle manure application in the Ethiopian highlands II. Maize yields and nutrient uptake (1999)
    Springer
    Biology and fertility of soils 28 (1999), S. 196-203 
    Details
    ISSN: 1432-0789
    Keywords: Key words Alley cropping ; Calcium ; Magnesium ; Nitrogen ; Phosphorus ; Leaf pruning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  The effects of Leucaena leucocephala and L. pallida prunings and cattle manure on maize nutrient uptake and yield were investigated in a hedgerow intercropping trial in the Ethiopian highlands. Hedgerow intercropping (also called alley cropping) is an agroforestry system in which trees are grown in dense hedges between alleys where short-cycle crops are grown. The hedges are pruned periodically during the cropping period and the prunings are added to the soil as green manure. For each leucaena species, the experiment had 16 treatments resulting from a factorial combination of four levels of leucaena leaf prunings (no prunings applied; first prunings applied; first and second prunings applied; first, second and third prunings applied), two levels of air-dried cattle manure (0 and 3 t dry matter ha–1) and two levels of N fertilizer (0 and 40 kg N ha–1 as urea). Uptake of N, P and K increased significantly with application of the three nutrient sources, but uptake of Ca and Mg either did not respond or decreased with application of prunings and manure. All the three factors increased maize grain and stover yields significantly, usually with no significant interactions between the factors. At least two applications of prunings were required to significantly increase nutrient uptake and maize yield. Maize in the row closest to the hedge did not respond to these nutrient inputs. It is concluded that hedgerow intercropping, with or without manure application, can increase crop yields moderately (to 2–3 t ha–1 maize grain yields) in the highlands, but P, Ca and Mg may have to be supplied from external sources if they are deficient in the soil. Additional N is still required for higher yields (〉4 t ha–1 maize grain yields). However, quantification of the competition effects of the trees is also required to confirm these results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003740050483
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  • 8
    Electronic Resource
    Electronic Resource
    Leucaena hedgerow intercropping and cattle manure application in the Ethiopian highlands III. Nutrient balances (1999)
    Springer
    Biology and fertility of soils 28 (1999), S. 204-211 
    Details
    ISSN: 1432-0789
    Keywords: Key words Alley cropping ; Calcium ; Magnesium ; Nitrogen ; Phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  Balances between nutrients applied or mineralized and nutrients removed in maize grain and stover were calculated in a hedgerow intercropping experiment in which Leucaena leucocephala and L. pallida prunings and cattle manure were applied. Hedgerow intercropping (also called alley cropping) is an agroforestry system in which trees are grown in dense hedges between alleys where short-cycle crops are grown. The hedges are pruned periodically during the cropping period and the prunings are added to the soil as green manure. In control treatments, nutrient depletion per season was in the order of 7–19 kg N ha–1, 4–12 kg P ha–1, 10–26 kg K ha–1, 0–2 kg Ca ha–1 and 3–6 kg Mg ha–1. N fertilizer reversed the depletion of N, but it accelerated the depletion of the other nutrients. Manure and at least two applications of leucaena prunings resulted in net positive balances of N, K, and Ca between amounts applied or mineralized and amounts removed by maize. The amounts of P and Mg applied with, or mineralized from, prunings or manure were insufficient to offset the negative balances of these nutrients.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003740050484
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  • 9
    Electronic Resource
    Electronic Resource
    Rainfall effects on erosion of earthworm casts and phosphorus transfers by water runoff (1999)
    Springer
    Biology and fertility of soils 30 (1999), S. 7-13 
    Details
    ISSN: 1432-0789
    Keywords: Key words Earthworm ; Surface casts ; Rainfall events ; Soil erosion ; Phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  We investigated whether, under a temperate climate and in a maize crop, earthworm casts could contribute to soil erosion and further favour the exportation of phosphorus by runoff waters. Recording of casts was made in compacted (wheel-tracks) and non-compacted inter-rows, for a 2-month period in spring. To assess the rainfall impact on cast evolution, half of the observation sites were protected against rain splash by a nylon mesh placed above the soil surface. The water runoff was collected and analysed for sediment contents and phosphorus concentration. The mean annual production of surface casts was calculated to be 34 kg (dry weight) year–1 kg–1 earthworm (fresh weight). Synchronization between cast erosion and rainfall events was shown under natural conditions (unprotected sites). The erosion rate was 4 times greater over rainy periods than dry ones, reaching 80% of cast numbers. It appeared that not the runoff effect but the splash effect, due to the kinetics of the drops, disrupted casts. Newly formed casts disappeared first, with the erosion rate decreasing twofold for casts more than 10 days old. Cast erosion and runoff, as well as worm casting activity, were greater under compacted sites than under non-compacted sites, indicating an influence of earthworms on soil erosion from compacted soils. The total phosphorus content was similar in casts and uningested soil (0.80 mg phosphorus g–1). Potential phosphorus losses from cast erosion was calculated to reach 25–49 mg phosphorus m–2 per rainfall event depending on soil compaction. The amounts of particulate phosphorus recovered in water runoff after each rainfall event varied from 1 mg to 11 mg phosphorus. These results are compared and discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003740050580
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  • 10
    Electronic Resource
    Electronic Resource
    Modelling nutrient fluxes from source to river load: a macroscopic analysis applied to the Rhine and Elbe basins (1999)
    Springer
    Hydrobiologia 410 (1999), S. 123-130 
    Details
    ISSN: 1573-5117
    Keywords: Nitrogen ; Phosphorus ; rivers ; modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In many European rivers, including the major streams of the Rhine and Elbe basins, the nutrient load (N and P) still exceeds target levels. In this paper, a model is presented that describes the river nutrient load as a function of nutrient sources, runoff and lithology in the upstream basin. The model was tested with independent data on nutrient sources (input) and nutrient river load (output) for 130 specific combinations of sub-basins and 5 year periods. A wide range of river systems within the Rhine and Elbe basins were included and the analysis covers a period of 25 years from 1970 to 1995. Most of the observed spatial and temporal variation in the average annual river nutrient load was successfully described by the model. It is therefore concluded that the model can be used to predict the effect of changes in nutrient sources (e.g. reduction of livestock numbers, further improvement of waste water treatment plants etc.) on the average annual nutrient loads of the rivers Rhine, Elbe and their main tributaries.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003783109031
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  • 11
    Electronic Resource
    Electronic Resource
    Intramolecular Donor-Assisted Cyclization of Organotin Compounds (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 887-898 
    Details
    ISSN: 1434-1948
    Keywords: Tin ; Phosphorus ; Intramolecular coordination ; O ligands ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: New intramolecularly coordinated organotin compounds containing the monoanionic O,C,O-coordinating ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}- have been synthesized by substitution reactions starting from organotin halides. In view of the enhanced reactivity of the intramolecularly coordinated compounds {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}SnR2R′ (2, R = Ph, R′ = CH2SiMe3; 3, R = R′ = Ph; 6, R = R′ = Cl), cationic tin species are suggested to occur as intermediates in the formation of the heterocyclic compounds [1(Sn),3(P)-Ph2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (8), [1(Sn), 3(P)-Ph(Me3SiCH2)SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (15), and {[1(Sn),3(P)-Cl2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)]C6H2}2 (16). The latter compounds are formed by intramolecular cyclizations of pentacoordinate cationic tin species under elimination of ethyl halide. Furthermore, the synthesis of [1(Sn),3(P)-Ph2SnOP(O)(OH)-5-tert-Bu-7-P(O)(OH)2]C6H2 (13) is described. Reaction of 8 with an excess of Me3SiBr leads to the unexpected formation of {2-[P(O)(OEt)(OSiMe3)]-4-tert-Bu-6-[P(O)(OEt)2]C6H2}SnPhBr2 (9) as a result of an O-Sn bond cleavage initiated by Me3SiBr and subsequent reaction of the intermediate with further Me3SiBr under Sn-C bond cleavage. The high donor capacity and the rigidity of the new ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}- are demonstrated by X-ray diffraction analyses of the tetraorganotin compound 2 and the monoorganotin trichloride 6. Furthermore, the molecular structures of the 2,3,1-oxaphosphastannoles 8 and 16 are discussed.
    Additional Material: 5 Ill.
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  • 12
    Electronic Resource
    Electronic Resource
    N-Thiophosphorylated and N-Phosphorylated Iminophosphoranes [R3P=N-P(X)R′2; × = O, S] as Models for Dendrimers: Synthesis, Reactivity and Crystal Structures (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 601-611 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Ferrocenes ; Phosphorylated iminophosphoranes ; Dendrimers ; Cations ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several R3P=N-P(X)R′2 and Fe[C5H4Ph2P=N-P(X)R′2]2 derivatives (X = S, O) are readily obtained from Staudinger reactions between phosphanes and N3-P(X)R′2. The P=N-P=X groups are easily alkylated on the × atom with methyl or isopropyl triflates. The alkylation induces a lengthening of the P-X bond, as shown by X-ray diffraction studies. This corresponds to a weakening of the P-X bond which can be cleaved with P(NMe2)3 to yield [P=N-P:] linkages. The presence of tricoordinated phosphorus atoms opens the way to a versatile reactivity, including the reaction with alkyl iodides and functionalized azides. These molecules are good models for screening which types of reagents and reactions could be used with macromolecules possessing also P=N-P=X linkages, such as dendrimers.
    Additional Material: 5 Ill.
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  • 13
    Electronic Resource
    Electronic Resource
    Formation of Calcium-Carbon Bonds From a Lewis Acid-Base Reaction of Calcium Bis[bis(trimethylsilyl)amide] and Tris(trimethylsilylmethyl)alane (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2209-2214 
    Details
    ISSN: 1434-1948
    Keywords: Aluminium ; Amides ; Calcium ; Metallacycles ; Phosphorus ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Treatment of calcium bis[bis(trimethylsilyl)amide] with two equivalents of tris(trimethylsilylmethyl)alane yields (Me3SiCH2)2Al-N(SiMe3)2 (1) and the dimer [(Me3Si)2N-Ca(μ-CH2SiMe3)2Al(CH2SiMe3)2]2 (2). The five-coordinate bridging carbon atoms show Ca-C bond lengths of 264 and 268 pm. A similar reaction with calcium bis[bis(trimethylsilyl)phosphanide] gives the dimer [(Me3SiCH2)2Al-P(SiMe3)2]2 (3) with crystallographic C2 symmetry. A calcium-containing species is not isolable, however, in the presence of DME - ether cleavage reactions and the formation of the centrosymmetric dimer [(Me3SiCH2)2Al-OCH2CH2OMe]2 (4) are observed. The central moiety is an Al2O2 cycle with fivefold coordinated aluminium centers.
    Additional Material: 4 Ill.
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  • 14
    Electronic Resource
    Electronic Resource
    Magnesiation of Triisopropylsilylphosphane: Synthesis and Structures of New Mg2nP2m Polyhedra (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2215-2220 
    Details
    ISSN: 1434-1948
    Keywords: Magnesium ; Metalation ; Phosphorus ; Polyhedra ; X-ray structures ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnesiation of triisopropylsilylphosphane with dibutylmagnesium in toluene yields the octanuclear complex [Mg8(PSiiPr3)6{P(H)SiiPr3}4] (1) which consists of MgPSiiPr3 units forming a hexagonal Mg6P6 prism, with two opposite Mg2P2 moieties capped by additional Mg[P(H)SiiPr3]2 groups. If a small amount of THF is present during the metalation reaction [(THF)4Mg6(PSiiPr3)6] (2) also containing a hexagonal Mg6P6 prism can be isolated. The magnesiation of H2P-SiiPr3 in tetrahydrofuran leads to the formation of the tetrameric complex [(THF)MgPSiiPr3]4(3) with a slightly distorted Mg4P4 cubane-like structure.The structures depend strongly on the steric strain caused by the trialkylsilyl substituents and the neutral coligands at the magnesium center. The highest steric strain, which is induced by coordination to every magnesium atom, leads to the smallest MgnPn polyhedron - the central Mg4P4 heterocubane moiety. In compounds 1 and 2 the hexagonal Mg6P6 prism is formed, however, with reduced steric strain as observed for 2 where the Mg-P bond lengths become more similar.
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  • 15
    Electronic Resource
    Electronic Resource
    The Dramatic Influence of Diamidoamine Ligands on the Structure and Reactivity of Low-Valent Tin and Bismuth Derivatives (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2295-2299 
    Details
    ISSN: 1434-1948
    Keywords: Lewis acids ; Bismuth ; Aluminum ; Phosphorus ; Tin ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dilithium salts of N-methyl-N′,N′′-bis(diisopropyl)- and -(trimethylsilyl)-diethylenetriamine 1a,b react with SnCl2 affording the corresponding stannylenes 2a,b in 60 and 80% yield, respectively. Compound 1b also reacts with BiCl3 to give the bismuth chloride 5 (90% yield). Derivatives 2b and 5 have a symmetrical bicyclic structure and are monomeric both in solution and in the solid state. When 2b is treated with BiCl3 or PCl3, an oxidation reaction leads to the hypercoordinated tin(IV) dichloride 3 (58% yield), or a transmetallation gives rise to the oniophosphane 4 (95% yield), respectively. Transmetalation reactions also occurred when 5 was treated with AlCl3, GaCl3 or SnCl2 affording the corresponding aluminum chloride 6 (81% yield), gallium chloride 7 (38% yield) or tin dichloride 3 (38% yield). The observed reactivity for 2 and 5 is compared to that reported for Veith's stannylene or bismuth chloride.
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  • 16
    Electronic Resource
    Electronic Resource
    Synthesis and Homomolecular Metalation of Trialkylsilylphosphanides of Calcium and Barium (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 743-750 
    Details
    ISSN: 1434-1948
    Keywords: Arsenic ; Barium ; Calcium ; Metalations ; NMR spectroscopy ; Phosphorus ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Metalation of triisopropylsilylphosphane with bis(tetrahydrofuran-O)calcium bis[bis(trimethylsilyl)amide] in tetrahydropyran (thp) in a molar ratio of 3:2 yields (Me3Si)2NCa[μ-P(H)SiiPr3]3Ca(thp)3 (1) containing a trigonal-bipyramidal Ca2P3 core, the metal atoms occupying apical positions. Reaction of two equivalents of triisopropylsilylphosphane or -arsane with bis(tetrahydrofuran-O)barium bis[bis(trimethylsilyl)amide] in tetrahydrofuran gives the corresponding bis(phosphanide) 2 and bis(arsanide) 3, compounds of the type (thf)3Ba[μ-E(H)SiiPr3]Ba(thf)2E(H)SiiPr3 with E = P, As. The equimolar reaction of (tri-tert-butylsilyl)phosphane with (thf)2Ba[N(SiMe3)2]2 in toluene yields heteroleptic dimeric (thf)2Ba[N(SiMe3)2][P(H)SitBu3] (4). Addition of a further equivalent of H2PSitBu3 leads to the formation of homoleptic (thf)nBa[P(H)SitBu3]2 (5). Dissolution of the latter in aromatic hydrocarbons leads to the elimination of H2PSitBu3, yielding dimeric (thf)Ba3(PSitBu3)2[P(H)SitBu3]2 (6). The inner core of 6 consists of the tetramer (BaPSitBu3)4 based on a Ba4P4 heterocubane unit, two opposite faces being capped with (thf)Ba[P(H)SitBu3]2 molecules.
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  • 17
    Electronic Resource
    Electronic Resource
    Cobalt Complexes with 1,3-Bis(trimethylsilyl)cyclopentadienyl and Substituent-Free Pn Ligands (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 945-949 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Pn ; C5H3(SiMe3)2 ligands ; Cobalt ; Coordination chemistry ; Crystallography ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermal or photochemical reaction of [Cp′′Co(CO)2] (1) [Cp′′ = C5H3(SiMe3)2-1,3] with white phosphorus (P4) gives [{Cp′′Co}2(P5-P5){CoCp′′}2] (2) and [{Cp′′Co}3P4(μ-CO)] (3) as well as [{Cp′′Co}2(μ-η2:η2-P2)2] (4). Cobalt complexes 2, 3, and 4 have been characterized by an X-ray crystal-structure determination.
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  • 18
    Electronic Resource
    Electronic Resource
    Insights into the Staudinger Reaction: Experimental and Theoretical Studies on the Stabilization of cis-Phosphazides (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1659-1664 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Iminophosphorane ; Staudinger reaction ; Heterocycles ; Ab initio calculations ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Staudinger-model reaction H3P (1) + HN3 (2) → H3P=NH (5) + N2 (6) has been investigated at the CCSD(T)/6-31G**//MP2(Full)/6-31G* level. Primary products formed in this reaction are the phosphazides H3P=N-N=NH (3) which exist as trans and cis isomers. In contrast to some previous assumptions, cis -3is 8.2 kcal mol-1 more stable than trans -3 but decomposes rather easily into the expected products H3P=NH and N2. This decomposition can be effectively hampered by intramolecular donor-acceptor interactions as shown by calculations on model compounds as well as by experiments. Thus the reaction of a methylene-σ3,λ3-phosphanyl-σ5,λ5-phosphorane with PhN3 led to a new four-membered heterocycle containing a thermally remarkable stable cis-phosphazide moiety.
    Additional Material: 4 Ill.
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  • 19
    Electronic Resource
    Electronic Resource
    Synthesis and Characterisation of tetrahedro-Tetraphosphorus Complexes of Rhenium - Evidence for the First Bridging Complex of White Phosphorus (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 931-933 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Rhenium ; 31P-NMR spectroscopy ; Tripodal polyphosphanes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reaction of white phosphorus with [(triphos)Re(CO)2(OTf)] (1) in dichloromethane affords the new tetraphosphorus complex [(triphos)Re(CO)2(η1-P4)](OTf) (2) [triphos = MeC(CH2PPh2)3; OTf = OSO2CF3]. Compound 2 reacts with a second equivalent of 1 to give the binuclear complex [{(triphos)Re(CO)2}2(μ,η1,η1-P4)](OTf)2 (3) in which a tetrahedro-P4 ligand behaves as tethering unit between two [(triphos)Re(CO)2]+ moieties. Complexes 2 and 3 represent the first soluble metal complexes of the tetraphosphorus molecule where the P4 ligand has not undergone any major modification.
    Additional Material: 1 Ill.
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  • 20
    Electronic Resource
    Electronic Resource
    Synthesis, X-ray Crystal Structures and Reactivity Towards Alkynes of Gold(I)-Phosphinine Complexes (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2233-2241 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Heterocycles ; Phosphinines ; Gold ; Cycloadditions ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The coordination behaviour of 2,6-disilyl-substituted phosphinines towards gold(I) has been examined. The reaction of the bis(trimethylsilyl)phosphinine 1 with [AuCl(SMe2)] gives the corresponding AuCl derivative 2. X-ray crystal structure analysis reveals that the aromaticity of the phosphinine ring is slightly reduced as a result of the poor π-back bonding ability of the AuCl fragment. The same phenomenon is observed in the cationic complex [Au(1)2][GaCl4] (3) which was readily prepared by reaction of two equivalents of 1 with [AuCl(SMe2)] followed by treatment with GaCl3 at low temperature. Reaction of 2,6-bis(phenylethynyldimethylsilyl)phosphinine (4) with the same precursor leads similarly to the complex [AuCl(4)] (5). Interestingly, this complex dimerizes upon crystallization to give the bis(phosphabarrelene) complex 6, also structurally characterized. The formation of 6 results from a [4 + 2] cycloaddition between one alkynyl group of each phosphinine with the other phosphinine subunit. The formation of the cationic complex [Au(4)][GaCl4] (8) occurs under classical conditions but it disproportionates to give the cationic complex [Au(4)2][GaCl4] (9) and colloidal gold deposition. The formation of 9 has been ascertained by treating 8 with one equivalent of ligand 4. Additionally, 9 can also be obtained in a straightforward fashion by treating two equivalents of 4 with [AuCl(SMe2)] followed by treatment with GaCl3 at low temperature. The structure of 9 has been elucidated. Despite a particular arrangement of the alkyne groups which encapsulate the gold coordination sphere, no gold-alkyne interactions are visible.
    Additional Material: 5 Ill.
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  • 21
    Electronic Resource
    Electronic Resource
    Studies of iron transport by arbuscular mycorrhizal hyphae from soil to peanut and sorghum plants (1998)
    Springer
    Mycorrhiza 8 (1998), S. 35-39 
    Details
    ISSN: 1432-1890
    Keywords: Key words Arbuscular mycorrhiza ; Iron ; Peanut ; Phosphorus ; Sorghum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The influence of an arbuscular mycorrhizal (AM) fungus on phosphorus (P) and iron (Fe) uptake of peanut (Arachis hypogea L.) and sorghum (Sorghum bicolor L.) plants was studied in a pot experiment under controlled environmental conditions. The plants were grown for 10 weeks in pots containing sterilised calcareous soil with two levels of Fe supply. The soil was inoculated with rhizosphere microorganisms only or with rhizosphere microorganisms together with an AM fungus (Glomus mosseae [Nicol. & Gerd.] Gerdemann & Trappe). An additional small soil compartment accessible to hyphae but not roots was added to each pot after 6 weeks of plant growth. Radiolabelled P and Fe were supplied to the hyphae compartment 2 weeks after addition of this compartment. After a further 2 weeks, plants were harvested and shoots were analysed for radiolabelled elements. In both plant species, P uptake from the labelled soil increased significantly more in shoots of mycorrhizal plants than non-mycorrhizal plants, thus confirming the well-known activity of the fungus in P uptake. Mycorrhizal inoculation had no significant influence on the concentration of labelled Fe in shoots of peanut plants. In contrast, 59Fe increased in shoots of mycorrhizal sorghum plants. The uptake of Fe from labelled soil by sorghum was particularly high under conditions producing a low Fe nutritional status of the plants. These results are preliminary evidence that hyphae of an arbuscular mycorrhizal fungus can mobilise and/or take up Fe from soil and translocate it to the plant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050208
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  • 22
    Electronic Resource
    Electronic Resource
    Effect of root exudate fractions from P-deficient and P-sufficient onion plants on root colonisation by the arbuscular mycorrhizal fungus Gigaspora margarita (1998)
    Springer
    Mycorrhiza 8 (1998), S. 67-70 
    Details
    ISSN: 1432-1890
    Keywords: Key words Allium cepa ; Appressorium ; Arbuscular mycorrhiza ; Root colonisation ; Phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The effect of root exudates from P-deficient onion on root colonisation by an arbuscular mycorrhizal fungus was examined. Onions (Allium cepa L.) were grown in solution culture at phosphorus concentrations of 0 (P0) and 2 (P2) mg P l–1. Root exudates were collected and fractionated with Amberlite XAD-4 resin to give EtOH and water soluble fractions. Onions inoculated with the arbuscular mycorrhizal fungus Gigaspora margarita Becker & Hall were grown with or without (control) root exudates and exudate fractions in a growth chamber. After 24 days, arbuscular mycorrhiza levels and appressoria formation had increased in plants treated with P0-root exudate or the P0-EtOH fraction when compared to corresponding P2 treatments or control plants. P0 and P2 water-soluble fractions did not significantly affect either aspect of fungal development. These results suggest that hydrophobic compounds found in root exudates from P-deficient onion increase appressorium formation and, therefore, enhance mycorrhiza development.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050214
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  • 23
    Electronic Resource
    Electronic Resource
    Patterns of arbuscular mycorrhiza colonisation of the roots of Hyacinthoides non-scripta after disruption of soil mycelium (1998)
    Springer
    Mycorrhiza 8 (1998), S. 87-91 
    Details
    ISSN: 1432-1890
    Keywords: Key words Acaulospora ; Hyacinthoides non-scripta ; Bluebell ; Disturbance ; Glomus ; Fine endophytes ; Phosphorus ; Scutellospora
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Early-season colonisation of new roots of Hyacinthoides non-scripta (L.) Chouard ex Rothm. was investigated to determine how arbuscular mycorrhizal symbiosis is re-established after the annual root system is shed. During the rootless phase in summer, colonies of bulbs were removed and replanted after the soil around and below the bulb had been mixed (major disturbance) so as to disrupt the external mycelium of arbuscular mycorrhizal (AM) fungi. As a minor disturbance treatment, top soil was removed, bulbs were turned or not in their growth position with as little other disturbance as possible, and the top soil replaced. Control plants were left undisturbed. Half of the plants were harvested 3–4 weeks after the onset of root emergence. Populations of all AM fungi in roots were greatly reduced by major disturbance, whilst those in other treatments and controls were unaffected. At the second harvest, in spring, when shoots had emerged, root colonisation by fine endophytes and Scutellospora morphotypes developed in all treatments, whereas that of Acaulospora morphotypes remained low after major disturbance. Disturbance treatments delayed the appearance, at the second harvest, of mycorrhizas with degenerate arbuscules. Leaf phosphorus concentration was unaffected by soil disturbance, possibly due to partial recovery of AM fungal populations or buffering by resources stored in the bulb.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050217
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  • 24
    Electronic Resource
    Electronic Resource
    Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.) (1998)
    Springer
    Theoretical and applied genetics 97 (1998), S. 777-783 
    Details
    ISSN: 1432-2242
    Keywords: Key words Rice ; QTL ; Phosphorus ; Use efficiency ; Deficiency tolerance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Phosphorus (P) deficiency of soils is a major yield-limiting factor in rice production. Increasing the P-deficiency tolerance of rice cultivars may represent a more cost-effective solution than relying on fertilizer application. The objective of this study was to identify putative QTLs for P-deficiency tolerance in rice, using 98 backcross inbred lines derived from a japonica×indica cross and genotyped at 245 RFLP marker loci. Lines were grown on P-deficient soil and P uptake, internal P-use efficiency, dry weight, and tiller number were determined. Three QTLs were identified for dry weight and four QTLs for P uptake, together explaining 45.4% and 54.5% of the variation for the respective traits. Peaks for both traits were in good agreement which was to be expected considering the tight correlation of r=0.96 between dry weight and P uptake. For both traits the QTL linked to marker C443 on chromosome 12 had a major effect. Two of the three QTLs detected for internal P-use efficiency, including the major one on chromosome 12, coincided with QTLs for P uptake; however, whereas indica alleles increased P uptake they reduced P-use efficiency. We concluded that this was not due to the tight linkage of two genes in repulsion but rather due to an indirect effect of P uptake on P-use efficiency. Most lines with high use efficiency were characterized by very low P uptake and dry weight and apparently experienced extreme P-deficiency stress. Their higher P-use efficiency was thus the result of highly sub-optimal tissue-P concentrations and did not represent a positive adaptation to low P availability. The number of tillers produced under P deficiency is viewed as an indirect indicator of P-deficiency tolerance in rice. In addition to the major QTL on chromosome 12 already identified for all other traits, two QTLs on chromosome 4 and 12 were identified for tiller number. Their position, however, coincided with QTLs for tiller number reported elsewhere under P-sufficient conditions and therefore appear to be not related to P-deficiency tolerance. In this study P-deficiency tolerance was mainly caused by differences in P uptake and not in P-use efficiency. Using a trait indirectly related to P-deficiency tolerance such as tiller number, we detected a major QTL but none of the minor QTLs detected for P uptake or dry weight.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050955
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  • 25
    Electronic Resource
    Electronic Resource
    Soil-plant interactions in a neotropical mangrove forest: iron, phosphorus and sulfur dynamics (1998)
    Springer
    Oecologia 115 (1998), S. 553-563 
    Details
    ISSN: 1432-1939
    Keywords: Key words Mangrove species zonation ; Sulfate reduction ; Pyrite formation ; Phosphorus ; Decomposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We examined soil porewater concentrations of sulfate, alkalinity, phosphorus, nitrogen, and dissolved organic carbon and solid phase concentrations of pyrite in relation to mangrove species distributions along a 3.1-km-long transect that traversed a 47.1-km2 mangrove forest in the Dominican Republic. Iron, phosphorus, and sulfur dynamics are closely coupled to the activity of sulfate-reducing bacteria, the primary decomposers in anoxic soils of mangrove ecosystems. Patterns in the chemistry data suggested that sulfate reduction rates and storage of reduced sulfur were greater in the inland basin forest dominated by Laguncularia racemosa than the Rhizophora mangle dominated forest of the lower tidal region. The distribution of Laguncularia was significantly correlated with concentrations of total phosphorus (r= 0.99) and dissolved organic carbon (r= 0.86), alkalinity (r= 0.60), and the extent of sulfate depletion (r= 0.77) in the soil porewater and soil pyrite concentrations (r= 0.72) across the tidal gradient. Leaf tissue chemistry of Laguncularia was characterized by lower C:N and C:P ratios that could fuel the higher rates of decomposition in the Laguncularia-dominated forest. We suggest that a plant-soil-microbial feedback contributes to the spatial patterning of vegetation and soil variables across the intertidal zone of many mangrove forest communities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004420050553
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  • 26
    Electronic Resource
    Electronic Resource
    Nutrient relations in calcareous grassland under elevated CO2 (1998)
    Springer
    Oecologia 116 (1998), S. 67-75 
    Details
    ISSN: 1432-1939
    Keywords: Key words Dinitrogen fixation ; Plant functional types ; legumes ; Nutrient limitation ; Phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Plant nutrient responses to 4 years of CO2 enrichment were investigated in situ in calcareous grassland. Beginning in year 2, plant aboveground C:N ratios were increased by 9% to 22% at elevated CO2 (P 〈 0.01), depending on year. Total amounts of N removed in biomass harvests during the first 4 years were not affected by elevated CO2 (19.9 ± 1.3 and 21.1 ± 1.3 g N m−2 at ambient and elevated CO2), indicating that the observed plant biomass increases were solely attained by dilution of nutrients. Total aboveground P and tissue N:P ratios also were not altered by CO2 enrichment (12.5 ± 2 g N g−1 P in both treatments). In contrast to non-legumes (〉98% of community aboveground biomass), legume C/N was not reduced at elevated CO2 and legume N:P was slightly increased. We attribute the less reduced N concentration in legumes at elevated CO2 to the fact that virtually all legume N originated from symbiotic N2 fixation (%Ndfa ≈ 90%), and thus legume growth was not limited by soil N. While total plant N was not affected by elevated CO2, microbial N pools increased by +18% under CO2 enrichment (P = 0.04) and plant available soil N decreased. Hence, there was a net increase in the overall biotic N pool, largely due increases in the microbial N pool. In order to assess the effects of legumes for ecosystem CO2 responses and to estimate the degree to which plant growth was P-limited, two greenhouse experiments were conducted, using firstly undisturbed grassland monoliths from the field site, and secondly designed `microcosm' communities on natural soil. Half the microcosms were planted with legumes and half were planted without. Both monoliths and microcosms were exposed to elevated CO2 and P fertilization in a factored design. After two seasons, plant N pools in both unfertilized monoliths and microcosm communities were unaffected by CO2 enrichment, similar to what was found in the field. However, when P was added total plant N pools increased at elevated CO2. This community-level effect originated almost solely from legume stimulation. The results suggest a complex interaction between atmospheric CO2 concentrations, N and P supply. Overall ecosystem productivity is N-limited, whereas CO2 effects on legume growth and their N2 fixation are limited by P.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004420050564
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  • 27
    Electronic Resource
    Electronic Resource
    Seasonal mycorrhizal colonization of winter wheat and its effect on wheat growth under dryland field conditions (1998)
    Springer
    Mycorrhiza 8 (1998), S. 139-144 
    Details
    ISSN: 1432-1890
    Keywords: Key words Winter wheat ; Mycorrhiza ; Phosphorus ; Dryland
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A field experiment was conducted to determine the seasonal patterns of arbuscular mycorrhiza (AM) in a dryland winter wheat (Triticum aestivum L.) system and to determine wheat growth and P uptake responses to inoculation with mycorrhizal fungus. Broadcast-incorporated treatments included (1) no inoculation with mycorrhizal fungus, with and without P fertilizer, and (2) mycorrhizal fungal inoculation at a rate of 5000 spores of Glomus intraradices (Schenck and Smith), per 30 cm in each row, with and without fertilizer P. Winter wheat was seeded within a day after treatments were imposed, and roots were sampled at five growth stages to quantify AM. Shoot samples were also taken for determination of dry matter, grain yield and yield components, and N and P uptake. No AM infection was evident during the fall months following seeding, which was characterized by low soil temperature, while during the spring, the AM increased gradually. Increases in wheat grain yields by enhanced AM were of similar magnitude to the response obtained from P fertilization. However, responses differed at intermediate growth stages. At the tillering stage, P uptake was mainly increased by P fertilization but not by fungal inoculation. At harvest, enhanced AM increased P uptake regardless of whether or not fertilizer P was added. The AM symbiosis increased with rising soil temperatures in the spring, in time to enhance late-season P accumulation and grain production.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050226
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  • 28
    Electronic Resource
    Electronic Resource
    Effect of phosphate and the arbuscular mycorrhizal fungus Glomus intraradices on disease severity of root rot of peas (Pisum sativum) caused by Aphanomyces euteiches (1998)
    Springer
    Mycorrhiza 8 (1998), S. 169-174 
    Details
    ISSN: 1432-1890
    Keywords: Key words Peas ; Aphanomyces euteiches ; Phosphorus ; PAGE ; Isozymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The effects of inorganic phosphate levels and the presence of arbuscular mycorrhiza on disease severity of Aphanomyces euteiches in pea roots were studied. Disease severity on roots and epicotyl as well as the oospore number within infected root tissue were correlated with the phosphorus (P) level in the growth medium. The arbuscular mycorrhizal fungus Glomus intraradices increased P uptake and the P concentration in the plant but reduced disease development in peas. Polyacrylamide gel electrophoresis followed by densitometry of glucose-6-phosphate dehydrogenase specific to A.euteiches was used to measure the activity of the pathogen in roots. The enzyme activity increased with disease severity and disease incidence, except in plants supplemented with P at the highest level, where a peak in activity was seen 12 days after inoculation with the pathogen, followed by a decrease in activity. The epicotyl of mycorrhizal plants showed a reduction in disease severity although this part of the plants was not mycorrhizal. Thus, an induced systemic factor may be responsible for increased resistance in mycorrhizal plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s005720050230
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  • 29
    Electronic Resource
    Electronic Resource
    Edaphic factors as determinants for the distribution of intrinsic antibiotic resistance in a cowpea rhizobia population (1998)
    Springer
    Biology and fertility of soils 27 (1998), S. 386-392 
    Details
    ISSN: 1432-0789
    Keywords: Key words Rhizobia ; Cowpea ; Antibiotic resistance ; Phosphorus ; Aluminium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  A large collection of cowpea rhizobia strains was obtained from soil samples collected from either a semi-arid or a tropical rain forest area located at about the same latitude in the north-eastern region of Brazil and evaluated for their intrinsic antibiotic resistance to eight commercial antibiotics. The aim of this study was to correlate antibiotic resistance of native rhizobia strains to edaphic-climatic factors as a way to establish suitable inoculants for specific areas. A large diversity regarding intrinsic antibiotic resistance was found, and 17 clusters were identified as varying from sensitive to gradually resistant up to 500 μg·ml–1 of the antibiotics tested. Clustering analysis did not show any pattern related to the geographic region where isolates have been obtained. On the other hand, an increase in the antibiotic-resistant rhizobia population was associated with an increase in soil P and Al contents. lsolates which were sensitive to spectinomycin, ampicillin, streptomycin, chloramphenicol and tetracycline were present at higher rates in soils devoid of Al. Rhizobia bacteria producing mucus type I (fluid and capable of spreading over the solid media) were found preferentially in soil with Al concentrations up to 36 mg·kg–1, diminishing quickly at higher levels.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003740050448
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  • 30
    Electronic Resource
    Electronic Resource
    Lattice Monte Carlo simulations as link between ab-initio calculations and macroscopic behavior of dopants and defects in silicon (1998)
    Springer
    Journal of computer-aided materials design 5 (1998), S. 81-88 
    Details
    ISSN: 1573-4900
    Keywords: Aggregation ; Arsenic ; Diffusion ; Lattice Monte Carlo ; Phosphorus ; Silicon ; Vacancy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract In this work, we show that lattice Monte Carlo simulations can be used to span the time and distance scales between underlying atomistic processes and macroscopic diffusion behavior. We use ab- initio calculations of binding energies versus configuration to calculate hopping rates of vacancies for use in lattice Monte Carlo (LMC) simulations of diffusion and aggregation in silicon. The LMC simulations consider the biased nature of vacancy hop frequencies in the neighborhood of dopants, with interactions up to sixth-nearest- neighbor distances included. We use these simulations to investigate the expected macroscopic diffusion behavior, as well as the process by which dopant/defect aggregation occurs. Specific phenomena investigated include collective behavior leading to greatly enhanced diffusivity at high doping levels, the time dependence of effective diffusivity due to the formation of dopant/vacancy clusters, and dopant fluxes in the presence of a vacancy gradient.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008689130758
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  • 31
    Electronic Resource
    Electronic Resource
    Comparison of nutrient losses into the water from rainbow trout culture based on fresh Baltic herring, moist and dry diets (1998)
    Springer
    Aquaculture international 6 (1998), S. 441-450 
    Details
    ISSN: 1573-143X
    Keywords: Cage culture ; Dietary lipid ; Dietary water ; Feeding frequency ; Moist diets ; Nitrogen ; Phosphorus ; Rainbow trout (Oncorhynchus mykiss)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The nutrient losses into the water from rainbow trout (Oncorhynchus mykiss) cage culture using locally caught low-fat Baltic herring, herring-based moist diets and fishmeal-based dry diets were estimated. Feeding with herring led to nitrogen and phosphorus losses into the water twice as high as those feeding with dry pellets (78–162 versus 37–39 g N and 15–39 versus 7–18 g P per kg growth). This was supported by direct measurements of ammonia and phosphate excretion. Increasing feeding frequencies resulted in increased nutrient losses irrespective of diet. Increasing dietary lipid level had a more pronounced effect in reducing the expected nutrient losses in dry pellets than herring. The reduction within the herring was approximately 18% on average for nitrogen and 25% for phosphorus losses. Dietary water content did not affect the nutrient losses. © Rapid Science Ltd. 1998
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    URL: http://dx.doi.org/10.1023/A:1009283401505
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  • 32
    Electronic Resource
    Electronic Resource
    Characterization of receptors with a new negative image: Use in molecular docking and lead optimization (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 321-336 
    Details
    ISSN: 0887-3585
    Keywords: surface characterization ; DOCK ; structure-based molecular design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design. Proteins 30:321-336, 1998. © 1998 Wiley-Liss, Inc.
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    Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 352-356 
    Details
    ISSN: 0887-3585
    Keywords: myoglobin ; nitric oxide ; ligand binding ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 Å resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112°. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the Nε atom of histidine64 is located 2.8 Å away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold. Proteins 30:352-356, 1998. © 1998 Wiley-Liss, Inc.
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    A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 372-380 
    Details
    ISSN: 0887-3585
    Keywords: protein modeling ; crystal structure ; conformation change ; prediction ; mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex. Proteins 30:372-380, 1998. © 1998 Wiley-Liss, Inc.
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    Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 388-400 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; free energy perturbation ; thermodynamics integration ; spherical solvent boundary potential ; cell multipole method ; Nosé-Hoover equation ; component analysis ; chymotrypsin inhibitor 2 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ΔΔG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388-400, 1998. © 1998 Wiley-Liss, Inc.
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    Proteolysis as a probe of thermal unfolding of cytochrome C (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 435-441 
    Details
    ISSN: 0887-3585
    Keywords: cytochrome c ; thermal unfolding ; proteolysis ; proteinase K ; thermolysin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent hydrogen exchange experiments on native cytochrome c implicate a sequential unfolding pathway in contrast to a simple two-state process. We have studied the heat-induced unfolding of this protein by using spectroscopic measurements to detect changes in conformation and proteolytic enzyme digestion to identify regions of the protein that are labile. Several spectroscopic profiles were monitored: CD at 222 nm, a measurement of secondary structure change in the protein, the absorbance at 280 nm, involving the local environment of Trp 59, and absorbance at 420 nm, the Soret band of the heme. The apparent Tm values for these probes differ, consistent with an unfolding pathway containing intermediates. The limited digestion by proteinase K is consistent with population of an intermediate state in unfolding. We find a single strong region of cleavage at low temperature with retention of structure in each fragment. Proteins 30:435-441, 1998. © 1998 Wiley-Liss, Inc.
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    Crystallographic and spectroscopic characterization of a molecular hinge: Conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 442-454 
    Details
    ISSN: 0887-3585
    Keywords: venom toxin ; protein-membrane interaction ; X-ray diffraction ; spectroscopy ; quaternary structural change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bothropstoxin I (BthTX-I) from the venom of Bothrops jararacussuis a myotoxic phospholipase A2 (PLA2) homologue which, although catalytically inactive due to an Asp49→Lys substitution, disrupts the integrity of lipid membranes by a Ca2+-independent mechanism. The crystal structures of two dimeric forms of BthTX-I which diffract X-rays to resolutions of 3.1 and 2.1 Å have been determined. The monomers in both structures are related by an almost perfect twofold axis of rotation and the dimer interfaces are defined by contacts between the N-terminal α-helical regions and the tips of the β-wings of partner monomers. Significant differences in the relative orientation of the monomers in the two crystal forms results in “open” and “closed” dimer conformations. Spectroscopic investigations of BthTX-I in solution have correlated these conformational differences with changes in the intrinsic fluorescence emission of the single tryptophan residues located at the dimer interface. The possible relevance of this structural transition in the Ca2+-independent membrane damaging activity is discussed. Proteins 30:442-454, 1998. © 1998 Wiley-Liss, Inc.
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    Structure-based design of model proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 10-20 
    Details
    ISSN: 0887-3585
    Keywords: protein design ; lattice model ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model. Proteins 31:10-20, 1998. © 1998 Wiley-Liss, Inc.
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    Modelling repressor proteins docking to DNA (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 535-549 
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    ISSN: 0887-3585
    Keywords: docking ; protein-DNA ; prediction ; structure ; base recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The docking of repressor proteins to DNA starting from the unbound protein and model-built DNA coordinates is modeled computationally. The approach was evaluated on eight repressor/DNA complexes that employed different modes for protein/ DNA recognition. The global search is based on a protein-protein docking algorithm that evaluates shape and electrostatic complementarity, which was modified to consider the importance of electrostatic features in DNA-protein recognition. Complexes were then ranked by an empirical score for the observed amino acid /nucleotide pairings (i.e., protein-DNA pair potentials) derived from a database of 20 protein/DNA complexes. A good prediction had at least 65% of the correct contacts modeled. This approach was able to identify a good solution at rank four or better for three out of the eight complexes. Predicted complexes were filtered by a distance constraint based on experimental data defining the DNA footprint. This improved coverage to four out of eight complexes having a good model at rank four or better. The additional use of amino acid mutagenesis and phylogenetic data defining residues on the repressor resulted in between 2 and 27 models that would have to be examined to find a good solution for seven of the eight test systems. This study shows that starting with unbound coordinates one can predict three-dimensional models for protein/DNA complexes that do not involve gross conformational changes on association. Proteins 33:535-549, 1998. © 1998 Wiley-Liss, Inc.
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    Influence of protein structure databases on the predictive power of statistical pair potentials (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 139-149 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; statistical potentials ; protein structure database ; assessing protein models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139-149, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 128-138 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; antitumor ; single chain Fv ; variable domains ; X-ray crystallography ; protein structure ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A recombinant Fv construct of the B1 monoclonal antibody that recognizes the LewisY-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the VH and VL domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues VL100 and VH44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023-1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6122 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the LewisY tetrasaccharide, Fuc-Gal-Nag-Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781-3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128-138, 1998. Published 1998 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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    Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 150-159 
    Details
    ISSN: 0887-3585
    Keywords: photosynthetic reaction center ; bacteriorhodopsin ; cytochrome C oxidase ; zipper ; packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Membrane-embedded protein domains frequently exist as α-helical bundles, as exemplified by photosynthetic reaction centers, bacteriorhodopsin, and cytochrome C oxidase. The sidechain packing between their transmembrane helices was investigated by a nearest-neighbor analysis which identified sets of interfacial residues for each analyzed helix-helix interface. For the left-handed helix-helix pairs, the interfacial residues almost exclusively occupy positions a, d, e, or g within a heptad motif (abcdefg) which is repeated two to three times for each interacting helical surface. The connectivity between the interfacial residues of adjacent helices conforms to the knobs-into-holes type of sidechain packing known from soluble coiled coils. These results demonstrate on a quantitative basis that the geometry of sidechain packing is similar for left-handed helix-helix pairs embedded in membranes and coiled coils of soluble proteins. The transmembrane helix-helix interfaces studied are somewhat less compact and regular as compared to soluble coiled coils and tolerate all hydrophobic amino acid types to similar degrees. The results are discussed with respect to previous experimental findings which demonstrate that specific interactions between transmembrane helices are important for membrane protein folding and/or oligomerization. Proteins 31:150-159, 1998. © 1998 Wiley-Liss, Inc.
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    Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 2-33 
    Details
    ISSN: 0887-3585
    Keywords: chevron plot ; energy landscape ; folding funnel ; kinetic trap ; lattice models ; non-Arrhenius behavior ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have “chevron plot” dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponental behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2-33, 1998. © 1998 Wiley-Liss, Inc.
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    Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 49-60 
    Details
    ISSN: 0887-3585
    Keywords: kohonen network ; mitochondrial processing peptidase (MPP) ; mitochondrial intermediate peptidase (MIP) ; neural network ; protein import ; sequence motif ; mitochondrial targeting ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps. Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs. Neural networks were used to define local sequence features around precursor cleavage sites. Proteins 30:49-60, 1998. © 1998 Wiley-Liss, Inc.
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    Don Caspar, TMV, and protein-protein interactions (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 109-112 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    A hybrid sequence approach to the paracelsus challenge (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 136-143 
    Details
    ISSN: 0887-3585
    Keywords: protein design ; protein structure ; circular dichroism ; trifluoroethanol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Inspired by the Paracelsus Challenge of Rose and Creamer (Proteins 19:1-3, 1994), we have designed a protein sequence that is 50% identical to an all-helical protein but is intended to fold into a largely β-sheet structure. Rather than attempt a de novo design, our strategy was to construct a hybrid sequence based on a helical “parent” protein (434 Cro) and a “target” protein with the desired fold (the B1 domain of protein G). The hybrid sequence (Crotein-G) is 50% identical to 434 Cro but is also 62% identical to the B1 domain of protein G. We also created a variant of Crotein-G (ZCrotein-G) that contains a potential His3Cys1 zinc binding site. At low protein concentrations and in the presence of 20% 2,2,2-trifluoroethanol (TFE) (v/v), the circular dichroism spectra of the designed proteins are distinct from that of 434 Cro and similar to that of the B1 domain of protein G. However, the proteins fail to denature in a cooperative manner. Furthermore, aggregation occurs at moderate protein concentrations or in the absence of TFE. Addition of zinc to ZCrotein-G does not promote structure formation. In summary, 434 Cro has been altered to something that may resemble the B1 domain of protein G, but the protein does not adopt a native structure. Proteins 30:136-143, 1998. © 1998 Wiley-Liss, Inc.
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    Monte Carlo simulation of denaturation of adsorbed proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 168-176 
    Details
    ISSN: 0887-3585
    Keywords: denaturation kinetics ; irreversible conformational changes ; metastable states ; folding temperature ; lattice model ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 × 3 × 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first-order law at T 〉 Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first-order kinetics. For the most interesting temperatures, that is, below Tf, the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of values of this rate constant (different values of kr correspond to the transitions to the altered state via different metastable states). Proteins 30:168-176, 1998. © 1998 Wiley-Liss, Inc.
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    Monte Carlo simulation of the kinetics of protein adsorption (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 177-182 
    Details
    ISSN: 0887-3585
    Keywords: adsorption ; irreversible conformational changes ; denaturation rate constant ; kinetic control ; diffusion control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Adsorption of proteins occurs via diffusion toward the interface, actual adsorption, and subsequent irreversible conformational changes resulting in denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kr. Meanwhile, recent Monte Carlo simulations indicate that, in general, the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of this rate constant (physically, different values of kr correspond to the transitions to the altered state via different metastable states). We have calculated the kinetics of irreversible adsorption of proteins with and without distribution of the denaturation rate constant kr in the limits when protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with distribution of kr are found to be close to those with a single-valued rate constant kr provided that the average value of kr in the former case is equal to kr for the latter case. This conclusion holds even for wide distributions of kr. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed. Proteins 30:177-182, 1998. © 1998 Wiley-Liss, Inc.
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    Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 228-231 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; local vs. non-local interactions ; secondary structure prediction ; fragment matching algorithms ; PDB ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: One of the most important questions in the protein folding problem is whether secondary structures are formed entirely by local interactions. One way to answer this question is to compare identical subsequences of proteins to see if they have identical structures. Such an exercise would also reveal a lower limit on the number of amino acids needed to form unique secondary structures. In this context, we have searched the April 1996 release of the Protein Data Bank for sequentially identical subsequences of proteins and compared their structures. We find that identical octamers can have different conformations. In addition, there are several examples of identical heptamers with different conformations, and the number of identical hexamers with different conformations has increased since the previous PDB releases. These observations imply that secondary structure can be formed entirely by non-local interactions and that an identical match of up to eight amino acids may not imply structural similarity. In addition to the larger context of the protein folding problem, these observations have implications for protein structure prediction methods. Proteins 30:228-231, 1998. © 1998 Wiley-Liss, Inc.
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    Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 249-263 
    Details
    ISSN: 0887-3585
    Keywords: antibody-antigen complex ; snake toxin ; protein docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The antibody Mα2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin α, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin α:Mα2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy,1 was docked to models of the variable fragment of the antibody combining site2 by using a method based on surface complementarity and maximization of buried surface area3,4 while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3. Proteins 30:249-263, 1998. © 1998 Wiley-Liss, Inc.
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    Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 287-294 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; side chain contact prediction ; lattice protein models ; CREB-binding protein ; KIX domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 Å. This is to be compared with the estimate of 12.9 Å that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). Proteins 30:287-294, 1998. © 1998 Wiley-Liss, Inc.
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    Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: Strategies and applications (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 74-89 
    Details
    ISSN: 0887-3585
    Keywords: mass spectrometry ; matrix-assisted laser desorption/ionization ; electrospray ; database searching ; gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The entire genomic DNA sequences of a number of prokaryotic and eukaryotic species are now available and many more, including the human genome, will be completed in the near future. The state-of-life of a cell at any given time, however, is defined by its protein composition, i.e., its proteome. Gel electrophoresis, mass spectrometry, and bioinformatics will be important tools for protein and proteome analysis in the post-genome era. Protein identification from electrophoretic gels by mass spectrometric peptide mapping or peptide sequencing combined with sequence database searching is established and has been applied to numerous biological systems. We describe current strategies and selected applications in molecular and cell biology. The next challenges are detailed structure/function analyses, which include studying the molecular composition of multiprotein complexes and characterization of secondary modifications of proteins. The advantages and limitations of a number of mass spectrometry-based strategies designed for microcharacterization of low amounts of protein from electrophoretic gels are discussed and illustrated by examples. Proteins Suppl. 2:74-89, 1998. © 1998 Wiley-Liss, Inc.
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    A fusion protein between serum amyloid A and staphylococcal nuclease - synthesis, purification, and structural studies (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 381-387 
    Details
    ISSN: 0887-3585
    Keywords: serum amyloid A ; fluorescence ; circular dichroism ; acute phase ; denaturation ; nuclease ; amyloidosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We developed a recombinant DNA system to overexpress a fusion protein between the small, minimally soluble acute phase serum protein, serum amyloid A (SAA), and the bacterial enzyme staphylococcal nuclease (SN). This fusion protein is very soluble and is immunoreactive to polyclonal anti-SAA antibodies. Tryptophan fluorescence shows smooth denaturation curves for the fusion protein in guanidinium HCl or potassium thiocyanate. Fluorescence also indicates that only a single tryptophan residue (of the four present) is accessible to iodide quenching and, presumably, is exposed on the surface of the fusion protein. Circular dichroism (CD) shows a significant signal indicating α-helix, which can be attributed to the SAA portion of the molecule; these are the first CD spectral data available for SAA. pH titration shows persistence of helix domains for the fusion protein at pH 3.0, in contrast to the denaturation of SN under the same conditions. (The entire fusion protein shows a random coil pattern below pH 3.0.) By exploiting the structural and solubility properties of SN, this fusion protein has provided the first structural data about SAA - the precursor of the amyloid deposits in secondary amyloidosis. This fusion protein should be useful for further physical and physiologic studies of SAA. Proteins 30:381-387, 1998. © 1998 Wiley-Liss, Inc.
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    The PDP: Past, present, and future (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 1-1 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Direct observation of an altered quaternary-structure transition in a mutant aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 383-390 
    Details
    ISSN: 0887-3585
    Keywords: time-resolved small-angle X-ray scattering ; allosterism ; domain closure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Time-resolved small-angle X-ray scattering (TR-SAXS) was used to monitor the structural changes that occur upon the binding of the natural substrates to a mutant version of the allosteric enzyme aspartate transcarbamoylase from Escherichia coli, in which the creation of a critical link stabilizing the R state of the enzyme is hindered. Previously, SAXS experiments at equilibrium showed that the structures of the unligated mutant enzyme and the mutant enzyme saturated with a bisubstrate analog are indistinguishable from the T and R state structures, respectively, of the wild-type enzyme (Tauc et al., Protein Sci. 3:1998-2004, 1994). However, as opposed to the wild-type enzyme, the combination of one substrate, carbamoyl phosphate, and succinate, an analog of aspartate, did not convert the mutant enzyme into the R state. By using TR-SAXS we have been able to study the transient steady-state during catalysis using the natural substrates rather than the nonreactive substrate analogs. The steady-state in the presence of saturating amount of substrates is a mixture of 60% T and 40% R structures, which is further converted entirely to R in the additional presence of ATP. These results provide a structural explanation for the reduced cooperativity observed with the mutant enzyme as well as for the stimulation by ATP at saturating concentrations of substrates. They also illustrate the crucial role played by domain motions and quaternary-structure changes for both the homotropic and heterotropic aspects of allostery. Proteins 31:383-390, 1998. © 1998 Wiley-Liss, Inc.
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    Structural investigation of C4b-binding protein by molecular modeling: Localization of putative binding sites (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 391-405 
    Details
    ISSN: 0887-3585
    Keywords: complement control protein ; protein modeling ; blood coagulation ; C4b-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one β-chain and seven α-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its α-chains and with protein S through its β-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP α-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the α-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions. Proteins 31:391-405, 1998. © 1998 Wiley-Liss, Inc.
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    Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 406-416 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; Brownian dynamics ; triose phosphate isomerase ; diffusion-control ; similarity index ; rate enhancement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406-416, 1998. © 1998 Wiley-Liss, Inc.
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    Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 434-444 
    Details
    ISSN: 0887-3585
    Keywords: hinge ; structural change ; xylose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a ‘hinge-bending’ motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. © 1998 Wiley-Liss, Inc.
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    Interaction of human SRY protein with DNA: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 417-433 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; sex-determining region Y (SRY) protein ; high mobility group (HMG) box ; DNA-binding proteins ; DNA bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG-DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein-DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG-DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417-433, 1998. © 1998 Wiley-Liss, Inc.
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    Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 453-459 
    Details
    ISSN: 0887-3585
    Keywords: quantum mechanical calculations ; substrate-enzyme interactions ; mutants ; functional role of amino acids ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The enzyme herpes simplex virus type 1 thymidine kinase (HSV1 TK) salvages thymidine into the DNA metabolism of the virus. In the active site, the thymine ring of the nucleoside binds in a pocket, formed by two residues, Tyr-172 and Met-128, in a sandwich-type orientation. To investigate the nature of the thymine-enzyme pocket interactions, we have carried out density functional theory calculations with gradient-corrected exchange-correlation functionals of models of the thymine-HSV1 TK adduct. Our calculations indicate that the role of Met-128 in the substrate fixation is purely steric and hydrophobic, while the substrate-Tyr-172 interaction is essentially electrostatic in nature. These findings are completely consistent with the available catalytic properties of mutants on the 128 position. Proteins 31:453-459, 1998. © 1998 Wiley-Liss, Inc.
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    Electrostatics, allostery, and activity of the yeast chorismate mutase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 445-452 
    Details
    ISSN: 0887-3585
    Keywords: chorismate mutase ; activity ; allosteric ; electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The predicted active site of chorismate mutase of baker's yeast Saccharomyces cerevisiae has been studied by continuum electrostatics, molecular surface/volume calculations, and molecular modeling. Our study shows that despite being subject to an allosteric transition, the enzyme's active-site pocket neither decreased in volume nor deformed significantly in shape between the active R state and the inactive T state. We find that the polar atmosphere in the pocket is responsible for the enzyme's affinity. A single amino acid, Glu23, can adequately account for the atmospheric variation. This residue swings into the active-site pocket from the R state to the T state. In the R state, Glu23 on helix H2 doubly pairs with Arg204 and Lys208 of H11, which is packed against H2. In the T state, a slide occurs between H11 and H2 such that Glu23 can no longer interact with Lys208 and competes with Asp24 for interacting with Arg204. Consequently, Glu23 is found in the T state to couple with Arg157, an active-site residue critical to substrate binding. The tandem sliding of H11 in both monomers profoundly changes the interactions in the dimer interface. The loop between H11 and H12 demonstrates the largest conformational change. Hence, we establish a connection between the allosteric transition and the activity of the enzyme. The conformational change in the transition is suggested to propagate into the active-site pocket via a series of polar interactions that result in polarity reversal in the active-site pocket, which regulates the enzyme's activity. Proteins 31:445-452, 1998. © 1998 Wiley-Liss, Inc.
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    Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 477-485 
    Details
    ISSN: 0887-3585
    Keywords: X-ray structure ; L-chain apoferritin ; metal binding sites ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 Å and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f′′ = 3.6 e-) of cadmium at 1.375 Å, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f′′ = 0.44 e-). Proteins 31:477-485, 1998. © 1998 Wiley-Liss, Inc.
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    The biology workbench - A seamless database and analysis environment for the biologist (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 39-48 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; antigen ; electrostatics ; binding ; finite difference ; Poisson-Boltzmann ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and rotamer counting for the sidechain entropy contribution. Comparison of experimental and calculated results indicate that because of pKa shifts in some of the mutated residues, primarily those involving Aspartate or Glutamate, proton uptake or release occurs in binding. When this effect was incorporated into the binding free energy calculations, the agreement with experiment improved significantly, and resulted in a mean error of about 1.9 kcal/mole. Thus these calculations predict that there should be a significant pH dependence to the change in binding caused by these mutations. The other major contributions to binding energy changes comes from solvation and charge charge interactions, which tend to oppose each other. Smaller contributions come from nonpolar interactions and sidechain entropy changes. The structures of the HyHel-10-HEL complexes with mutant HEL were obtained by modeling, and the effect of the modeled structure on the calculations was also examined. “Knowledge based” modeling and automatic generation of models using molecular mechanics produced comparable results. Proteins 33:39-48, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase KAtomic coordinates have been deposited with the Protein Data Bank, Brookhaven National Laboratory. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 30-38 
    Details
    ISSN: 0887-3585
    Keywords: lactoferrin ; proteinase K ; complex, hydrolysis ; structure ; inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine proteinases such as trypsin, chymotrypsin, and pepsin hydrolyze lactoferrin into two unequal halves while proteinase K divides this protein into two equal halves. In the first step of hydrolysis by proteinase K, the C- and N-lobes, each having a molecular weight of approximately 40 kDa, are generated. In the next step, the lobes are further hydrolyzed into small molecular weight peptides. The proteinase K isolated from the hydrolyzed product does not show enzymatic activity suggesting that the enzyme is inhibited. Furthermore, the hydrolysis experiments on N-lobe and C-lobe showed that the inhibitory fragment came from the C-lobe. The purified lactoferrin fragment was found to be a decapeptide with an amino acid sequence of H2N-Val-Ala-Gln-Gly-Ala-Ala-Gly-Leu-Ala-COOH. The complex formed between proteinase K and lactoferrin fragment was crystallized by microdialysis. The crystals belonged to the monoclinic space group P21with cell dimensions a = 44.4 Å, b = 38.6 Å, c = 79.2 Å, β = 105.8o and Z = 2. The crystal structure has been determined at 2.4 Å resolution. It has been refined to an R factor of 0.163 for 9044 reflections. The Lf-fragment forms several intermolecular interactions with proteinase K. The Ser-224 Oγ and His-57 Nε2 move away to a distance of 3.68 Å in the complex. In the crystal structure, Gln-3I (I indicates inhibitor i.e., lactoferrin fragment) is involved in a direct intermolecular interaction with a symmetry related proteinase K molecule through a strong hydrogen bond with Asp-254. The mode of intermolecular interactions in the complex conformational features of the enzyme and placement of the fragment with respect to the enzyme resemble with the molecular complex of proteinase K with its natural inhibitor PKI3 from wheat. Proteins 33:30-38, 1998. © 1998 Wiley-Liss, Inc.
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    Dictionary of recurrent domains in protein structures (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 88-96 
    Details
    ISSN: 0887-3585
    Keywords: fold classification ; substructures ; Dali ; protein families ; structural similarity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures. Proteins 33:88-96, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 97-106 
    Details
    ISSN: 0887-3585
    Keywords: antigenic peptides ; class I MHC molecules ; HLA-A2 complexes ; hydrogen bonds ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structures of class I major histocompatibility complex (MHC) molecules complexed with antigenic peptides revealed a network of hydrogen bonds between the charged amino- and carboxyl-termini of the peptides and conserved MHC residues at both ends of the peptide binding site. These interactions were shown to contribute substantially to the stability of class I MHC/peptide complexes by thermal denaturation studies using synthetic peptides in which either the amino- or carboxyl-terminal group is substituted by a methyl group. Here we report crystal structures of HLA-A*0201 complexed with these terminally modified synthetic peptides showing that they adopt the same bound conformation as antigenic peptides. A number of variations in peptide conformation were observed for the terminally modified peptides, including in one case, a large conformational difference in four central peptide residues that is apparently caused by the lattice contact. This is reminiscent of the way binding a T-cell receptor changed the conformation of central residues of an MHC-bound peptide. The structures determined identify which conserved hydrogen bonds are eliminated in terminally substituted peptides and suggest an increased energetic importance of the interactions at the peptide termini for MHC-peptide stability. Proteins 33:97-106, 1998. © 1998 Wiley-Liss, Inc.
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    AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 26-42 
    Details
    ISSN: 0887-3585
    Keywords: intermolecular restraints ; solid-state NMR ; symmetric multimer ; branch and bound ; amyloid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of β-amyloid (an ordered aggregate). Proteins 32:26-42, 1998. © 1998 Wiley-Liss, Inc.
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    Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 204-217 
    Details
    ISSN: 0887-3585
    Keywords: rotamer libraries ; energy minimization ; self consistent mean-field theory ; torsion space ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native-like backbone folds and the positioning of side chains upon these backbones. The prediction of side-chain conformation in this context is challenging, because at best only the near-native global fold of the protein is known. To test the effect of displacements in the protein backbones on side-chain prediction for folds generated ab initio, sets of near-native backbones (≤ 4 Å Cα RMS error) for four small proteins were generated by two methods. The steric environment surrounding each residue was probed by placing the side chains in the native conformation on each of these decoys, followed by torsion-space optimization to remove steric clashes on a rigid backbone. We observe that on average 40% of the χ1 angles were displaced by 40° or more, effectively setting the limits in accuracy for side-chain modeling under these conditions. Three different algorithms were subsequently used for prediction of side-chain conformation. The average prediction accuracy for the three methods was remarkably similar: 49% to 51% of the χ1 angles were predicted correctly overall (33% to 36% of the χ1+2 angles). Interestingly, when the inter-side-chain interactions were disregarded, the mean accuracy increased. A consensus approach is described, in which side-chain conformations are defined based on the most frequently predicted χ angles for a given method upon each set of near-native backbones. We find that consensus modeling, which de facto includes backbone flexibility, improves side-chain prediction: χ1 accuracy improved to 51-54% (36-42% of χ1+2). Implications of a consensus method for ab initio protein structure prediction are discussed. Proteins 33:204-217, 1998. © 1998 Wiley-Liss, Inc.
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    Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 119-134 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; proton transfer ; enzyme catalysis ; mutations ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism. Proteins 33:119-134, 1998. © 1998 Wiley-Liss, Inc.
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    Sequence and structure conservation in a protein core (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 358-366 
    Details
    ISSN: 0887-3585
    Keywords: homologous proteins ; superfamilies ; sequence conservation ; protein structure ; protein evolution ; sequence-structure relationships ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In order to study structural aspects of sequence conservation in families of homologous proteins, we have analyzed structurally aligned sequences of 585 proteins grouped into 128 homologous families. The conservation of a residue in a family is defined as the average residue similarity in a given position of aligned sequences. The residue similarities were expressed in the form of log-odd substitution tables that take into account the environments of amino acids in three-dimensional structures. The protein core is defined as those residues that have less then 7% solvent accessibility. The density of a protein core is described in terms of atom packing, which is investigated as a criterion for residue substitution and conservation. Although there is no significant correlation between sequence conservation and average atom packing around nonpolar residues such as leucine, valine and isoleucine, a significant correlation is observed for polar residues in the protein core. This may be explained by the hydrogen bonds in which polar residues are involved; the better their protection from water access the more stable should be the structure in that position. Proteins 33:358-366, 1998. © 1998 Wiley-Liss, Inc.
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    Extraction of geometrically similar substructures: Least-squares and Chebyshev fitting and the difference distance matrix (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 320-328 
    Details
    ISSN: 0887-3585
    Keywords: structural similarity ; optimal superposition ; common substructure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In analysis, comparison and classification of conformations of proteins, a common computational task involves extractions of similar substructures. Structural comparisons are usually based on either of two measures of similarity: the root-mean-square (r.m.s.) deviation upon optimal superposition, or the maximal element of the difference distance matrix. The analysis presented here clarifies the relationships between different measures of structural similarity, and can provide a basis for developing algorithms and software to extract all maximal common well-fitting substructures from proteins.Given atomic coordinates of two proteins, many methods have been described for extracting some substantial (if not provably maximal) common substructure with low r.m.s. deviation. This is a relatively easy task compared with the problem addressed here, i.e., that of finding all common substructures with r.m.s. deviation less than a prespecified threshold. The combinatorial problems associated with similar subset extraction are more tractable if expressed in terms of the maximal element of the difference distance matrix than in terms of the r.m.s. deviation. However, it has been difficult to correlate these alternative measures of structural similarity. The purpose of this article is to make this connection.We first introduce a third measure of structural similarity: the maximum distance between corresponding pairs of points after superposition to minimize this value. This corresponds to fitting in the Chebyshev norm. Properties of Chebyshev superposition are derived.We describe relationships between the r.m.s. and minimax (Chebyshev) deviations upon optimal superposition, and between the Chebyshev deviation and the maximal element of the difference distance matrix. Combining these produces a relationship between the r.m.s. deviation upon optimal superposition and the maximal element of the difference distance matrix. Based on these results, we can apply algorithms and software for finding subsets of the difference distance matrix for which all elements are less than a specified bound, either to select only subsets for which the r.m.s.deviation is less than or equal to a specified threshold, or to select subsets that include all subsets for which the r.m.s. deviation is less than or equal to a threshold. Proteins 33:320-328, 1998. © 1998 Wiley-Liss, Inc.
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    Flexible docking using tabu search and an empirical estimate of binding affinity (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 367-382 
    Details
    ISSN: 0887-3585
    Keywords: ligand-protein docking ; molecular recognition ; tabu search ; empirical scoring function ; binding affinity prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367-382, 1998. © 1998 Wiley-Liss, Inc.
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    Folding-unfolding energy change of a simple sphere model protein and an energy landscape of the folding process (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 408-416 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; potential energy curve ; two state model ; semi-empirical calculation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have calculated the free energy of a spherical model of a protein or part of a protein generated in the way of protein folding. Two spherical models are examined; one is a homogeneous model consisting of only one residue type - hydrophobic. The other is a heterogeneous model consisting of two residue types - strong hydrophobic and weak hydrophobic. Both models show a folding transition state, and the latter model reproduces the trend of the experimental folded-unfolded energy change. The heterogeneous model suggests that in the folding process of a protein of more than 70 residues, a specific region of the protein folds first to form a stable region, then the other residues follow the folding process. The energy landscape of folding of a small protein is approximately a funnel model, whereas a flatter energy landscape is suggested for larger proteins of more than 55-70 residues. Proteins 33:408-416, 1998. © 1998 Wiley-Liss, Inc.
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    Structural model for family 32 of glycosyl-hydrolase enzymes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 383-395 
    Details
    ISSN: 0887-3585
    Keywords: glycosidases ; protein structure prediction ; correlated mutations ; sequence space ; phylogenic relationships ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structural model is presented for family 32 of the glycosyl-hydrolase enzymes based on the beta-propeller fold. The model is derived from the common prediction of two different threading methods, TOPITS and THREADER. In addition, we used a correlated mutation analysis and prediction of active-site residues to corroborate the proposed model. Physical techniques (circular dichroism and differential scanning calorimetry) confirmed two aspects of the prediction, the proposed all-beta fold and the multi-domain structure. The most reliable three-dimensional model was obtained using the structure of neuraminidase (1nscA) as template. The analysis of the position of the active site residues in this model is compatible with the catalytic mechanism proposed by Reddy and Maley (J. Biol. Chem. 271:13953-13958, 1996), which includes three conserved residues, Asp, Glu, and Cys. Based on this analysis, we propose the participation of one more conserved residue (Asp 162) in the catalytic mechanism. The model will facilitate further studies of the physical and biochemical characteristics of family 32 of the glycosyl-hydrolases. Proteins 33:383-395, 1998. © 1998 Wiley-Liss, Inc.
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    Molecular dynamics simulations of epidermal growth factor and transforming growth factor-α structures in water (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 396-407 
    Details
    ISSN: 0887-3585
    Keywords: AMBER ; epidermal growth factor ; transforming growth factor-alpha ; conformation ; receptor binding ; domain movement ; weakly polar interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: AMBER v. 4.1 force field in 1.5 ns NPT molecular dynamics simulations of murine epidermal growth factor (mEGF), human epidermal growth factor (hEGF), and human transforming growth factor-α (hTGF-α) structures with explicit TIP3P solvation were used to investigate differences in backbone stability, changes in secondary structure, interdomain flexibility, and weakly polar interactions. Backbone root mean square deviations of sections of each peptide show that the most stable regions in mEGF and hEGF are the A-, B-, and C-loops, whereas the most stable regions in hTGF-α are the A- and B-loops. The secondary structure in the B-loops of mEGF and hEGF differ significantly from the nuclear magnetic resonance (NMR) structures of mEGF and hEGF. The position and type of turns in the B-loop of mEGF and hEGF increase the interstrand distance of the antiparallel β-sheets thereby disrupting their structure. The interdomain flexibility of simulated hTGF-α structure is greater than in either mEGF or hEGF. The φ, ψ dihedrals of hTGF-α occupy two distinct populations of phase space corresponding to either a C7eq or an α-helical conformation. This change in dihedral angle is stabilized by Phe15 with Arg42 and Phe17 with Arg42 N-π weakly polar interactions that are present only in hTGF-α but not in mEGF or hEGF. Proteins 33:396-407, 1998. © 1998 Wiley-Liss, Inc.
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    Analysis of domain motions by approximate normal mode calculations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 417-429 
    Details
    ISSN: 0887-3585
    Keywords: protein energy surface ; crambin ; lysozyme ; ATCase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The identification of dynamical domains in proteins and the description of the low-frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low-frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low-frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi-rigid domains. The methods are validated by application to three well-studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins. Proteins 33:417-429, 1998. © 1998 Wiley-Liss, Inc.
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    Helix-helix packing angle preferences for finite helix axes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 457-459 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger. Proteins 33:457-459, 1998. © 1998 Wiley-Liss, Inc.
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    A homology model for the human theta-class glutathione transferase T1-1 (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 444-454 
    Details
    ISSN: 0887-3585
    Keywords: hGSTT1-1 ; homology modeling ; menaphthyl sulfate ; dichloromethane ; dehalogenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A manual threading approach is used to model the human glutathione transferase T1-1 based on the coordinates of the related Theta class enzyme T2-2. The low level of sequence identity (about 20%), found in the C-terminal extension in conjunction with a relative deletion of about five residues makes this a challenging modeling problem. The C-terminal extension contributes to the active site of the molecule and is thus of particular interest for understanding the molecular mechanism of the enzyme. Manual docking of known substrates and non-substrates has implicated potential candidates for the T1-1 catalytic residues involved in the dehalogenation and epoxide-ring opening activities. These include the conserved Theta class residues Arg 107, Trp 115, and the conserved GSTT1 subclass residue His 176. Also, the residue at position 234 is implicated in the modulation of T1-1 activity with different substrates between species. Proteins 33:444-454, 1998. © 1998 Wiley-Liss, Inc.
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    Intersubunit hydrogen bond acts as a global molecular switch in Escherichia coli aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 430-443 
    Details
    ISSN: 0887-3585
    Keywords: pyrimidine biosynthesis ; protein crystallography ; allostery ; long-range interactions ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tyr 165 in the catalytic subunit of Escherichia coli aspartate transcarbamoylase (ATCase, EC 2.1.3.2) forms an intersubunit hydrogen bond in the T state with Glu 239 in the 240s loop of a second catalytic subunit, which is broken in the T to R transition. Substitution of Tyr 165 by Phe lowers substrate affinity by approximately an order of magnitude and alters the pH profile for enzyme function. We have determined the crystal structure of Y165F at 2.4 Å resolution by molecular replacement, using a wild-type T state structure as the probe, and refined it to an R value of 25.2%. The Y165F mutation induces a global conformational change that is in the opposite direction to the T to R transition and therefore results in an extreme T state. The two catalytic trimers move closer by ∼0.14 Å and rotate by ∼0.2°, in the opposite direction to the T→R rotation; the two domains of each catalytic chain rotate by ∼2.1°, also in the opposite direction to the T→R transition; and the 240s loop adopts a new conformation. Residues 229 to 236 shift by ∼2.4 Å so that the active site is more open. Residues 237 to 244 rotate by ∼24.1°, altering interactions within the 240s loop and at the C1-C4 and C1-R4 interfaces. Arg 167, a key residue in domain closure and interactions with L-Asp, swings out from the active site to interact with Tyr 197. This crystal structure is consistent with the functional properties of Y165F, expands our knowledge of the conformational repertoire of ATCase, and indicates that the canonical T state does not represent an extreme. Proteins 33:430-443, 1998. © 1998 Wiley-Liss, Inc.
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    A hierarchical method for generating low-energy conformers of a protein-ligand complex (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 475-495 
    Details
    ISSN: 0887-3585
    Keywords: docking ; landscape ; dynamics ; dielectric ; affinity ; binding ; methotrexate ; thermolysin ; dihydrofolate reductase ; HIV protease ; generalized Born ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented. Proteins 33:475-495, 1998. © 1998 Wiley-Liss, Inc.
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    Energy landscape of a native protein: Jumping-among-minima model (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 496-517 
    Details
    ISSN: 0887-3585
    Keywords: energy landscape ; hierarchical conformational substates ; molecular dynamics ; normal mode analysis ; principal component analysis ; jumping-among-minima model ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496-517, 1998. © 1998 Wiley-Liss, Inc.
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    Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 518-534 
    Details
    ISSN: 0887-3585
    Keywords: structure databank ; superfold ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage - whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture - eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518-534, 1998. © 1998 Wiley-Liss, Inc.
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    The slow step of folding of Staphylococcus aureus PC1 β-lactamase involves the collapse of a surface loop rate limited by the Trans to Cis isomerization of a non-proline peptide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 550-557 
    Details
    ISSN: 0887-3585
    Keywords: mutagenesis ; c.d. spectroscopy ; unfolding ; Ω-loop ; molten-globule ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We wished to test the hypothesis that the non proline cis to trans isomerization of the peptide bond at position 167 in the S. aureus β-lactamase PC1 exerts a significant controlling effect on the folding pathway of this enzyme. The previous data presented in support of this hypothesis could not rule out the effect of factors unrelated to non-proline cis/trans isomerization. We have used the plasmid pET9d to direct soluble overproduction of the S. aureus β-lactamase PC1 and a site-directed mutant (Ile 167 to Pro) in Escherichia coli. Following purification the proteins were subjected to a comparative analysis of the kinetics of unfolding and refolding using the techniques of near- and far-UV circular dichroism spectroscopy and fluorescence spectroscopy in conjunction with “double-jump” experiments. Results show that the fully-unfolded I167P mutant enzyme retains 20% of molecules in a fast-refolding form and that slower-refolding molecules fold faster than the recombinant wild-type enzyme. The final stage of folding involves folding of the Ω-loop into a conformation essential for enzymatic activity. In support of the original hypothesis, the folding of this Ω-loop is rate limited by the isomerization of the Glu 166-Ile 167 peptide bond. Proteins 33:550-557, 1998. © 1998 Wiley-Liss, Inc.
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    Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 116-127 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; X-ray crystallography ; essential dynamics ; lysozyme ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consists of an N- and C-terminal domain connected by a long helix. The analysis of the distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates concertedly with the C-terminal domain, while the domain fluctuation with second largest amplitude corresponds to a twisting mode of the two domains, with the N-terminal helix rotating concertedly with the N-terminal domain. For the closure mode, the difference in hinge-bending angle between the most open and most closed X-ray structure along this mode is 49 degrees. In the MD simulation that shows the largest fluctuation along this mode, a rotation of 45 degrees was observed. Although the twisting mode has much less freedom than the closure mode in the distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations. Proteins 31:116-127, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 86
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    Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 558-566 
    Details
    ISSN: 0887-3585
    Keywords: Drosophila melanogaster couch potato protein ; Werner's syndrome ; restrained molecular dynamics ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by “homology distance constraints,” while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good conformational energies and are physically reasonable. The effects of misalignment of the unknown and the template sequences were also explored in order to determine the feasibility of this homology modeling method for distinguishing possible sequence alignments based on considerations of the resulting conformational energies of modeled structures. Differences in the alignments of the unknown and the template sequences result in significant differences in the conformational energies of the calculated homology models. These results suggest that conformational energies and residual constraint violations in these homology-constrained simulated annealing calculations can be used as criteria to distinguish between correct and incorrect sequence alignments and chain folds. Proteins 33:558-566, 1998. © 1998 Wiley-Liss, Inc.
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  • 87
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    Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of β-glucosidase A from Bacillus polymyxa (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 567-576 
    Details
    ISSN: 0887-3585
    Keywords: bacterial cellobiase ; mutated β-glucosidase ; family 1 ; thermoresistance ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The increasing development of the biotechnology industry demands the design of enzymes suitable to be used in conditions that often require broad resistance against adverse conditions. β-glucosidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a well-characterized enzyme, belonging to glycosyl hydrolase family 1. Its natural substrate is cellobiose, but is also active against various artificial substrates. In its native state has an octameric structure. Its subunit conserves the general (α/β)8 barrel topology of its family, with the active site being in a cavity defined along the axis of the barrel. Using random-mutagenesis, we have identified several mutations enhancing its stability and it was found that one them, the E96K substitution, involved structural changes. The crystal structure of this mutant has been determined by X-ray diffraction and compared with the native structure. The only difference founded between both structures is a new ion pair linking Lys96 introduced at the N-terminus of helix α2, to Asp28, located in one of the loops surrounding the active-site cavity. The new ion pair binds two segments of the chain that are distant in sequence and, therefore, this favorable interaction must exert a determinant influence in stabilizing the tertiary structure. Furthermore, analysis of the crystallographic isotropic temperature factors reveals that, as a direct consequence of the introduced ion pair, an unexpected decreased mobility of secondary structure units of the barrel which are proximal to the site of mutation is observed. However, this effect is observed only in the surrounding of one of the partners forming the salt bridge and not around the other. These results show that far-reaching effects can be achieved by a single amino acid replacement within the protein structure. Consequently, the identification and combination of a few single substitutions affecting stability may be sufficient to obtain a highly resistant enzyme, suitable to be used under extreme conditions. Proteins 33:567-576, 1998. © 1998 Wiley-Liss, Inc.
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  • 88
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    Mass spectrometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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  • 89
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    Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase from Desulfovibrio vulgaris hildenborough (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 590-600 
    Details
    ISSN: 0887-3585
    Keywords: [Fe] hydrogenase ; protein-protein interaction ; BIAcore analysis ; crystallization ; cooperativity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrogenases from Desulfovibrio are found to catalyze hydrogen uptake with low potential multiheme cytochromes, such as cytochrome c3, acting as acceptors. The production of Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough was improved with respect to the growth phase and media to determine the best large-scale bacteria growth conditions. The interaction and electron transfer from Fe-only hydrogenase to multiheme cytochrome has been studied in detail by both BIAcore and steady-state measurements. The electron transfer between [Fe] hydrogenase and cytochrome c3 appears to be a cooperative phenomenon (h = 1.37). This behavior could be related to the conductivity properties of multihemic cytochromes. An apparent dissociation constant was determined (2 × 10-7 M). The importance of the cooperativity for contrasting models proposed to describe the functional role of the hydrogenase/cytochrome c3 complex is discussed. Presently, the only determined structure is from [NiFe] hydrogenase and there are no obvious similarities between [NiFe] and [Fe] hydrogenase. Furthermore, no crystallographic data are available concerning [Fe] hydrogenase. The first results on crystallization and X-ray crystallography are reported. Proteins 33:590-600, 1998. © 1998 Wiley-Liss, Inc.
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  • 90
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    Surface properties of adipocyte lipid-binding protein: Response to lipid binding, and comparison with homologous proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 577-589 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; accessible surface area ; fatty acid binding proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Adipocyte lipid-binding protein (ALBP) is one of a family of intracellular lipid-binding proteins (iLBPs) that bind fatty acids, retinoids, and other hydrophobic ligands. The different members of this family exhibit a highly conserved three-dimensional structure; and where structures have been determined both with (holo) and without (apo) bound lipid, observed conformational changes are extremely small (Banaszak, et al., 1994, Adv. Prot. Chem. 45, 89; Bernlohr, et al., 1997, Annu. Rev. Nutr. 17, 277). We have examined the electrostatic, hydrophobic, and water accessible surfaces of ALBP in the apo form and of holo forms with a variety of bound ligands. These calculations reveal a number of previously unrecognized changes between apo and holo ALBP, including: 1) an increase in the overall protein surface area when ligand binds, 2) expansion of the binding cavity when ligand is bound, 3) clustering of individual residue exposure increases in the area surrounding the proposed ligand entry portal, and 4) ligand-binding dependent variation in the topology of the electrostatic potential in the area surrounding the ligand entry portal. These focused analyses of the crystallographic structures thus reveal a number of subtle but consistent conformational and surface changes that might serve as markers for differential targeting of protein-lipid complexes within the cell. Most changes are consistent from ligand to ligand, however there are some ligand-specific changes. Comparable calculations with intestinal fatty-acid-binding protein and other vertebrate iLBPs show differences in the electrostatic topology, hydrophobic topology, and in localized changes in solvent exposure near the ligand entry portal. These results provide a basis toward understanding the functional and mechanistic differences among these highly structurally homologous proteins. Further, they suggest that iLBPs from different tissues exhibit one of two predominant end-state structural distributions of the ligand entry portal. Proteins 33:577-589, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 91
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    Structural models of the bovine papillomavirus E5 protein (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 601-612 
    Details
    ISSN: 0887-3585
    Keywords: platelet-derived growth factor receptor ; E5 protein ; bovine papillomavirus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The bovine papillomavirus E5 protein is thought to be a type II integral membrane protein that exists as a disulfide-linked homodimer in transformed cells. Polarized-infrared measurements show that the E5 dimer in membrane bilayers is largely α-helical and has a transmembrane orientation. Computational searches of helix-helix conformations reveal two possible low-energy dimer structures. Correlation of these results with previous mutagenesis studies on the E5 protein suggests how the E5 dimer may serve as a molecular scaffold for dimerization and ligand-independent activation of the PDGF-β receptor. We propose that on each face of the E5 dimer a PDGF-β receptor molecule interacts directly with Gln17 from one E5 monomer and with Asp33 from the other E5 monomer. This model accounts for the requirement of Gln17 and Asp33 for complex formation and explains genetic results that dimerization of the E5 protein is essential for cell transformation. Proteins 33:601-612, 1998. © 1998 Wiley-Liss, Inc.
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  • 92
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    Dissection of multi-protein complexes using mass spectrometry: Subunit interactions in transthyretin and retinol-binding protein complexes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 3-11 
    Details
    ISSN: 0887-3585
    Keywords: mass spectrometry ; time-of-flight ; nanoflow electrospray ; transthyretin ; retinol binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Complexes formed between transthyretin and retinol-binding protein prevent loss of retinol from the body through glomerular filtration. The interactions between these proteins have been examined by electrospray ionization combined with time-of-flight mass analysis. Conditions were found whereby complexes of these proteins, containing from four to six protein molecules with up to two ligands, are preserved in the gas phase. Analysis of the mass spectra of these multimeric species gives the overall stoichiometry of the protein subunits and provides estimates for solution dissociation constants of 1.9 ± 1.0 × 10-7 M for the first and 3.5 ± 1.0 × 10-5 M for the second retinol-binding protein molecule bound to a transthyretin tetramer. Dissociation of these protein assemblies within the gas phase of the mass spectrometer shows that each retinol-binding protein molecule interacts with three transthyretin molecules. Mass spectral analysis illustrates not only a correlation with solution behavior and crystallographic data of a closely related protein complex but also exemplifies a general method for analysis of multi-protein assemblies. Proteins Suppl. 2:3-11, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 93
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    GLASS: A tool to visualize protein structure prediction data in three dimensions and evaluate their consistency (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 339-351 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; ab initio methods ; fold recognition ; molecular graphics ; model evaluation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: When a protein sequence does not share any significant sequence similarity with a protein of known structure, homology modeling cannot be applied. However, many novel and interesting methods, such as secondary structure prediction, fold recognition, and prediction of long-range interactions, are being developed and have been shown to be reasonably successful in predicting protein structures from sequence data and evolutionary information. The a priori evaluation of the correctness of a prediction obtained by one of these methods is however often problematic. Consequently, it is important to use all available information provided by as many different methods as possible and all the available experimental data about the protein of interest, since the consistency of the results is indicative of the reliability of the prediction. Hence the need has arisen for suitable tools able to compare results provided by different methods and evaluate their consistency. We have therefore constructed GLASS, a general platform to read, visualize, compare, and evaluate prediction results from many different sources and to project these prediction results into three dimensions. In addition, GLASS allows the comparison of selected parameters calculated for a model with the distribution observed in real protein structures, thus providing an easy way to test new methods for evaluating the likelihood of different structural models. GLASS can be considered as a “workbench” for structural predictions useful to both experimentalists and theoreticians. Proteins 30:339-351, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 94
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    IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 357-371 
    Details
    ISSN: 0887-3585
    Keywords: membrane ; protein ; structure ; prediction ; hydrophobicity ; computer ; magainin ; melittin ; 18A ; M2δ ; PGLa ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The lipid bilayer is crucial for the folding of integral membrane proteins. This article presents an empirical method to account for water-lipid interfaces in the insertion of molecules interacting with bilayers. The interactions between the molecule and the bilayer are described by restraint functions designed to mimic the membrane effect. These functions are calculated for each atom and are proportional to the accessible surface of the latter. The membrane is described as a continuous medium whose properties are varying along the axis perpendicular to the bilayer plane. The insertion is analyzed by a Monte Carlo procedure applied to the restraint functions. The method was successfully applied to small α peptides of known configurations. It provides insights of the behaviors of the peptide dynamics that cannot be obtained with statistical approaches (e.g., hydropathy analysis). Proteins 30:357-371, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 18 Ill.
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  • 95
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    Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum modelYury N. Vorobjev is on leave from the Novosibirsk Institute of Bioorganic Chemistry, Novosibirsk, Russia. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 399-413 
    Details
    ISSN: 0887-3585
    Keywords: protein stability ; conformational free energy ; structure discrimination ; molecular dynamics ; molecular surface ; continuum solvent model ; continuum dielectric model ; boundary element method ; protein entropy ; quasi-harmonic approximation ; deliberately misfolded protein structures ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods - SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element - have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances. Proteins 32:399-413, 1998. © 1998 Wiley-Liss, Inc.
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  • 96
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    Statistical mechanics of protein folding by exhaustive enumeration (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 425-437 
    Details
    ISSN: 0887-3585
    Keywords: theory of protein folding ; folding funnel ; folding thermodynamics ; folding kinetics ; conformation space ; sequence/structure compatibility ; thermal denaturation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: It is hard to construct theories for the folding of globular proteins because they are large and complicated molecules having enormous numbers of nonnative conformations and having native states that are complicated to describe. Statistical mechanical theories of protein folding are constructed around major simplifying assumptions about the energy as a function of conformation and/or simplifications of the representation of the polypeptide chain, such as one point per residue on a cubic lattice. It is not clear how the results of these theories are affected by their various simplifications. Here we take a very different simplification approach where the chain is accurately represented and the energy of each conformation is calculated by a not unreasonable empirical function. However, the set of amino acid sequences and allowed conformations is so restricted that it becomes computationally feasible to examine them all. Hence we are able to calculate melting curves for thermal denaturation as well as the detailed kinetic pathway of refolding. Such calculations are based on a novel representation of the conformations as points in an abstract 12-dimensional Euclidean conformation space. Fast folding sequences have relatively high melting temperatures, native structures with relatively low energies, small kinetic barriers between local minima, and relatively many conformations in the global energy minimum's watershed. In contrast to other folding theories, these models show no necessary relationship between fast folding and an overall funnel shape to the energy surface, or a large energy gap between the native and the lowest nonnative structure, or the depth of the native energy minimum compared to the roughness of the energy landscape. Proteins 32:425-437, 1998. © 1998 Wiley-Liss, Inc.
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  • 97
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    Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 232-243 
    Details
    ISSN: 0887-3585
    Keywords: turkey lysozyme ; human lysozyme ; crystal structure ; protein structure ; structure refinement ; protein crystal ; atomic resolution ; rigid-body motion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystal structures of turkey egg lysozyme (TEL) and human lysozyme (HL) were refined by full-matrix least-squares method using anisotropic temperature factors. The refinement converged at the conventional R-values of 0.104 (TEL) and 0.115 (HL) for reflections with Fo 〉 0 to the resolution of 1.12 Å and 1.15 Å, respectively. The estimated r.m.s. coordinate errors for protein atoms were 0.031 Å (TEL) and 0.034 Å (HL). The introduction of anisotropic temperature factors markedly reduced the R-value but did not significantly affect the main chain coordinates. The degree of anisotropy of atomic thermal motion has strong positive correlation with the square of distance from the molecular centroid. The ratio of the radial component of thermal ellipsoid to the r.m.s. magnitude of three principal components has negative correlation with the distance from the molecular centroid, suggesting the domination of libration rather than breathing motion. The TLS model was applied to elucidate the characteristics of the rigid-body motion. The TLS tensors were determined by the least-squares fit to observed temperature factors. The profile of the magnitude of reproduced temperature factors by the TLS method well fitted to that of observed Beqv. However, considerable disagreement was observed in the shape and orientation of thermal ellipsoid for atoms with large temperature factors, indicating the large contribution of local motion. The upper estimate of the external motion, 67% (TEL) and 61% (HL) of Beqv, was deduced from the plot of the magnitude of TLS tensors determined for main chain atoms which were grouped into shells according to the distance from the center of libration. In the external motion, the translational portion is predominant and the contribution of libration and screw motion is relatively small. The internal motion, estimated by subtracting the upper estimate of the external motion from the observed temperature factor, is very similar between TEL and HL in spite of the difference in 54 of 130 amino acid residues and in crystal packing, being suggested to reflect the intrinsic internal motion of chicken-type lysozymes. Proteins 30:232-243, 1998. © 1998 Wiley-Liss, Inc.
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  • 98
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    Mapping the active site of factor Xa by selective inhibitors: An NMR and MD study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 264-274 
    Details
    ISSN: 0887-3585
    Keywords: factor Xa ; serine proteinases ; blood coagulation ; active site inhibitors ; transferred NOE ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of two selective inhibitors, Ac-Tyr-Ile-Arg-Ile-Pro-NH2 and Ac-(4-Amino-Phe)-(Cyclohexyl-Gly)-Arg-NH2, in the active site of the blood clotting enzyme factor Xa was determined by using transferred nuclear Overhauser effect nuclear magnetic resonance (NMR) spectroscopy. They represent a family of peptidic inhibitors obtained by the screening of a vast combinatorial library. Each structure was first calculated by using standard computational procedures (distance geometry, simulated annealing, energy minimization) and then further refined by systematic search of the conformation of the inhibitor docked in the active site and repeating the simulated annealing and energy minimization. The final structure was optimized by molecular dynamics simulations of the inhibitor-complex in water. The NMR restraints were kept throughout the refinement. The inhibitors assume a compact, very well defined conformation, embedded into the substrate binding site not in the same way as a substrate, blocking thus the catalysis. The model allows to explain the mode of action, affinity, and specificity of the peptides and to map the active site. Proteins 30:264-279, 1998. © 1998 Wiley-Liss, Inc.
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  • 99
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    Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomersThe opinions expressed in this article are those of the authors and do not reflect the views or policies of the DHHS or the U.S. Government. The mention of trade names, commercial products, or organizations does not imply endorsement of the U.S. Government. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 159-174 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; flexible docking ; protein-ligand interaction ; induced fit ; structure-based drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Here we dock a ligand onto a receptor surface allowing hinge-bending domain/substructural movements. Our approach mimics and manifests induced fit in molecular recognition. All angular rotations are allowed on the one hand, while a conformational space search is avoided on the other. Rather than dock each of the molecular parts separately with subsequent reconstruction of the consistently docked molecules, all parts are docked simultaneously while still utilizing the position of the hinge from the start. Like pliers closing on a screw, the receptor automatically closes on its ligand in the best surface-matching way. Movements are allowed either in the ligand or in the larger receptor, hence reproducing induced molecular fit. Hinge bending movements are frequently observed when molecules associate. There are numerous examples of open versus closed conformations taking place upon binding. Such movements are observed when the substrate binds to its respective enzyme. In particular, such movements are of interest in allosteric enzymes. The movements can involve entire domains, subdomains, loops, (other) secondary structure elements, or between any groups of atoms connected by flexible joints. We have implemented the hinges at points and at bonds. By allowing 3-dimensional (3-D) rotation at the hinge, several rotations about (consecutive or nearby) bonds are implicitly taken into account. Alternatively, if required, the point rotation can be restricted to bond rotation. Here we illustrate this hinge-bending docking approach and the insight into flexibility it provides on a complex of the calmodulin with its M13 ligand, positioning the hinges either in the ligand or in the larger receptor. This automated and efficient method is adapted from computer vision and robotics. It enables utilizing entire molecular surfaces rather than focusing a priori on active sites. Hence, allows attaining the overall optimally matching surfaces, the extent and type of motions which are involved. Here we do not treat the conformational flexibility of side-chains or of very small pieces of the molecules. Therefore, currently available methods addressing these issues and the method presented here, are complementary to each other, expanding the repertoire of computational docking tools foreseen to aid in studies of recognition, conformational flexibility and drug design. Proteins 32:159-174, 1998. © 1998 Wiley-Liss, Inc.
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  • 100
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    Effects of the T→R transition on the electrostatic properties of E. coli aspartate transcarbamylaseDr. Allewell was supported by the University of Minnesota. The facilities of the Minnesota Supercomputer Center were used for some calculations. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 200-210 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; allostery ; modeling ; signal transduction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Aspartate transcarbamylase is a large (310 kD), multisubunit protein that binds substrates cooperatively and undergoes a large change in quaternary structure when substrates bind. The forces that drive this transition are poorly understood. We evaluated the electrostatic component of these forces by using finite difference and multigrid methods to solve the nonlinear Poisson-Boltzmann equation for complexes of the enzyme with several substrates and substrate analogs. The results have been compared with calculations for the unliganded protein. While pK½ values of most ionizable residues fall within 3 pH units of values for model compounds, 31 have pK½ values that fall outside the range 0-17. Many of these residues are at the active site, where they interact with the highly charged substrate, in the 80s loop or 240s loop or interact with these loops. The pK½ values of eight ionizable residues related by the twofold molecular axes differ by more than 3 pH units, providing additional evidence for asymmetry within the crystal. As in the unliganded structure, a set of residues forms a network in which ionizable groups with Wij values greater than 2 kcal-m-1 are separated by distances greater than 5 Å. Some residues participate in this network in both the unliganded and N-phosphonacetyl-L-aspartate (PALA)-liganded structure, while others are found in only one structure. The network is more extensive in the PALA-liganded structure than in the unliganded structure, but consists of two separate networks in the two halves of the molecule. Proteins 32:200-210, 1998. © 1998 Wiley-Liss, Inc.
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