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  • 2010-2014
  • 1995-1999  (1,350)
  • 1955-1959
  • 1890-1899
  • 1995  (1,350)
  • Biochemistry and Biotechnology  (1,318)
  • Brassica napus
  • Industrial Chemistry
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  • 2010-2014
  • 1995-1999  (1,350)
  • 1955-1959
  • 1890-1899
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  • 1
    ISSN: 1432-2145
    Keywords: Brassica napus ; SLR1 genes ; Pollination ; Stigma-specific
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-2145
    Keywords: Brassica napus ; Brassica oleracea ; Pollen-stigma interaction ; Pollen protein synthesis ; Pollen protein phosphorylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A technique is described which permits the in vivo study of protein synthesis and phosphorylation in the pollen of Brassica spp. during the early stages of the pollen-stigma interaction. In Brassica napus and B. oleracea, compatible pollination is followed by a dramatic activation of protein synthesis in the pollen involving the synthesis of approximately 40 proteins. After incompatible pollinations in B. oleracea, virtually no newly synthesised polypeptides were detected in the pollen except for a small group of high molecular weight proteins which were not normally synthesised during compatible pollinations. Both compatible and incompatible pollinations were followed by the appearance of newly phosphorylated proteins in the pollen; these fell into four distinct groups. In B. oleracea, the number of phosphorylated proteins and the degree of phosphorylation of individual proteins within the four groups differed between compatible and incompatible pollinations. One group of phosphorylated proteins appeared to correspond with the small group of high molecular weight polypeptides which were synthesised in pollen after incompatible pollinations. These findings are discussed in the perspective of cell signalling during the pollen-stigma interaction in Brassica and also in terms of their possible implication in sporophytic self-incompatibility.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1573-1561
    Keywords: Ceutorhynchus assimilis ; cabbage seed weevil ; Coleoptera ; Curculionidae ; Brassica napus ; oilseed rape ; volatiles ; isothiocyanates ; EAG ; SCR ; GC-EAG ; GC-SCR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The response of theCeutorhynchus assimilis antenna to volatiles in air entrainment-derived extracts of oilseed rape,Brassica napus, was studied using coupled gas chromatography (GC)-electroantennography (EAG) and coupled GC-single cell recording (SCR). By means of these techniques and coupled gas chromatography-mass spectrometry (GC-MS), 25 active compounds were identified, including isoprenoids and compounds derived from fatty acids and amino acids. Some of the latter, the isothiocyanates and goitrin, and probably indole and benzyl cyanide, are catabolites of glucosinolates. The electrophysiological activity of the identified compounds was confirmed by EAG using a physiologically discriminating dose, and by SCR studies. The importance of the combined use of the EAG and SCR techniques was demonstrated, since specific olfactory cells were located for five compounds that did not elicit significant EAG responses. The majority of the olfactory cells from which single cell recordings were obtained showed very high specificity, and in numerous recordings there were consistent pairings of specific cell types.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1573-5028
    Keywords: Anther ; Brassica napus ; Brassica rapa ; Ca2+-binding protein ; cDNA cloning ; pollen allergen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Thirteen cDNA clones encoding IgE-binding proteins were isolated from expression libraries of anthers of Brassica rapa L. and B. napus L. using serum IgE from a patient who was specifically allergic to Brassica pollen. These clones were divided into two groups, I and II, based on the sequence similarity. All the group I cDNAs predicted the same protein of 79 amino acids, while the group II predicted a protein of 83 amino acids with microheterogeneity. Both of the deduced amino acid sequences contained two regions with sequence similarity to Ca2+-binding sites of Ca2+-binding proteins such as calmodulin. However flanking sequences were distinct from that of calmodulin or other Ca2+-binding proteins. RNA-gel blot analysis showed the genes of group I and II were preferentially expressed in anthers at the later developmental stage and in mature pollen. The recombinant proteins produced in Escherichia coli was recognized in immunoblot analysis by the IgE of a Brassica pollen allergic patient, but not by the IgE of a non-allergic patient. The cDNA clones reported here, therefore, represent pollen allergens of Brassica species.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1573-5028
    Keywords: Brassica napus ; cold acclimation ; cold-regulated genes ; tonoplast ATPase ; abscisic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA clone, pBN59, was isolated by differential screening of a cDNA library of winter Brassica napus during cold acclimation. Nucleotide sequence of BN59 was found to be homologous to that encoding the 70 kDa subunit of the vacuolar H+-ATPase in plants. Transcripts hybridizing to BN59 accumulated during exposure to low temperatures and to the exogenous application of abscisic acid (ABA). Western blot analyses also indicated an increase in the 70 kDa subunit during cold acclimation. The accumulation of an endomembrane H+-ATPase is consistent with the observation of osmotic adjustment, increases in endogenous ABA and the proliferation of endomembranes during cold acclimation.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 27 (1995), S. 541-551 
    ISSN: 1573-5028
    Keywords: abscisic acid ; Brassica napus ; cold ; drought ; salinity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract During droughting plants activate a number of genes involved in adaptation to water stress. We have isolated one such gene, btg-26, from Brassica napus. Expression of btg-26 is induced in leaf tissue within 72 h of withholding water. At 81% relative water content (RWC), when the plant is just beginning to show signs of wilting, expression is already increased six-fold over levels found in leaf tissue from fully hydrated plants. btg-26 expression reaches a maximum eleven-fold induction at 63% RWC, then transcript levels decrease as RWC continues to drop. btg-26 is also activated in plants exposed to high salinity, low temperature, heat shock and the plant hormone abscisic acid. Analysis of the deduced amino acid sequence revealed similarity to the dehydrogenase family of enzymes. These results suggest that btg-26 encodes a protein whose function may be required early during general osmotic stress in some unknown adaptive metabolic pathway.
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  • 7
    ISSN: 1573-5028
    Keywords: Brassica napus ; cell division cycle ; cyclin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to investigate the role of cell division in plant development, we isolated several plant genes which encode homologues of animal and yeast cell cycle regulators known as cyclins. Through the use of degenerate primers and the polymerase chain reaction (PCR) we isolated a Brassica sequence which showed homology to the ‘cyclin box’ functional domain found within cyclin proteins. Southern blot analysis indicated that Brassica napus has a large number of genes containing cyclin box-related sequences. This was further supported by the isolation of cyclin box sequences from six different genomic clones. In addition, we have isolated two different cyclin cDNA clones, BnCYC1 and BnCYC2, from a Brassica napus shoot apical cDNA library. Both of the cDNA clones contain a ‘destruction box’ regulatory domain similar to animal mitotic cyclins. Northern blot analysis using BnCYC2 shows mRNA levels which correlate well with the level of cell division in various tissues. Messenger RNA abundance was highest in 1–3 mm leaves, root tips and shoot apices. The mRNA detected using BnCYC1 was restricted to young leaves and the shoot apex, suggesting divergent, organ-specific roles for cyclin family members. The results demonstrate that the plant cyclin gene family is more extensive than previously demonstrated and consists of genes expressed in all dividing tissues as well as a subset of developmentally specific members.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Plant molecular biology 27 (1995), S. 863-874 
    ISSN: 1573-5028
    Keywords: Brassica napus ; glucosinolates ; myrosinase ; thioglucoside glucohydrolase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A full-length cDNA clone defining the new myrosinase gene family MC in Brassica napus was isolated and sequenced. Southern hybridization showed that the MC family probably consists of 3 or 4 genes in B. napus. MC genes are expressed in the developing seed, but not in the vegetative tissues investigated. In situ hybridizations to developing seeds showed that the MC genes are expressed in the myrosin cells of the embryo axis and the cotyledons. Complexes with myrosinase and myrosinase-binding protein (MBP) were purified and characterized. Sequencing of peptides from myrosinases occurring in the complexes showed that the 70 kDa myrosinase is encoded by the MC genes, whereas the 65 kDa myrosinase is encoded by the MB genes. This is in contrast to the 75 kDa myrosinase which occurs in free form and is encoded by the MA genes. Deglycosylations of the myrosinase complexes and the free myrosinase showed that the molecular sizes of the myrosinases could be reduced significantly by this treatment, and that the size differences between the different myrosinases are mainly due to differences in glycosylation.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-2242
    Keywords: Brassica napus ; Cruciferin ; Antisense ; Seed storage protein ; Amino-acid composition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The levels of certain essential amino acids, in particular cysteine, lysine and methionine, in the seed storage protein of a commercial spring variety of rape, Brassica napus, have been increased by the introduction of an antisense gene for cruciferin, which is the most abundant storage protein in rapeseed. The antisense construct contained part of the cruA gene in an inverted orientation, and the gene was driven by the 5′ flanking region of the gene for napin such that antisense RNA was expressed in a seed-specific manner. The construct was introduced by Agrobacterium-mediated gene transfer. In self-pollinated seeds (T1 seeds) of transgenic plants there was a reduction in the levels of the α1β1 and α2/3β2/3 subunits of cruciferin, whereas the level of the α4β4 subunit was unchanged. The total protein and lipid contents of transgenic seeds did not differ significantly from that of normal seeds. Seeds with reduced amounts of cruciferin accumulated higher amounts of napin than non-transformed seeds, but the level of oleosin was unaffected. Amino-acid analysis of the seed storage protein revealed that T1 seeds with reduced amounts of cruciferin contained higher relative levels of three essential amino acids, namely, lysine, methionine and cysteine, with increases of 10%, 8% and 32% over the respective levels in non-transgenic seeds (B. napus cv Westar).
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-2242
    Keywords: Aliphatic glucosinolates ; Brassica napus ; Restriction fragment length polymorphism (RFLP) ; Genomic mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report the RFLP mapping of quantitative trait loci (QTLs) which regulate the total seed aliphaticglucosinolate content in Brassica napus L. A population of 99 F1-derived doubled-haploid (DH) recombinant lines from a cross between the cultivars Stellar (low-glucosinolate) and Major (high-glucosinolate) was used for singlemarker analysis and the interval mapping of QTLs associated with total seed glucosinolates. Two major loci, GSL-1 and GSL-2, with the largest influence on total seed aliphatic-glucosinolates, were mapped onto LG 20 and LG 1, respectively. Three loci with smaller effects, GSL-3, GSL-4 and GSL-5, were tentatively mapped to LG 18, LG 4 and LG 13, respectively. The QTLs acted in an additive manner and accounted for 71 % of the variation in total seed glucosinolates, with GSL-1 and GSL-2 accounting for 33% and 17%, respectively. The recombinant population had aliphatic-glucosinolate levels of between 6 and 160 μmoles per g-1 dry wt of seed. Transgressive segregation for high seed glucosinolate content was apparent in 25 individuals. These phenotypes possessed Stellar alleles at GSL-3 and Major alleles at the four other GSL loci demonstrating that low-glucosinolate genotypes (i.e. Stellar) may possess alleles for high glucosinolates which are only expressed in particular genetic backgrounds. Gsl-elong and Gsl-alk, loci which regulate the ratio of individual aliphatic glucosinolates, were also mapped. Gsl-elong-1 and Gsl-elong-2, which control elongation of the α-amino-acid precursors, mapped to LG 18 and LG 20 and were coincident with GSL loci which regulate total seed aliphatic glucosinolates. A third tentative QTL, which regulates side-chain elongation, was tentatively mapped to LG 12. Gsl-alk, which regulates H3CS-removal and side-chain de-saturation, mapped to LG 20.
    Type of Medium: Electronic Resource
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  • 11
    ISSN: 1432-2242
    Keywords: Brassica napus ; Restriction fragment length polymorphism ; Vernalization ; Days-to-flowering ; Linkage map
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Rapeseed cultivars (Brassica napus L.) can be classified into annual and biennial groups according to their requirement for vernalization in order to induce flowering. The genetic control of these phenotypic differences is not well understood, but this information could be valuable for the design of breeding approaches to accelerate rapeseed improvement. In order to map loci controlling this variation, a doubled haploid population, derived from a cross between annual and biennial cultivars, was evaluated for vernalization requirement and days-to-flowering in a replicated field experiment using three treatments: no vernalization, 4 weeks of vernalization and 8 weeks of vernalization. A linkage map of 132 RFLP loci was used to locate loci controlling these traits. Marker segregation in one region of linkage group 9 was strongly associated with the annual/biennial growth habit in the unvernalized treatment and with days-to-flowering in all three treatments. Two other regions with smaller effects on days-to-flowering were also identified.
    Type of Medium: Electronic Resource
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 91 (1995), S. 756-761 
    ISSN: 1432-2242
    Keywords: Brassica napus ; Dwarfing gene ; Bulked segregant analysis ; Near-isogenic lines ; Genetic mapping ; RAPD markers ; RFLP markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We mapped the dwarf Bzh gene in B. napus with RAPD and RFLP markers. Research of the linked markers proceeded in two ways: a random approach through the construction of a detailed genetic map and targeting of the dwarf gene using both near-isogenic lines (NILs) and the bulked segregant analysis (BSA) method. The BSA approach was the most efficient in finding DNA markers linked to Bzh, whereas the efficiency of the NILs approach was limited by a too great similarity of the genetic background between the dwarf donor parent and the recurrent lines. Eight RAPD markers were identified as linked to Bzh, the closest being at 0.8±0.7 cM. The random genetic mapping approach added markers and extended the linkage group containing Bzh. This work represents the first step towards a better understanding of the dwarf mutation, the development of marker-assisted selection, and the cloning of the underlying gene responsible for dwarfing.
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 91 (1995), S. 1129-1136 
    ISSN: 1432-2242
    Keywords: Brassica napus ; somatic hybrids ; protoplast fusion ; Erucic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Novel Brassica napus somatic hybrids have been created through protoplast fusion of B. oleracea var. botrytis and B. rapa var. oleifera genotypes selected for high erucic acid (22:1) content in the seed oil. Fifty amphidiploids (aacc) and one putative hexaploid (aacccc) hybrid were recovered in one fusion experiment. Conversely, only one amphidiploid and numerous regenerates with higher DNA contents were produced in a similar fusion using a different B. rapa partner. Hybridity was confirmed by morphology, isozyme expression, flow cytometry, and DNA hybridization. Analysis of organellar DNA revealed a distinct bias toward the inheritance of chloroplasts from the B. rapa (aa) genome. All amphidiploids set self-pollinated seed. A erucic acid content as high as 57.4% was found in the seed oil of one regenerated plant. Fatty acid composition was stable in the R1 generation and was coupled with increased female fertility. Other novel agronomic characters in the hybrids recovered include large seed size, lodging resistance, and non-shattering seed pods.
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  • 14
    ISSN: 1432-2242
    Keywords: Microspore culture ; Responsiveness genes ; Comparative mapping ; Doubled haploid populations ; Brassica napus ; Segregation distortion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLP segregation analyses were performed on a F2 population and two F1 microspore-derived populations from the same cross between a microspore culture-responsive parent (‘Topas’) and a non-responsive parent (‘Westar’). A total of 145 loci were detected with 87 cDNA clones. Eighty-two markers were common across all three populations. A total of 66 markers was assembled into 18 linkage groups and 16 markers remained unlinked. Segregation distortions were significant for 29% of the markers in the F2 population and 23% and 31% in microspore-derived populations M3 and M5, respectively. An equivalent number of markers showed biased segregation towards each parental allele in the F2 population while more markers showed a significant deviation from the expected Mendelian ratio towards the responsive parent in both microspore-derived populations. Different subsets of markers showed segregation distortions in the three populations indicating that the selective pressures leading to microsporederived plants are different from those acting during selfing of the F1. Linkage groups 1 and 18 were identified as putative chromosomal regions associated with microspore-culture responsiveness.
    Type of Medium: Electronic Resource
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  • 15
    ISSN: 1432-2242
    Keywords: Brassica napus ; DNA mapping ; Leptosphaeria maculans ; Quantitative trait loci ; Restriction fragment length polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We report the tagging of genes involved in blackleg resistance, present in the French cultivar Crésor of B. napus, with RFLP markers. A total of 218 cDNA probes were tested on the parental cultivars Crésor (resistant) and Westar (susceptible), and 141 polymorphic markers were used in a segregating population composed of 98 doubled-haploid lines (DH). A genetic map from this cross was constructed with 175 RFLP markers and allowed us to scan for specific chromosomal associations between response to blackleg infection and RFLP markers. Canola residues infested with virulent strains of Leptosphaeria maculans were used as inoculum and a suspension of pycnidiospores from cultures of L. maculans, including the highly virulent isolate Leroy, was sprayed to increase disease pressure. QTL mapping suggested that a single chromosomal region was responsible for resistance in each of the four environments tested. This QTL accounted for a high proportion of the variation of blackleg reaction in each of the assays. A second QTL, responsible for a small proportion of the variation of blackleg reaction, was present in one of four year-site assays. A Mendelian approach, using blackleg disease ratings for classifying DH lines as resistant or susceptible, also allowed us to map resistance in the region of the highly significant LOD scores observed in each environment by interval mapping. Results strongly support the presence of a single major gene, named LmFr 1 controlling adult plant resistance to blackleg in spring oil-seed rape cultivar Crésor. Several RFLP markers were found associated with LmFr 1.
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 90 (1995), S. 665-670 
    ISSN: 1432-2242
    Keywords: Brassica napus ; Self-incompatibility S-allele ; Interspecific hybridization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Thirty Brassica napus lines have been developed through interspecific hybridization of B. oleracea and B. campestris lines with defined S-allele constitutions. These lines, which represent 29 different S-allele combinations, were tested in a diallel of test-pollinations to determine the activity of the introgressed S-alleles and intergenomic dominance relationships. Some consistent trends were observed: B. oleracea S-alleles high in the dominance series (e.g. S8, S14, S29) were always active in the resynthesized B. napus lines, whereas recessive S-alleles (S2, S15) lost their activity in some test combinations. The B. campestris S-alleles were active in most cases, although 2 alleles were partially inactivated by the recessive B. oleracea allele S15.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 91 (1995), S. 62-67 
    ISSN: 1432-2242
    Keywords: Brassica napus ; Resynthesized rapeseed ; Genetic distance ; Isozymes ; Allozymes ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract It has frequently been suggested to use the resynthesis of rapeseed (Brassica napus) from B. campestris and B. oleracea to broaden its genetic base. The objective of the present study is twofold: (1) to compare the genetic variation within resynthesized rapeseed with a world-wide collection of oilseed rape cultivars, and (2) to compare genetic distances estimated from RFLP markers with distances estimated from a relatively small number of allozyme markers. We investigated 17 resynthesized lines and 24 rapeseed cultivars. Genetic distances were estimated either based on the electrophoresis of seven allozymes, with a total of 38 different bands, or based on RFLP data of 51 probe/enzyme combinations, with a total of 355 different bands. The results of allozyme and RFLP analyses agreed reasonably well. Genetic distances, estimated from two independent sets of RFLP data with 25 and 26 probe/enzyme combinations respectively, were highly correlated; hence about 50 RFLP markers are sufficient to characterize rapeseed material with a large genetic diversity. The cultivars were clustered into three groups: (1) spring rapeseed of European and Northern American origin, (2) winter rapeseed of European and Northern American origin, and (3) rapeseed of Asian origin. Several of the resynthesized rapeseed lines were similar to European winter rapeseed cultivars, whereas others had quite unique patterns. It is concluded, that resynthesized rapeseed is a valuable source for broadening the genetic variation in present breeding material of Brassica napus. However, different lines differ widely in their suitability for this purpose.
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  • 18
    ISSN: 1432-2242
    Keywords: Brassica napus ; RFLP ; Erucic acid genes ; Oil content ; QTL mapping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A F1 microspore-derived DH population, previously used for the development of a rapeseed RFLP map, was analysed for the distribution of erucic acid and seed oil content. A clear three-class segregation for erucic acid content could be observed and the two erucic acid genes of rapeseed were mapped to two different linkage groups on the RFLP map. Although the parents of the segregating DH population showed no significant difference in seed oil content, in the DH population a transgressive segregation in oil content was observed. The segregation closely followed a normal distribution, characteristic of a quantitative trait. Using the program MAPMAKER/QTL, three QTLs for seed oil content could be mapped on three different linkage groups. The additive effects of these QTLs explain about 51% of the phenotypic variation observed for this trait in the DH population. Two of the QTLs for oil content showed a close association in location to the two erucic acid genes, indicating a direct effect of the erucic acid genes on oil content.
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  • 19
    ISSN: 1615-6102
    Keywords: Androgenesis ; Brassica napus ; Microspore culture ; Pollen embryogenesis ; Protein phosphorylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The monoclonal antibody MPM-2, which interacts with a mitosis-specific phosphorylated epitope, has been used to study phosphorylation of proteins in microspores and pollen ofBrassica napus. One- (1-D) and two-dimensional (2-D) immunoblots revealed that MPM-2 recognized a family of phosphorylated proteins in freshly isolated microspores and pollen. The same set of phosphorylated proteins was found after 8 h of culture at embryogenie (32 °C) and non-embryogenic (18 °C) conditions. Two major spots were observed on 2-D immunoblots, one of which (Mr≈75 kDa, pI≈5.1) co-localized with the 70 kDa heat shock protein. Immunolabelling of sectioned microspores and pollen showed that MPM-2 reactive epitopes were predominantly observed in the nucleoplasm from G1 until G2-phase, and in the cytoplasm during mitosis. This may be due to a cell cycle related translocation of phosphoproteins from the nucleus to the cytoplasm, or alternate phosphorylation and dephosphorylation in nucleus and cytoplasm. Detectability of epitopes on sections depended on the embedding procedure. Cryo processing revealed epitope reactivity in all stages of the cell cycle whereas polyethylene glycol embedded material showed no labelling in the cytoplasm during mitosis. Processing might reduce the antigenicity of cytoplasmic MPM-2 detectable proteins, probably due to dephosphorylation. The MPM-2 detectable epitope was observed in all cells investigated, irrespective of culture conditions, and its intracellular distribution depended on the cell cycle stage and was not related to the developmental fate of the microspores and pollen.
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  • 20
    ISSN: 1615-6102
    Keywords: Brassica napus ; Embryogenesis ; Heat shock ; Induction ; Microspore embryogenesis ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Brassica napus cv. Topas microspores, isolated and cultured near the time of the first pollen mitosis and subjected to a heat treatment of 24 h, can be induced to develop into haploid embryos. This is a study of microspore structure during induction and embryo determination. Early during the 32.5 °C incubation period the nucleus moved away from the edge of the cell, and granules, 30 to 60 nm in diameter, appeared in the mitochondria and as a cluster in the cytoplasm. Cells divided symmetrically and at the end of the heat treatment, acquired the features of induced bicellular structures described previously. The features persisted as the cells divided randomly within the exine for 4–7 days following heat induction. Multicellular structures released from the exine underwent periclinal divisions resulting in protoderm differentiation of the globular embryo, thus determining embryo development. The cytoplasm of early heart-stage embryos contains abundant polyribosomes. Non-embryogenic development was indicated by large accumulations of starch and/or lipid and thickened cell walls or an unorganized pattern of cell division following release of the multicellular structures from the exine. Embryogenesis is discussed in terms of induction, embryo determination and development.
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  • 21
    ISSN: 1572-9788
    Keywords: 2S Albumin ; Brassica napus ; chimeric seed storage protein gene ; co-transformation ; T-DNA insertion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract UsingAgrobacterium tumefaciens-mediated gene transfer, 14 T0Brassica napus plants carrying one of three chimeric 2S albumin seed protein genes were obtained after co-transformation with theneo gene. Plants were made homozygous using either cell haploid culture or, for single-copy plants, traditional crossing methods. Sixty-five percent of kanamycin-resistant plants contained at least one copy of the seed protein gene, and multiple copies were usually at a single locus. In the majority of cases, at least one copy of theneo gene was linked to an introduced 2S albumin gene, demonstrating that co-transformation is not a reliable way to obtain lines without the marker gene linked to the gene of interest. In 3 T0 plants sequences derived from beyond the left border of the vector were integrated in the plant genome, in two cases partially rearranged, confirming that T-DNA insertion is not always precise. Procedures for efficiently determining this are described. This work highlights the extra steps needed to prepare transgenic lines for field studies and potential further breeding.
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  • 22
    Electronic Resource
    Electronic Resource
    Springer
    Plant and soil 175 (1995), S. 251-255 
    ISSN: 1573-5036
    Keywords: Brassica napus ; Ca/Na ratio ; K/Na ratio ; rapeseed yield ; salinity ; sodicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Rapeseed (Brassica napus) is a crop relatively tolerant to salt and sodium. Our objective was to study the interactions between Na, K and Ca and their relationship with its yield under the isolated effects of soil salinity or sodicity. Two experiments were carried out using pots filled with the Ah horizon of a Typic Natraquoll. There were three salinity levels (2.3 dS m-1; 6.0 dS m-1 and 10.0 dS m-1) and three sodicity levels, expressed as sodium adsorption ratios (SAR: 12; 27 and 44). The soil was kept near field capacity. As soil salinity increased, the K/Na and Ca/Na ratios in the tissues decreased markedly but yields and aerial biomass production were not affected. As soil SAR value increased, the K/Na and Ca/Na ratios in plants and K-Na and Ca-Na selectivities decreased. Plants could not maintain their Ca concentration in soil with a high SAR. The grain yield and biomass production diminished significantly in the highest SAR treatment. Our results are consistent with those showing detrimental osmotic effects of salts in Brassica napus. Conversely, under sodicity, the K/Na and Ca/Na ratios in plant tissues decreased considerably, in accordance with grain and biomass production. These results show that the effects of sodicity are different from those of salinity.
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  • 23
    ISSN: 1573-5036
    Keywords: Brassica napus ; canola ; nitrogen nutrition ; irrigation ; 15N isotope ; oilseed rape
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The seasonal course of nitrogen uptake, incorporation and remobilization in different shoot components of winter oilseed rape (Brassica napus L.) was studied under field conditions including three rates of 15N labelled nitrogen application (0, 100 or 200 kg N ha-1) and two irrigation treatments (rainfed or watered at a deficit of 20 mm). The total amount of irrigation water applied was 260 mm, split over 13 occasions in a 7-week-period ranging from 1 week before onset of flowering until 4 weeks after flowering. Nitrogen application and irrigation increased plant growth and nitrogen accumulation. Irrespective of N and irrigation treatment more than 50% of total shoot N was present in the stem when flowering started. At the end of flowering, pod walls were the main N store containing about 30–40% of shoot N. The quantities of N remobilized from stems and pod walls amounted in all treatments to about 70% of the N present in these organs at mid-flowering. At harvest, stem and pod walls each contained about 10% of total shoot N, the remaining 80% being incorporated into seeds. The main component contributing to the response of seed N accumulation to nitrogen application and irrigation was pods in axillary racemes. Up to 20 kg N ha-1, corresponding to about 10% of final shoot N content, was lost from the plants by leaf drop. Irrigation increased the recovery at harvest of applied N from 30% to about 50%, while the level of N application did not affect the N recovery. 15N labelled (fertilizer derived) nitrogen constituted a greater proportion of the N content in old leaves than in young leaves and increased with age in the former, but not in the latter. Relative to soil N, fertilizer derived N also contributed more to the N content of vegetative than to that of reproductive shoot components. Small net changes in shoot N content after flowering reflected a balance between N import and export, leading to continuous dilution of 15N labelled N with unlabelled N.
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  • 24
    ISSN: 1573-5044
    Keywords: Brassica napus ; B. campestris ; B. oleracea ; cotyledon protoplasts ; callus formation and growth ; plant regeneration
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cotyledons from twelve cultivars of Brassica; B. napus (Westar, Eureka, Global, Pivot and Narc 82); B. campestris: (Arlo, Sonja, Bunyip and Wonk Bok) and B. oleracea (Phenomenal Early, Sugar Loaf and Earliball) were used for protoplast isolation and culture in a comparative study of cell colony and callus formation, and plant regeneration. The formation of cell colonies and callus from protoplast cultures were significantly influenced by the light conditions of seed germination. All twelve cultivars showed callus formation from protoplast cultures derived from cotyledons of seedlings grown in dark for 3 days followed by 1 day dim light (dark/dim light-grown). Callus was obtained in all five liquid media used: modified K8P(1), modified K8P(2), modified MS, modified B and modified NN. In contrast, only six cultivars exhibited callus formation from the protoplasts isolated from cotyledons of seedlings germinated under light conditions for 7 days (light-grown) and in only three media: modified K8P(1), modified MS, modified B. Callus, derived from protoplast cultures isolated from dark/dim light-grown cotyledons and grown on K3 or MS series solid media for about 1 month, could develop shoots when further transferred onto MS series regeneration media. All five cultivars of B. napus, three of the four cultivars of B. campestris (Arlo, Sonja and Bunyip) and one of the three cultivars of B. oleracea (Sugar Loaf) exhibited shoot regeneration from protoplast cultures within 2–3 months after protoplast isolation. The frequency of shoot regeneration ranged among 1–22.5%. A high degree of reproducibility was observed in cultivars Westar, Eureka, Global, Arlo, Bunyip and Sugar Loaf. In contrast, among the six cultivars that formed callus in protoplast culture derived from light-grown cotyledons, only three cultivars from B. napus (Westar, Eureka, Global) exhibited shoot regeneration 5.5 months after protoplast isolation. Regenerated shoots from cultivars Westar, Eureka and Bunyip and Sugar Loaf, which derived from protoplasts of dark/dim light germinated seedling and were induced to root on rooting media, survived in soil and grew to produce silique and set seeds.
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  • 25
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    Springer
    Euphytica 81 (1995), S. 283-289 
    ISSN: 1573-5060
    Keywords: Key words ; Brassica napus ; field trial ; gene dispersal ; genetic modification ; pollination ; oil seed rape
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary A field trial was carried out with oil seed rape plants that had been genetically modified to contain genes coding for marker characters (β-glucuronidase, kanamycin resistance and asulam resistance). The aim of the experiment was to examine a method of studying gene dispersal in an agricultural environment. The central area of the field plot comprised 150 genetically modified plants and 450 plants not expressing the marker genes. These were surrounded by additional non-expressing plants. The plants were allowed to freely cross pollinate and a sample of the resultant progeny from non-expressing plants were screened for expression of the marker characters and for the presence of the introduced genes (by PCR). Limited gene dispersal was detected and the frequency of modified seedlings amongst the progeny of a plant appeared to have been strongly influenced by the genotype of the immediately adjacent plants.
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  • 26
    ISSN: 1573-5060
    Keywords: Brassica napus ; flower-culture method ; intergeneric cross ; oilseed rape ; radish ; Raphanus sativus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Hybridization between radish and oilseed rape has been cumbersome, requiring elaborate embryo rescue techniques. With a modified flower culture method, we have achieved successful hybridization between radish and (transgenic) oilseed rape without the laborious and technically demandingin vitro ovule or embryo rescue techniques. The hybrid nature of the intergeneric hybrids was demonstrated using morphological traits, and DNA analyses. The described method will facilitate the generation ofRaphanobrassica hybrids useful for biosafety studies of the potential for transgenes to spread in weedyCruciferae as well as for breeding programs aimed at introducing useful radish genes, e.g. nematode resistance genes, into oilseed rape.
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  • 27
    ISSN: 1573-5044
    Keywords: Brassica napus ; β-glucuronidase ; polymerase chain reaction ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Approximately 2,000 embryogenic uninuclear microspores of rapeseed (Brassica napus) cv. Topas were intranuclearly injected with a chimaeric β-glucuronidase (Escherichia coli Uid A) gene. Stable integration had not occurred among 55 plants that were regenerated. Coinjection of the dye Lucifer Yellow and detection of injected DNA by the polymerase chain reaction revealed high frequencies of transfer. However, the amount of DNA injected was less than 20 copies, which may have been insufficient for stable transformation of microspores.
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  • 28
    ISSN: 1573-5044
    Keywords: Hypocotyl protoplast ; Brassica napus ; somatic embryogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A simple protocol has been developed for high frequency protoplast regeneration via somatic embryogenesis in B. napus. Protoplasts isolated from hypocotyl tissue of 8–12 day old seedlings of Brassica napus ISN706 (AACC) when cultured in KM(A) medium resulted in divisions with a, frequency ranging from 30–35%. Regeneration of plantlets was possible by both organogenesis and embryogenesis. Nearly 80% of the call transferred on to MS medium supplemented with 5.0 mg l-1 2iP, 0.1 mg l-1 NAA, 0.001 mg l-1 GA3, 0.5 g l-1 PVP and 0.5 g l-1 MES displayed somatic embryogenesis. The somatic embryos developed into normal plantlets, and also displayed secondary, repetitive embryogenesis.
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  • 29
    ISSN: 1573-5079
    Keywords: Brassica napus ; chloroplast ; fructose-1,6-bisphosphatase ; rapeseed ; recombinant enzyme ; reductive activation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In chloroplasts, the light-modulated fructose-1,6-bisphosphatase catalyzes the formation of fructose 6-bisphosphate for the photosynthetic assimilation of CO2 and the biosynthesis of starch. We report here the construction of a plasmid for the production of chloroplast fructose-1,6-bisphosphatase in a bacterial system and the subsequent purification to homogeneity of the genetically engineered enzyme. To this end, a DNA sequence that coded for chloroplast fructose-1,6-bisphosphatase of rapeseed (Brassica napus) leaves was successively amplified by PCR, ligated into the Ndel/EcoRI restriction site of the expression vector pET22b, and introduced into Escherichia coli cells. When gene expression was induced by isopropyl-β-d-thiogalactopyranoside, supernatants of cell lysates were extremely active in the hydrolysis of fructose 1,6-bisphosphate. Partitioning bacterial soluble proteins by ammonium sulfate followed by anion exchange chromatography yielded 10 mg of homogeneous enzyme per 1 of culture. Congruent with a preparation devoid of contaminating proteins, the Edman degradation evinced an unique N-terminal amino acid sequence [A-V-A-A-D-A-T-A-E-T-K-P-]. Gel filtration experiments and sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the (recombinant) rapeseed chloroplast fructose-1,6-bisphosphatases was a tetramer [160 kDa] comprised of four identical subunits. Like other chloroplast fructose-1,6-bisphosphatases, the recombinant enzyme was inactive at 1 mM fructose 1,6-bisphosphate and 1 mM Mg2+ but became fully active after an incubation in the presence of either 10 mM dithiothreitol or 1 mM dithiothreitol and chloroplast thioredoxin. However, at variance with counterparts isolated from higher plant leaves, the low activity observed in absence of reductants was not greatly enhanced by high concentrations of fructose 1,6-bisphosphate (3 mM) and Mg2+ (10 mM). In the catalytic process, all chloroplast fructose-1,6-bisphosphatases had identical features; viz., the requirement of Mg2+ as cofactor and the inhibition by Ca2+. Thus, the procedure described here should prove useful for the structural and kinetic analysis of rapeseed chloroplast fructose-1,6-bisphosphatase in view that this enzyme was not isolated from leaves.
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  • 30
    ISSN: 1573-1561
    Keywords: Jasmonate ; Brassica napus ; canola ; toughness ; glucosinolate ; structure-activity ; analogue ; defense
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Jasmonic acid (JA) has potent activity in enhancing cotyledon toughness and stimulating the biosynthesis of 3-indolymethyl glucosinolate in seedlings of canola,Brassica napus L. Structure-activity relationships among cyclopentane analogs of JA revealed that maximum activity in both systems was achieved when an acetyl side chain (or a methylated acetyl side chain) occurred at the C-1 ring position, ann-pentenyl side chain at the C-2 ring position, and a keto group at the C-3 ring position. Although coronatine and coronafacic acid both possess a cyclopentane ring with a keto group at the C-3 position, only coronatine was active inB. napus seedlings. Coronatine, a chlorosis-inducing toxin essential to the infectivity of pathovars ofPseudomonas syringae, acted as a complete molecular mimic of JA and had the same stimulatory effect on specific indole glucosinolates inBrassica species, thereby casting doubt on the hypothesis that indole glucosinolates serve in bacterial pathogen defense. Similarities and differences for structural requirements for activity among several diverse physiological systems affected by jasmonates likely reflect species-, tissue-, and developmental-specific differences.
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  • 31
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    Plant cell, tissue and organ culture 40 (1995), S. 255-270 
    ISSN: 1573-5044
    Keywords: anther/microspore culture ; Brassica napus ; colchicine ; embryogenesis ; microtubules ; pollen mitosis I
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In an attempt to discover the biological basis of microspore derived embryogenesis, the effect of the antimicrotubule agent colchicine on anther and free microspore embryogenesis was investigated. The microtubule inhibitor colchicine promoted embryogenesis from cultured anthers, both with regard to the number of anthers responding and the number of embryos being produced per anther. A similar promotional response was also observed with cultured microspores. Although the parameters for cultured anthers and free microspores differed, administration of the drug for a short period immediately prior to pollen mitosis I seems to exert the maximum promotional effect. Of the five cultivars of Brassica napus studied, all responded to colchicine treatment. However, the drug did release more embryogenic potential in poor-responding varieties (i.e. Lirawell and Optima) than in the highest responding variety (Topas). Colchicine also resulted in increased embryogenic response in microspores cultured at lower temperatures. These results are considered in terms of models proposed to explain the switch in microspore development from a gametophytic to a sporophytic pathway. The use ofcolchicine as agent to promote embryogenesis in previously recalcitrant species other than Brassica is also discussed.
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  • 32
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    Biotechnology and Bioengineering 48 (1995), S. 631-638 
    ISSN: 0006-3592
    Keywords: Saccharomyces cerevisiae ; fermentation ; on-line simulation ; state estimation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In order to study and control fermentation processes, indirect on-tine measurements and mathematical models can be used. In this article we present a mathematical on-line model for fermentation processes. The model is based on atom and partial mass balances as well as on equations describing the acid-base system. The model is brought into an adaptive form by including transport equations for mass transfer and unstructured expressions for the fermentation kinetics. The state of the process, i.e., the concentrations of biomass, substrate, and products, can be estimated on-line using the balance part of the model completed with measurement equations for the input and output flows of the process. Adaptivity is realized by means of on-line estimation of parameters in the transport and kinetic expressions using recursive regression analysis. These expressions can thus be used in the model as valid equations enabling prediction of the process. This makes model-based automation of the process and testing of the validity of the measurement variables possible. The model and the on-line principles are applied to a 3.5-L laboratory tormentor in which Saccharomyces cerevisiae is cultivated. The experimental results show that the model-based estimation of the state and the predictions of the process correlate closely with high-performance liquid chromatography (HPLC) analyses. © 1995 John Wiley & Sons, Inc.
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  • 33
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    Biotechnology and Bioengineering 48 (1995), S. 659-666 
    ISSN: 0006-3592
    Keywords: methanogenic activity ; ethylene ; dechlorination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Kinetics were determined for methanogenic activity and chlorinated ethylene dehalogenation by a methanol-enriched, anaerobic sediment consortium. The culture reductively dechlorinated perchloroethylene (PCE) to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), vinylchloride (VC), and ethylene and ethane. The absence : of methanol or the addition of 2-bromoethanesulfonic. acid in the presence of methanol suppressed both methanogenic activity and dechlorination. In contrast, acetate production continued in the presence of 2-bromoethanesulfonic acid. These results suggest that dechlorination was strongly linked to methane formation and not to acetate production. A kinetic model, developed to describe both methanogenesis and dechlorination, successfully predicted experimentally measured concentrations of biomass, methane, substrate, and chlorinated ethylenes. The average maximum specific dehalogenation rates for PCE, TCE, 1,1-DCE, and VC were 0.9 ± 0.6, 0.4 ± 0.1, 12 ± 0.1, and 2.5 ± 1.7 μmol contaminant/ g. DW/day, respectively. This pattern for dechlorination rates is distinctly different than that reported for transition metal cofactors, where rates drop by approximately one order of magnitude as each successive chlorine is removed. The experimental results and kinetic analysis suggest that it will be impractical to targeting methanol consuming methanogenic organisms for in situ ground-water restoration. © 1995 John Wiley & Sons, Inc.
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  • 34
    ISSN: 0006-3592
    Keywords: bovine serum albumin ; growth factor ; hollow-fiber culture ; perfusion culture ; antibody production rate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effects of the high-molecular-weight growth factors, transferrin and bovine serum albumin (BSA), on antibody production were analyzed quantitatively in continuous hollow-fiber cultivation over a period of 60 days. Transferrin enhanced cell growth but had no significant effect on the specific antibody production rate, whereas BSA significantly enhanced antibody production. The antibody production rate was increased 4- and 14-fold respectively by feeding BSA at 2 and 5 g L-1 into the EC side of the system (the side connected to the cell-containing outer part of the hollow-fiber unit) compared with the production achieved without BSA. Addition of 5 g L1 BSA into the IC side of the system (the side connected to the inner part of the hollow-fiber unit) resulted in a 2.5-fold increase in the antibody production rate. The effect of BSA was also analyzed using the perfusion culture system with a separation unit. When fresh medium containing either 2 or 5 g L-1 BSA was fed into the reactor, both the specific growth rate and specific death rate increased, while the specific antibody production rate was increased 2- and 25-fold, respectively, by feeding BSA at these two concentrations compared with no addition. Comparing the two systems, the increase in the antibody production rate achieved with the hollow-fiber system was threefold greater than that in the perfusion culture system with the same concentration of BSA feeding. © 1995 John Wiley & Sons, Inc.
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  • 35
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 132-140 
    ISSN: 0887-3585
    Keywords: protein folding ; protein stability ; mutational effects ; φ, ψ distribution ; Ramachandran map ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Changes in amino acid side chains have long been recognized to alterthe range and distribution of φ, ψ angles found in the main chain of polypeptides. Altering the range and distribution of φ, ψ angles also alters the conformational entropy of the flexible denatured state and may thus stabilize or destabilize it relative to the comparatively conformationally rigid native state. A database of 12,320 residues from 61 nonhomologous, high resolution crystal structures was examined to determine the φ, ψ conformational preferences of each of the 20 amino acids. These observed distributions in the native state of proteins are assumed to also reflect the distributions found in the denatured state. The distributionswere used to approximate the energy surface for each residue, allowing the calculation of relative conformational entropies for each residue relative to glycine. In the most extreme case, replacement of glycine by proline, conformational entropy changes will stabilize the native state relative to the denatured state by -0.82 ± 0.08 kcal/mol at 20°C. Surprisingly, alanine is found to be the most ordered residue other than proline. This unexpected result is a result of the high percentage of alanines found in helical conformations. This either indicates that the observed distributions in the native state do not reflect the distributions in the denatured state, or that alanine is much more likely to adopt a helical conformation in the denatured state than residues with longer side chains. Among those residues with φ, ψ angles compatible with helix incorporation the percentage of alanines actually in helices is very similar to other residues. This and the consistent ordering of alanine relative to other residues regardless of secondary structure are evidence that φ, ψ distributions in native states reflect those in the denatured states. © 1995 Wiley-Liss, Inc.
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  • 36
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 154-167 
    ISSN: 0887-3585
    Keywords: iron-sulfur proteins ; electron transfer ; oxidation-reduction potentials ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations of Clostridium pasteurianum rubredoxin in the oxidized and reduced forms have been performed. Good agreement between both forms and crystal data has been obtained (rms deviation of backbone atoms of 1.06 and 1.42 Å, respectively), which was due in part to the use of explicit solvent and counterions. The reduced form exhibits an unexpected structural change: the redox site becomes much more solvent-accessible, so that water enters a channel between the surface and the site, but with little actual structural rearrangement (the rms deviation of backbone atoms between the oxidized and reduced is 0.77 Å). The increase in solvent accessibility is also seen, although to a much lesser extent, between the oxidized and reduced crystal structures of Pyrococcus furiosus rubredoxin, but no high resolution crystal or nuclear magnetic resonance solution data exist for reduced C. pasteurianum rubredoxin. The electrostatic potential at the iron site and fluctuations in the potential, which contribute to both the redox and electron transfer properties, have also been evaluated for both the oxidized and the reduced simulations. These results show that the backbone plays a significant role (62-70 kcall/mol/e) and the polar sidechains contribute relatively little (0-4 kcal/mol/e) to the absolute electrostatic potential at the iron of rubredoxin for both forms. However, both groups contribute significantly to the change in redox state by becoming more polarized and more densely packed around the redox site upon reduction. Furthermore, these results show that the solvent becomes much more polarized in the reduced form than in the oxidized form, even excluding the penetrating water. Finally, the simulation indicates that the contribution of the charged side chains to the electrostatic potential is largely canceled by that of the counterions. © 1995 Wiley-Liss, Inc.
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  • 37
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 191-192 
    ISSN: 0887-3585
    Keywords: lipopolysaccharide ; lipid A ; endotoxin ; protein structure ; acyltransferase ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of UDP-N-acetylglucosamine O-acyltransferase (lpxA) fromEscherichia coli have been obtained from solutions of sodium/potassium phosphate and dimethylsulfoxide. These crystals belong to the cubic space group P213 (a = 99.0 Å), diffract X-raysto approximately 2.5 Å resolution and contain one subunit of the enzyme in the asymmetric unit. © 1995 Wiley-Liss, Inc.
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  • 38
    ISSN: 0887-3585
    Keywords: hydrophobic moment ; peptide-cell ; membrane interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Multiple linear regression was used to quantify the dependence of the antimicrobial activity of 13 peptides upon three calculated or experimentally determined parameters: mean hydrophobicity, mean hydrophobic moment, and α-helix content. Mean hydrophobic moment is a measure of the amphiphilicity of peptides in an α-helical conformation. Antimicrobial activity was quantified as the reciprocal of the measured minimal inhibitory concentration (MIC) against Escherichia coli. One of the peptides was magainin 2, and the remainder were novel peptides designed for this study. The multiple linear regression results revealed that the amphiphilicity of the peptides was the most important factor governing anti-microbial activity compared to mean hydrophobicity orα-helix content. A better regression cf the data was obtained using In(1/MIC + constant) as the dependent variable than with either 1/MIC or In(1/MIC). These results should be useful in designing peptides with higher antimicrobial activity. © 1995 Wiley-Liss, Inc.
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  • 39
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 168-181 
    ISSN: 0887-3585
    Keywords: aspartic proteinase ; enzyme kinetics ; rule-based model ; chromogenic assay ; synthetic substrate ; inhibitor ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Aspartic proteinases are produced in the human body by a variety of cells. Some of these proteins, examples of which are pepsin, gastricsin, and renin, are secreted and exert their effects in the extracellular spaces. Cathepsin D and cathepsin E on the other hand are intracellular enzymes. The least characterized of the human aspartic proteinases is cathepsin E. Presented here are results of studies designed to characterize the binding specificities in the active site of human cathepsin E with comparison to othermechanistically similar enzymes. A peptide series based on Lys-Pro-Ala-Lys-Phe*Nph-Arg-Leu was generatedto elucidate the specificity in the individual binding pockets with systematic substitutions in the P5- P2 and P2′-P3′ based on charge, hydrophobicity, and hydrogen bonding. Also, to explore the S2 binding preferences, asecond series of peptides based on Lys-Pro-Ile-Glu-Phe*Nph-Arg-Leu was generated with systematic replacements in the P2 position. Kinetic parameters were determined forboth sets of peptides. The results were correlated to a rule-based structural model of human cathepsin E, constructed on the known three-dimensional structures of several highly homologous aspartic proteinases; porcine pepsin, bovine chymosin, yeast proteinase A, human cathepsin D, andmouse and human renin. Important specificity-determining interactions were found in the S3 (Glu13) and S2 (Thr-222, Gln-287, Leu-289, Ile-300)subsites. © 1995 Wiley-Liss, Inc.
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  • 40
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    Proteins: Structure, Function, and Genetics 22 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 41
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 193-196 
    ISSN: 0887-3585
    Keywords: urea cycle ; frog ; liver ; carbamyl phosphate synthetase ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Carbamoyl phosphate synthetase I (ammonia; E C 6.3.4.16) was purified from the liver of Rana catesbeiana (bullfrog). Crystals of the protein have been obtained at 22°C by the hanging drop vapor diffusion technique, with polyethylene glycol as precipitant. Tetragonal crystals of about 0.3 × 0.3 × 0.7 mm diffract at room temperature to at least 3.5 Å using a conventional source and are stable to X-radiation for about 12 h. Therefore, these crystals are suitablefor high resolution studies. The space group is P41212 (or its enantiomorph P43212), with unit cell dimensions a = b = 291.6 Å and c = 189.4 Å. Density packing considerations areconsistent with the presence of 4-6 monomers (Mr of the monomer, 160,000) in the asymmetric unit. Amino-terminal sequence of the enzyme and of a chymotryptic fragment of 73.7 kDa containing the COOH-terminus has been obtained. The extensive sequence identity with rat and human carbamoyl phosphate synthetase I indicates the relevance for mammals of structural data obtained with the frog enzyme. © 1995 Wiley-Liss, Inc.
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  • 42
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 199-209 
    ISSN: 0887-3585
    Keywords: chaperonins ; electron microscopy ; FTIR ; molecular modeling ; structure prediction ; contact prediction ; active site prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of the GroES monomer and its interaction with GroEL has been predicted using a combination of prediction tools and experimental data obtained by biophysical [electron microscope (EM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR)] and biochemical techniques. The GroES monomer, according to the prediction, is composed of eight β-strands forming a β-barrel with loose ends. In the model, β-strands 5-8 run along the outer surface of GroES, forming an antiparallel β-sheet with β4 loosely bound to one of the edges. β-strands 1-3 would then be parallel and placed in the interior of the molecule. Loops 1-3 would face the internal cavity of the GroEL-GroES complex, and together with conserved residues in loops 5 and 7, would form the active surface interacting with GroEL. © 1995 Wiley-Liss, Inc.
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  • 43
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 226-244 
    ISSN: 0887-3585
    Keywords: photosynthesis ; protein structure ; homology modeling ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The reaction center (RC) from the photosynthetic bacterium Rhodobacter (Rb.) capsulatus has been the subject of a considerable amount of molecular biological and spectroscopic work aimed at improving our understanding of the primary steps of photosynthesis. However, no three-dimensional structure is available for this protein. We present here a model obtained by combining information from the structure of the highly homologous RC from Rhodopseudomonas (Rps.) viridis with molecular mechanics and simulated annealing calculations. In the Rb. Capsulatus model the orientations of the bacteriochlorophyll monomer and the bacteriopheophytin on the branch inactive in electron transfer differ significantly from those in the RCs of Rps. Viridis and Rb. Sphaeroides. The bacteriopheophytin orientational difference is in good accord with previous linear dichroism measurements. A comparison is made of interactions between the pigments and the protein environment that may be of functional significance in Rps. viridis, Rb. sphaeroides, and Rb. capsulatus. © 1995 Wiley-Liss, Inc.
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  • 44
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 210-225 
    ISSN: 0887-3585
    Keywords: serpin-proteinase complex ; mutants ; deamidation ; α-helix-β-sheet conversion ; homology modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The mechanism of formation and the structures of serpin-inhibitor complexes are not completely understood, despite detailed knowledge of the structures of a number of cleaved and uncleaved inhibitor, noninhibitor, and latent serpins. It has been proposed from comparison of inhibitor and noninhibitor serpins in the cleaved and uncleaved forms that insertion of strand s4A into preexisting β-sheet A is a requirement for serpin inhibitor activity. We have investigated the role of this strand in formation of serpin-proteinase complexes and in serpin inhibitor activity through homology modeling of wild type inhibitor, mutant substrate, and latent serpins, and of putative serpin-proteinase complexes. These models explain the high stability of the complexes and provide an understanding of substrate behavior in serpins with point mutations in s4A and of latency in plasmingoen activator inhibitor I. © 1995 Wiley-Liss, Inc.
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  • 45
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 259-266 
    ISSN: 0887-3585
    Keywords: homology search ; phosphodiesterases ; sequence analysis ; structure prediction ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of glycerol-3-phosphate cytidylyltransferase from B. subtilis (TagD) is about to be solved. Here, we report a testable structure prediction based on the identification by sequence analysis of a superfamily of functionally diverse but structurally similar nucleotide-binding enzymes. We predict that TagD is a member of this family. The most conserved region in this superfamily resembles the ATP-binding HiGH motif of class I aminoacyI-tRNA synthetases. The predicted secondary structure of cytidylyltransferase and its homologues is compatible with the α/β topography of the class I aminoacyl-tRNA synthetases. The hypothesis of similarity of fold is strengthened by sequence-structure alignment and 3D model building using the known structure of tyrosyl tRNA synthetase as template. The proposed 3D model of TagD is plausible both structurally, with a well packed hydrophobic core, and functionally, as the most conserved residues cluster around the putative nucleotide binding site. If correct, the model would imply a very ancient evolutionary link between class I tRNA synthetases and the novel cytidylyltransferase superfamily. © 1995 Wiley-Liss, Inc.
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  • 46
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 267-272 
    ISSN: 0887-3585
    Keywords: α-keratin ; intermediate filaments ; epidermal keratin ; vimentin ; keratinopathies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In intermediate filaments (IF) both epidermal keratin and vimentin molecules have been shown to have an eight residue head to-tail overlap between the rod domains of similarly directed molecules. In the case of the epidermal keratins this region has also been shown to have particular structural/functional significance since it represents a hot-spot for mutations in the four keratinopathies characterized to date. While there is good evidence that this head-to-tail overlap is present in IF containing Type III, IV, and V chains, as well as in the epidermal keratin IF (Ib/IIb), there are no data currently available for the hard α-keratin IF (Ia/IIa). Using a variety of data derived from X-ray diffraction and crosslinking studies, as well as theoretical modeling, it is now possible to demonstrate that the overlap region is not a feature of hard α-keratin IF. Indeed, it is shown that there is a nine residue gap between consecutive parallel molecules in the IF. An explanation for this observation is presented in terms of compensating disulfide bonds that occur both within the IF, and between the IF and the matrix in which the IF are embedded. © 1995 Wiley-Liss, Inc.
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  • 47
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 245-258 
    ISSN: 0887-3585
    Keywords: bacterial muramidase ; peptidoglycan ; structure comparison ; sequence motifs ; structure/function relationships ; evolutionary relationships ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli is a bacterial exo-muramidase that cleaves the cell wall peptidoglycan, producing 1,6-anhydro-muropeptides. The X-ray structure of SLT70 showed that one of its domains is structurally related to lysozyme, although there is no obvious similarity in amino acid sequence. To relate discrete structural features to differences in reaction mechanism and substrate/product specificity, we compared the threedimensional structure of the catalytic domain of SLT70 with the structures of three typical representatives of the lysozyme superfamily: chicken-type hen egg-white lysozyme, goosetype swan egg-white lysozyme, and phage-type lysozyme from bacteriophage T4. We find a particularly close relationship between the catalytic domain of SLT70 and goose-type lysozyme, with not only a significant similarity in overall structure, but even a weak homology in amino acid sequence. This finding supports the notion that the goose-type lysozyme takes up a central position in the lysozyme superfamily and that it is structurally closest to the lysozyme ancestors. The saccharide-binding groove is the most conserved part in the four structures, but only two residues are absolutely preserved: the “catalytic” glutamic acid and a structurally required glycine. The “catalytic” aspartate is absent in SLT70, a difference that can be related to a different mechanism of cleavage of the β-1,4-glycosidic bond. The unique composition of amino acids at the catalytic site, and the observation of a number of differences in the arrangements of secondary structure elements, define the catalytic domain of SLT70 as a novel class of lysozymes. Its fold is expected to be exemplary for other bacterial and bacteriophage muramidases with lytic transglycosylase activity. © 1995 Wiley-Liss, Inc.
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  • 48
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 273-283 
    ISSN: 0887-3585
    Keywords: globular proteins ; protein structure analysis ; optimal rigid body superposition ; three-dimensional structural motif ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein structures are routinely compared by their root-mean-square deviation (RMSD) in atomic coordinates after optimal rigid body superposition. What is not so clear is the significance of different RMSD values, particularly above the customary arbitrary cutoff for obvious similarity of 2-3 Å. Our earlier work argued for an intrinsic cutoff for protein similarity that varied with the number of residues in the polypeptide chains being compared. Here we introduce a new measure, ρ, of structural similarity based on RMSD that is independent of the sizes of the molecules involved, or of any other special properties of molecules. When ρ is less than 0.4-0.5, protein structures are visually recognized to be obviously similar, but the mathematically pleasing intrinsic cutoff of ρ〉1.0 corresponds to overall similarity in folding motif at a level not usually recognized until smoothing of the polypeptide chain path makes it striking. When the structures are scaled to unit radius of gyration and equal principle moments of inertia, the comparisons are even more universal, since they are no longer obscured by differences in overall size and ellipticity. With increasing chain length, the distribution of ρ for pairs of random structures is skewed to higher values, but the value for the best 1% of the comparisons rises only slowly with the number of residues. This level is close to an intrinsic cutoff between similar and dissimilar comparisons, namely the maximal scaled ρ possible for the two structures to be more similar to each other than one is to the other's mirror image. The intrinsic cutoff is independent of the number of residues or points being compared. For proteins having fewer than 100 residues, the 1% ρ falls below the intrinsic cutoff, so that for very small proteins, geometrically significant similarity can often occur by chance. We believe these ideas will be helpful in judging success in NMR structure determination and protein folding modeling. © 1995 Wiley-Liss, Inc.
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  • 49
    ISSN: 0887-3585
    Keywords: PCB degrading enzyme ; dioxygenase ; crystallization ; polychlorinated biphenyl ; selenomethionine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals have been obtained for a 2,3-dihydroxybiphenyl dioxygenase (conventionally called BphC) from a polychlorinated biphenyl (PCB)-degrader, Pseudomonas sp. strain KKS1O2. The crystals were grown using both ammonium sulfate and MPD as the precipitating agents. The crystals belonged to a tetragonal space group (I422) and diffracted to 2.5 Å. © 1995 Wiley-Liss, Inc.
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  • 50
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 287-289 
    ISSN: 0887-3585
    Keywords: DNA repair ; PCR ; Bacillus subtilis ; herpes simplex virus ; protein-protein interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The uracil-DNA glycosylase inhibitory protein (UGI) from the bacterio-phage PBS-l has been cloned and overexpressed. The nucleotide sequence is identical to that for the previously described PBS-2 inhibitor. The recombinant PBS-l UGI inhibits the uracil-DNA glycosylase from herpes simplex virus type-l (HSV-l UDGase), and a complex between the HSV-l UDGase and PBS-l UGI has been crystallized. The crystals have unit cell dimensions a = 143.21 Å, c = 40.78 Å and are in a polar hexagonal space group. There is a single complex in the asymmetric unit with a solvent content of 62% by volume and the crystals diffract to 2.5Å on a synchrotron radiation source. © 1995 Wiley-Liss, Inc.
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  • 51
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 290-292 
    ISSN: 0887-3585
    Keywords: macroH2A ; specialized nucleosomes ; fusion protein ; crystallization ; X-ray diffraction ; noncrystal-lographic symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Histone macroH2A has a novel hybrid structure consisting of a large nonhistone region and a region that closely resembles a full-length histone H2A. One key to understanding macroH2A function is determining the structure and function of its nonhistone region. The nonhistone region of one of the two known macroH2A subtypes was expressed in Escherichia coli and purified using affinity and molecular sieve chromatography. Crystals of the protein suitable for structural studies were grown from polyethylene glycol solutions by vapor equilibration techniques. The crystals belong to the hexagonal space group P64 (or its enantiomorph P62) with unit cell parameters: a = b = 106.2 Å, c = 125.9 Å, α = β = 90°, and γ = 120°. There are four molecules in the asymmetric unit. Self-rotation function studies revealed three twofold noncrystallographic rotation axes related approximately by 222 symmetry. These crystals have 47% solvent content and diffract to 3.8 Å resolution. © 1995 Wiley-Liss, Inc.
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  • 52
    ISSN: 0887-3585
    Keywords: aldolase ; protein complex crystallization ; crystallization screening ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray quality crystals of class I deoxyribose-5-phosphate aldolase from Escherichia coli have been obtained for the unliganded enzyme and in complex with its substrate, 2-deoxyribose-5-phosphate. The enzyme catalyzes the reversible cleavage of 2-deoxyribose-5-phosphate to acetaldehyde and D-glyceraldehyde-3-phosphate. The unliganded and complex crystals are prismatic long rods and belong to the orthorhombic space group P212121 with cell dimensions a = 183.1 Å, b = 61.4 Å, c = 49.3 Å and a = 179.2 Å, b = 60.5, Å, c = 49.1 Å, respectively. Two molecules in the asymmetric unit are related by a noncrystallo-graphic 2-fold axis. The crystals are stable in the X-ray beam and diffract to at least 2.6 Å. A new method, reverse screening, designed to minimize protein utilization during the screening process was used to determine supersaturation and crystallization conditions. © 1995 Wiley-Liss, Inc.
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  • 53
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    Proteins: Structure, Function, and Genetics 22 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 54
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 73-75 
    ISSN: 0887-3585
    Keywords: thioesterase ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thioesterase II from rat mammary gland has been crystallized in the presence of decanoic acid by the vapor diffusion method. The crystals belong to the orthorhombic space group P212121, and have cell dimensions, a = 52.7 Å, b = 78.0 Å, and c = 133.6 Å. The asymmetric unit likely consists of two protein monomers based on predictions from its calculated Matthews coefficient. Crystals typically diffract to at least 2.5 Å resolution and are suitable for X-ray crystallographic analysis. © 1995 Wiley-Liss, Inc.
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  • 55
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 76-78 
    ISSN: 0887-3585
    Keywords: arthritis ; cartilage ; crystallization ; link protein ; proteoglycan aggregate ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cartilage extracellular matrix link protein, having molecular mass of approximately 40 kDa, is a metalloprotein that binds divalent cations and is only soluble in low ionic strength solutions. The link protein was purified from bovine trachea and has been crystallized by a vapor diffusion method using PEG 3350 as precipitant. The crystal symmetry is P1, and the unit cell dimensions are a = 43.55, b = 53.11, c = 60.10 Å, α = 90.44, β = 106.21, γ = 101.51°. The VM of 1.8 Å3/Da is consistent with the presence of two molecules of the link protein in the asymmetric unit. The crystals diffract X-rays from a synchrotron source to 1.7 Å resolution. © 1995 Wiley-Liss, Inc.
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  • 56
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 100-109 
    ISSN: 0887-3585
    Keywords: protein structure ; RNA structure ; lattice model ; chain connectivity ; self-avoiding ; dynamic programming ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An algorithm based on dynamic programming gives the lattice models having the minimal RMS deviations from the actual folds of protein (RNA, etc.) chains for a given lattice and a given orientation of the macromolecule relative to the lattice. The algorithm is applicable for 3-D lattices of any kind. The accuracy of the lattice approximation increases when the distance between neighbor chain links is not rigidly fixed. Special repulsive potentials facilitate generation of self-avoiding lattice chains. The results of model building show the efficiency and precisionof this proposed general method when compared with others. © 1995 Wiley-Liss, Inc.
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  • 57
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 70-73 
    ISSN: 0887-3585
    Keywords: cell cycle protein ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The cell cycle regulatory protein CksHs1 has been crystallized in a form suitable for X-ray studies. CksHsl crystals were grown in the presence of vanadate, a phos-phatase inhibitor, but were also obtained with phosphate or tungstate as a cofactor. They belong to the hexagonal space group P6122 with unit cell dimensions: a=b=94 Å, c=131.6 Å, and γ =120. The crystals grown in the presence of vanadate diffract X-rays to at least 2.8 Å. Molecular replacement results from the homologous human CksHs2 structure reveal that a dimer forms the crystal habit, giving the unusual Vm value of 4.4 Å3/Da or a solvent content of 72%. © 1995 Wiley-Liss, Inc.
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  • 58
    ISSN: 0887-3585
    Keywords: glucocorticoid receptor ; DNA binding domain ; mutant ; yeast ; transcription factor ; transactivation ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Regulation of gene expression involves a large number of transcription factors with unique DNA-binding properties. Many transcription factors belong to families of related proteins that bind to similar but distinct sequences. In this study we have analyzed how amino acid substitutions at a single position in the DNA-binding domain modulate the DNA binding specificity within the nuclear receptor family of transcription factors. All possible amino acids were introduced at the first position in the DNA recognition helix, and the specificities of the mutants were analyzed using response elements containing all combinations of bases at two variable base pair positions. All mutant proteins were functional in DNA binding, and could be divided into classes of mutants with different response element specificities. By combining functional data with analysis of the structural effects of the mutations by molecular modeling, we could identify both prohibitive steric interactions as well as positive interactions, such as hydrogen bonds, that function as important determinants for specificity. Only the residues found naturally in the glucocorticoid and estrogen receptors, glycine and glutamate, produce unique binding specificities. The specificities of the other mutants overlap with each other somewhat but the substitutions clearly have potential to contribute to diversity within the nuclear receptor family. © 1995 Wiley-Liss, Inc.
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  • 59
    ISSN: 0887-3585
    Keywords: antiparallel β-sheet ; twist ; protein folding ; side chain interactions ; branched amino acids ; cystine-rich proteins ; side chain packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cross-strand pair correlations are calculated for residue pairs in antiparallel β-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. Thestrongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β- and γ-branched residues inthe non-H-bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded β- and γ-branched residue pairs, (2) the handedness of the observed enantiomers of chiral β-branched side chains, and (3) the handedness of the twist of β-sheet. These findings have implications for the formation of β-sheets during protein folding and the mechanism by which the sheet becomes twisted. © 1995 Wiley-Liss, Inc.
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  • 60
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 472-490 
    ISSN: 0887-3585
    Keywords: drug design ; FKBP ; FK506 ; immunophilin ; MCSS ; DLD ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site. © 1995 Wiley-Liss, Inc.
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  • 61
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 491-501 
    ISSN: 0887-3585
    Keywords: antibody structure ; viral neutralization ; human rhinovirus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the complex between the Fab fragment of a human rhinovirus serotype 2 (HRV2) neutralizing antibody (8F5) and a cross-reactive synthetic peptide derived from the viral capsid protein VP2 has been recently determined by crystallographic methods.1 The conformation adopted by the peptide was very similar to and could be superimposed onto the corresponding region of the viral protein VP2 of human rhinovirus 1A (HRV1A) whose three-dimensional structure is known.2 The structure of the Fab fragment determined in the complex was docked onto the viral capsid using the superimposition transformation found for the peptide. In the resulting model the Fab protrudes almost radially to about 60 Å from the surface of the virion without any major steric problem. The Fab fragment was then placed on each one of the 60 equivalent epitopes using the T = 1 icosahedral symmetry of the virus. The closest pairs of Fab fragments are related by viral 2-fold axes and run almost parallel to each other without clashing. These axes of symmetry from the viral particle could thus be coincident with the dyad axes of the antibodies. Furthermore, comparison of the three-dimensional structure of the Fab/peptide complex with the structure of the Fab fragment alone3 indicates that the flexibility of the antibody's elbow would facilitate bivalent attachment to the same viral particle. In accordance with the docking results, experimental determination of the stoichiometry of binding yielded a ratio of 30 IgG molecules per virion also suggesting bivalent attachment of antibody 8F5 onto the viral particle. The neutralization of viral infectivity, being neither aggregation (this paper) nor inhibition of receptor binding,4 might be mainly achieved by reducing viral spread from cell to cell and/or inhibition of uncoating. © 1995 Wiley-Liss, Inc.
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  • 62
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 502-509 
    ISSN: 0887-3585
    Keywords: microtubules ; molecular motors ; electron cryomicroscopy ; decorated microtubules ; microtubule organization ; structure of microtubule/motor domain complexes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To obtain an overall three-dimensional picture of the interaction between microtubules and the motor proteins of the kinesin family it will be necessary to take account of both atomic resolution structures obtained by X-ray crystallography and medium resolution reconstructions obtained by electron cryomicroscopy. We examine the problems associated with obtaining the required structural information from electron micrographs of vitreous ice-embedded microtubules decorated with motor domains. We find that the minus-end directed motor, ncd, decorates microtubules with an 80 Å periodicity as for kinesin. Our theoretical analysis and experiments with ncd illustrate the difficulty in determining unambiguously the surface lattice organization by diffraction analysis of micrographs. 3D reconstructions of decorated microtubules are required to accurately locate the motor domains. Helical diffraction theory is not usually applicable because microtubules are cylindrical structures that rarely have complete helical symmetry. We propose using a back-projection method based on the long pitch helices formed by individual protofilaments. Model reconstructions show that this approach is feasible. © 1995 Wiley-Liss, Inc.
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  • 63
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 525-535 
    ISSN: 0887-3585
    Keywords: DNA-protein interaction ; crystal structure ; transcription factor ; gene regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Many transcription factors have an α-helix that binds to DNA bases in a specific fashion. The DNA-binding geometry of these recognition helices varies substantially. We define a set of parameters to describe the binding geometry of recognition helices and analyze specific stereochemical elements that determine particular geometries. Because the convex surface of the helix must fit into the concave surface of the DNA major groove, the number of degrees of freedom of the recognition helix is reduced from a possible six to a single angle, which we call α. The chemically interacting DNA bases and amino acid residues must lie along a common line and have the same spacing along it. This pairing of base positions with residue positions seems to restrict the binding geometry further to a set of discrete values for α. © 1995 Wiley-Liss, Inc.
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  • 64
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 510-524 
    ISSN: 0887-3585
    Keywords: lectin ; demetallized ; peptide bond isomerization ; inter-dimer interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of demetallized concanavalin A has been determined at 2.5 Å resolution and refined to a crystallographic R-factor of 18%. The lectin activity of concanavalin A requires the binding of both a transition metal ion, generally Mn2+, and a Ca2+ ion in two neighboring sites in close proximity to the carbohydrate binding site. Large structural differences between the native and the metal-free lectin are observed in the metal-binding region and consequently for the residues involved in the specific binding of saccharides. The demetallization invokes a series of conformational changes in the protein backbone, apparently initiated mainly by the loss of the calcium ion. Most of the Mn2+ ligands retain their position, but the Ca2+ binding site is destroyed. The Ala207-Asp208 peptide bond, in the β-strand neighboring the metal-binding sites, undergoes a cis to trans isomerization. The cis conformation for this bond is a highly conserved feature among the leguminous lectins and is critically maintained by the Ca2+ ion in metal-bound concanavalin A. A further and major change adjacent to the isomerized bond is an expansion of the loop containing the monosaccharide ligand residues Leu99 and Tyr100. The dispersion of the ligand residues for the monosaccharide binding site (Asn14, Agr228, Asp208, Leu99, and Tyr100) in metalfree concanavalin A abolishes the lectin's ability to bind saccharides. Since the quaternary structure of legume lectins is essential to their biological role, the tetramer formation was analyzed. In the crystal (pH 5), the metal-free concanavalin A dimers associate into a tetramer that is similar to the native one, but with a drastically reduced number of inter-dimer interactions. This explains the tetramer dissociation into dimers below pH values of 6.5. © 1995 Wiley-Liss, Inc.
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  • 65
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 536-547 
    ISSN: 0887-3585
    Keywords: water ; hydrophobicity ; hydration ; X-ray crystallography ; solvation ; ordered solvent ; molecular recognition ; water-protein interactions ; drug and inhibitor design ; protein surface analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Water-protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen-bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively-charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side-chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U-75875 inhibitor complexes. © 1995 Wiley-Liss, Inc.
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  • 66
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 226-236 
    ISSN: 0887-3585
    Keywords: doeking ; Monte Carlo ; LexA repressor ; DNA binding domain ; protein-DNA interaction ; solution structure ; molecular recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structural model for the interaction of the LexA repressor DNA binding domain (DBD) with operator DNA is derived by means of Monte Carlo docking. Protein-DNA complexes were generated by docking the LexA repressor DBD NMR solution structure onto both rigid and bent B-DNA structures while giving energy bonuses for contacts in agreement with experimental data. In the resulting complexes, helix III of the LexA repressor DBD is located in the major groove of the DNA and residues Asn-41, Glu-44, and Glu-45 form specific hydrogen bonds with bases of the CTGT DNA sequence. Ser-39, Ala-42, and Asn-41 are involved in a hydrophobic interaction with the methyl group of the first thymine base. Residues in the loop region connecting the two β-sheet strands are involved in nonspecific contacts near the dyad axis of the operator. The contacts observed in the docked complexes cover the entire consensus CTGT half-site DNA operator, thus explaining the specificity of the LexA repressor for such sequences. In addition, a large number of nonspecific interactions between protein and DNA is observed. The agreement between the derived model for the LexA repressor DBD/DNA complex and experimental biochemical results is discussed. © 1995 Wiley-Liss, Inc.
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  • 67
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 256-260 
    ISSN: 0887-3585
    Keywords: α/β - barrel ; α/β - hyperboloid - 8 ; three-dimensional structure ; local tight packing of hydrophobic groups ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of β-hyperboloid-8 was conducted. This analysis shows that the disposition of amino acid side chains at the real β-structure's surface is unique. If we sign the mean distance between adjacent β-strands as “a,” and the mean distance along β-strand between Cα atoms, whose side chains are directed to one side of the β-sheet, as “b,” the ratio b/a = √2 very precisely. This ratio ensures the most efficient packing of side hydrophobic groups at the outer surface of β-hyperboloid-8, forming, at the same time, the second by efficiency packing at its inner surface. © 1995 Wiley-Liss, Inc.
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  • 68
    ISSN: 0887-3585
    Keywords: carboxylate ; magnesium ; hydration ; ligand ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The first coordination shell of an Mg(II) ion in a model protein environment is studied. Complexes containing a model carboxylate, an Mg(II) ion, various ligands (NH3, H2S, imidazole, and formaldehyde) and water of hydration about the divalent metal ion were geometry optimized. We find that for complexes with the same coordination number, the unidentate carboxylate-Mg(II) ion is greater than 10 kcal mol-1 more stable than the bidentate orientation. Imidazole was found to be the most stable ligand, followed in order by NH3 formaldehyde, H2O, and H2S. © 1995 Wiley-Liss, Inc.
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  • 69
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 97-110 
    ISSN: 0887-3585
    Keywords: bovine pancreatic trypsin inhibitor ; cluster analysis ; conformational searching ; molecular dynamics ; protein tertiary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using energy minimization and cluster analysis, we have analyzed a 1020 ps molecular dynamics trajectory of solvated bovine pancreatic trypsin inhibitor. Elucidation of conformational sub states in this way both illustrates the degree of conformational convergence in the simulation and reduces the structural data to a tractable subset. The relative movement of structures upon energy minimization was used to estimate the sizes of features on the protein potential energy surface. The structures were analyzed using their pairwise root-mean-square Cα deviations, which gave a global measure of conformational changes that would not be apparent by monitoring single degrees of freedom. At time scales of 0.1 ps, energy minimization detected sharp transitions between energy minima separated by 0.1 Å rms deviation. Larger conformational clusters containing these smaller minima and separated by 0.25 Å were seen at 1 ps time scales. Both of these small features of the conformational landscape were characterized by movements in loop regions associated with small, correlated backbone dihedral angle shifts. On a nanosecond time scale, the main features of the protein energy landscape were clusters separated by over 0.7 Å rms deviation, with only seven of these sub states visited over the 1 ns trajectory. These substates, discernible both before and after energy minimization, differ mainly in a monotonic pivot of the loop residues 11-18 over the course of the simulation. This loop contains lysine 17, which specifically binds to trypsin in the active site. The trajectory did not return to previously visited clusters, indicating that this trajectory has not been shown to have completely sampled the conformational substates available to it. Because the apparent convergence to a single region of conformation space depends on both the time scale of observation and the size of the conformational features examined, convergence must be operationally defined within the context of the simulation. © 1995 Wiley-Liss, Inc.
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  • 70
    ISSN: 0887-3585
    Keywords: antibody-protein complex ; influenza virus hemagglutinin ; protein recognition ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fab fragments from two different monoclonal antibodies (BH151 and HC45) which bind to the same antigenic region of the influenza hemagglutinin were crystallized as complexes with the hemagglutinin. The complexes crystallize in PEG 600, pH 6.0, and PEG 2000, pH 8.5, respectively. Both crystals belong to space group P321, with very similar unit cell dimensions. © 1995 Wiley-Liss, Inc.
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  • 71
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 187-190 
    ISSN: 0887-3585
    Keywords: cytokine ; BCRF1 ; protein structure ; crystal seeding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of recombinant human interleukin 10 have been grown from solutions of ammonium sulfate. The crystals are tetragonal, space group P41212 or P43212; the unit cell axes are a = 36.5 Å and c = 221.9 Å. There is the equivalent of one polypeptide chain in the asymmetric unit. The crystals are stable to X-rays and diffract to at least 2.5 Å resolution. © 1995 Wiley-Liss, Inc.
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  • 72
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 345-350 
    ISSN: 0887-3585
    Keywords: methyltransferase ; methylesterase ; protein modification ; S-adenosyl-L-methionine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacterial chemotaxis receptor modifying enzymes from Salmonella typhimurium have been crystallized using microseeding techniques. The crystals of the S-adenosyl-L-methionine-dependent methyl transferase, CheR, belong to the monoclinic space group P21 with cell constants a = 55.1 Å, b = 48.1 Å, c = 63.1 Å, β = 112.3°. The crystals of the catalytic domain of the methylesterase, CheB, belong to the trigonal space group P3221 or P3121 with unit cell dimensions of a = b = 63.4 Å, c = 86.8 Å. Both crystals contain one molecule per asymmetric unit and have calculated Matthews' volumes of 2.4 Å3/Da. © 1995 Wiley-Liss, Inc.
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  • 73
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    Proteins: Structure, Function, and Genetics 21 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 74
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 1-10 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein phosphatase ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A bona fide consensus prediction for the secondary and supersecondary structure of the serine-threonine specific protein phosphatases is presented. The prediction includes assignments of active site segments, an internal helix, and a region of possible 310 helical structure. An experimental structure for a member of this family of proteins should appear shortly, allowing this prediction to be evaluated. © 1995 Wiley-Liss, Inc.
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  • 75
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 11-21 
    ISSN: 0887-3585
    Keywords: phage display ; protein stability ; genetic selection ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method has been developed to select proteins that are thermodynamically destabilized yet still folded and functional. The DNA encoding the B1 IgG-binding domain from Group G Streptococcus (Strp G) has been fused to gene III of bacteriophage M13. The resulting fusion protein is displayed on the surface of the phage thus enabling the phage to bind to IgG molecules. In addition, these phage exhibit a small plaque phenotype that is reversed by mutations that destabilize the Strp G domain. By selecting phage with large plaque morphology that retain their IgG-binding function, it is possible to identify mutants that are folded but destabilized compared with wild-type Strp G. Such mutants can be divided into three general categories: (1) those that disrupt packing of hydrophobic side chains in the protein interior; (2) those that destabilize secondary structure; and (3) those that alter specific hydrogen bonds involving amino acid side chains. A number of the mutants have been physically characterized by circular dichroism and nuclear magnetic resonance and have been shown to have structures similar to wild-type Strp G but stabilities that were decreased by 2-5 kcal/mol. © 1995 Wiley-Liss, Inc.
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  • 76
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 30-39 
    ISSN: 0887-3585
    Keywords: protein-protein interaction ; protein-DNA interaction ; microcalorimetry ; heat capacity changes ; entropy ; accessible surface area ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The affinity of two molecules for each other and its temperature dependence are determined by the change in enthalpy, free enthalpy, entropy, and heat capacity upon dissociation. As we know the forces that stabilize-protein-protein or protein-DNA association and the three-dimensional structures of the complex, we can in principle derive values for each one of these parameters. The calculation is done first in gas phase by molecular mechanics, then in solution with the help of hydration parameters calibrated on small molecules. However, estimates of enthalpy and entropy changes in gas phase have excessively large error bars even under the approximation that the components of the complex associate as rigid bodies. No reliable result can be expected at the end. The fit to experimental values derived from binding and calorimetric measurements is poor, except for the dissociation heat capacity. This parameter can be attributed mostly to the hydration step and it correlates with the size of the interface. Many protein-protein complexes have interface areas in the range 1200-2000 Å2 and only small conformation changes, so the rigid body approximation applies. It is less generally valid in protein-DNA complexes, which have interfaces covering 2200-3100 Å2, large dissociation heat capacities, and affect both the conformation and the dynamics of their components. © 1995 Wiley-Liss, Inc.
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  • 77
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 68-69 
    ISSN: 0887-3585
    Keywords: microtubule motors ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The motor domain of the kinesin homolog ncd has been crystallized in the presence of MgATP by the vapor diffusion method using polyethylene glycol as the precipitant. The crystals belong to the orthorhombic space group I222 with unit cell dimensions a = 127.1 Å, b = 122.3 Å, c = 68.0 Å, and there is one ncd molecule per asymmetric unit. The crystals diffract X-ray to at least 2.3 Å and are appropriate for high-resolution structure determination. © 1995 Wiley-Liss, Inc.
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  • 78
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 40-56 
    ISSN: 0887-3585
    Keywords: zinc parameterization ; effective force-field ; four-coordination ; five-coordination ; reaction mechanism ; ligand exchange ; bond length constraint ; ligand dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force-field reproduces excellently the geometry of quantum chemically optimized zinc complexes as well as the crystallographic geometry of the active site of alcohol dehydrogenase and small organic structures. The parameterization is used in molecular dynamics simulations and molecular mechanical energy minimizations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. The active-site zinc ion seems to prefer four-coordination over five-coordination by at least 36 kJ/mol. The only stable binding site of a fifth ligand at the active-site zinc ion is opposite to the normal substrate site, in a narrow cavity behind the zinc ion. Only molecules of the size of water or smaller may occupy this site. There are large fluctuations in the geometry of the zinc coordination sphere. A four-coordinate water molecule alternates frequently (every 7 ps) between the substrate site and the fifth binding site and even two five coordinate water molecules may interchange ligation sites without prior dissociation. Ligand exchange at the zinc ion probably proceeds by a dissociative mechanism. The results show that it is essential to allow for bond stretching degrees of freedom in molecular dynamics simulations to get a correct description of the dynamics of the metal coordination sphere; bond length constraints may restrict the accessible part of the phase space and therefore lead to qualitatively erroneous results. © 1995 Wiley-Liss, Inc.
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  • 79
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 81-99 
    ISSN: 0887-3585
    Keywords: protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe LINUS, a hierarchic procedure to predict the fold of a protein from its amino acid sequence alone. The algorithm, which has been implemented in a computer program, was applied to large, overlapping fragments from a diverse test set of 7 X-ray-elucidated proteins, with encouraging results. For all proteins but one, the overall fragment topology is well predicted, including both secondary and supersecondary structure. The algorithm was also applied to a molecule of unknown conformation, groES, inwhich X-ray structure determination is presently ongoing. LINUS is an acronym for Local Independently Nucleated Units of Structure. The procedure ascends the folding hierarchy in discrete stages, with concomitant accretion of structure at each step. The chain is represented by simplified geometry and folds under the influence of a primitive energy function. The only accurately described energetic quantity in this work is hard sphere repulsion-the principal forceinvolved in organizing protein conformation [Richards, F. M. Ann. Rev. Biophys. Bioeng. 6:151-176, 1977]. Among other applications, the method is a natural tool for use in the human genome initiative. © 1995 Wiley-Liss, Inc.
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  • 80
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 110-118 
    ISSN: 0887-3585
    Keywords: protein folding ; guanidine hydrochloride denaturation ; molten globule ; folding/unfolding kinetics ; proline isomerization ; slow-folding forms ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The TEM-1 β-lactamase is a globular protein containing 12 proline residues. The folding mechanism of this enzyme was investigated by kinetic and equilibrium experiments with the help of fluorescence spectroscopy and circular dichroism. The equilibrium denaturation of the protein induced by guanidine hydrochloride occurs in two discrete steps, indicating the existence of a thermodynamically stable intermediate state. Thisstate is 5.2 ± 0.4 kcal/mol less stable than the native conformation and 5.7 ± 0.2 kcal/mol more stable than the fully denaturedprotein. This intermediate state exhibits a high content of native secondary structure elements but is devoid of specific tertiary organization; its relation to the “molten globule” is discussed. Refolding kinetic experimentsrevealed the existence of a transient intermediate conformation between thethermodynamically stable intermediate and the native protein. This transient intermediate appears rapidly during the folding reaction. It exhibits a secondary structure content very similar to that of the native protein and has also recovered a significant amount of tertiary organisation. The final refolding step of the TEM-1 β-lactamase, leading to the native enzyme, is dominated by two major slow kinetic phases which probablyreflect a very complex process kinetically limited by proline cis/transisomerization. © 1995 Wiley-Liss, Inc.
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  • 81
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    Proteins: Structure, Function, and Genetics 21 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 82
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 74-77 
    ISSN: 0887-3585
    Keywords: crystallization ; membrane protein ; X-ray diffraction ; atomic resolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Fv fragment of a monoclonal antibody, 7E2 (IgG1, κ, murine), which is directed against the integral membrane protein cytochrome c oxidase (EC 1.9.3.1) from Paracoccus denitrificans, was cloned and produced in Escherichia coli. Crystals suitable for highresolution X-ray analysis were obtained by microdialysis under low salt conditions. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 51.51 Å, b = 56.15 Å, c = 99.86 Å (1 Å = 0.1 nm) and contain one F v fragment per asymmetric unit. Using synchrotron radiation diffraction data were collected up to 1.28 Å resolution. This high resolution is very unusual for a heterodimeric protein. The crystals should open the way for refining not only the atomic positions, but also for obtaining information about internal dynamics. © 1995 Wiley-Liss, Inc.
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  • 83
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 78-81 
    ISSN: 0887-3585
    Keywords: T = 3 plant virus ; tymovirus ; protein crystallization ; X-ray diffraction ; synchrotron radiation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Turnip yellow mosaic virus (TYMV) was purified from Chinese cabbage and crystallized in a form that permits high resolution structural analysis using X-ray diffraction. The crystals have a hexagonal bipyramidal morphology and often achieve dimensions of 1.0 × 1.0 × 0.5 mm. The crystals appear to be of hexagonal space group P6222 with a = b = 525 Å, c=315 Å, but we cannot strictly rule out the possibility that the space group is P622. They appear different than any crystals of TYMV previously reported. There are three T = 3 virus particles in the unit cell, which implies that one quarter of the particle, or 45 protein subunits, comprises the asymmetric unit of the crystal. Native data have been collected using synchrotron radiation to a resolution of 3.2 Å. © 1995 Wiley-Liss, Inc.
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  • 84
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 83-90 
    ISSN: 0887-3585
    Keywords: cytochrome c ; thermodynamics ; antibody binding ; microcalorimetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper we study the binding of two monoclonal antibodies, E3 and E8, to cytochrome c using high-sensitivity isothermal titration calorimetry. We combine the calorimetric results with empirical calculations which relate changes in heat capacity to changes in entropy which arise from the hydrophobic effect. The change in heat capacity for binding E3 is -350 ± 60 cal K-1 mol-1 while for E8 it is -165 ± 40 cal K-1 mol-1. This result indicates that the hydrophobic effect makes a much larger contribution for E3 than for E8. Since the total entropy change at 25°C is very similar for both antibodies, it follows that the configurational entropy cost for binding E3 is much larger than for binding E8 (-77 ± 15 vs. -34 ± 11 cal K-1 mol-1). These results illustrate a case of entropy compensation in which the cost of restricting conformational degrees of freedom is to a large extent compensated by solvent release. We also show that the thermodynamic data can be used to make estimates of the surface area changes that occur upon binding. The results of the present study are consistent with previous hydrogen-deuterium exchange data, detected using 2D NMR, on the two antibody-antigen interactions. The NMR study indicated that protection from exchange is limited to the binding epitope for E8, but extends beyond the epitope for E3. These results were interpreted as suggesting that a larger surface area was buried on cytochrome c upon binding to E3 than to E8, and that larger changes in configurational entropy occur upon binding of E3 than E8. These findings are confirmed by the present study using isothermal titration calorimetry. © 1995 Wiley-Liss, Inc.
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  • 85
    ISSN: 0887-3585
    Keywords: transhydrogenase ; NAD binding ; prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A three-dimensional structure of the NAD site of Escerichia coli transhydrogenase has been predicted. The model is based on analysis of conserved residues among the transhydrogenases from five different sources, homologies with enzymes using NAD as cofactors or substrates, hydrophilicity profiles, and secondary structure predictions. The present model supports the hypothesis that there is one binding site, located relatively close to the N-terminus of the α-subunit. The proposed structure spans residues α145 to α287, and it includes five β-strands and five α-helices oriented in a typical open twisted α/β conformation. The amino acid sequence following the GXGXXG dinucleotide binding consensus sequence (residues α172 to α177) correlates exactly to a typical fingerprint region for ADP binding βαβ folds in dinucleotide binding enzymes. In the model, aspartic acid α195 forms hydrogen bonds to one or both hydroxyl groups on the adenosine ribose sugar moiety. Threonine α196 and alanine α256, located at the end of βB and βD, respectively, create a hydrophobic sandwich with the adenine part of NAD buried inside. The nicotinamide part is located in a hydrophobic cleft between αA and βE. Mutagenesis work has been carried out in order to test the predicted model and to determine whether residues within this domain are important for proton pumping directly. All data support the predicted structure, and no residue crucial for proton pumping Was detected. Since no three-dimensional structure of transhydrogenase has been solved, a well based tertiary structure prediction is of great value for further experimental design in trying to elucidate the mechanism of the energy-linked proton pump. © 1995 Wiley-Liss, Inc.
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  • 86
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 118-126 
    ISSN: 0887-3585
    Keywords: O-glyeosylation ; Ser-conjugated substrate ; Thr-conjugated substrate ; nonapeptide ; reduced 8-D space ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The specificity of UDP-Gal-NAc:polypeptide N-acetylgalactosaminytransferase (GalNAc-transferase) is consistent with the existence of an extended site composed of nine subsites, denoted by P4, P3, P2, P1, P0, P1′, P2′, P3′, and P4′, where the acceptor at P0 is being either Ser or Thr. To predict whether a peptide will react with the enzyme to form a Ser- or Thr-conjugated glycopeptide, a vector projection method is proposed which uses a training set of amino acid sequences surrounding 90 Ser and 106 Thr O-glycosylation sites extracted from the National Biomedical Research Foundation Protein Database. The model postulates independent interactions of the 9 amino acid moieties with their respective binding sites. The high ratio of correct predictions vs. total predictions for the data in both the training and the testing sets indicates that the method is self-consistent and efficient. It provides a rapid means for predicting O-glycosylation and designing effective inhibitors of GalNAc-transferase. © 1995 Wiley-Liss, Inc.
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  • 87
    ISSN: 0887-3585
    Keywords: crystals ; X-ray structure ; (α/β)8 barrel protein ; 222 molecular symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Sweet potato β-amylase is a tetramer of identical subunits, which are arranged to exhibit 222 molecular symmetry. Its subunit consists of 498 amino acid residues (Mr 55,880). It has been crystallized at room temperature using polyethylene glycol 1500 as precipitant. The crystals, growing to dimensions of 0.4 mm × 0.4 mm × 1.0 mm within 2 weeks, belong to the tetragonal space group P42212 with unit cell dimensions of a = b = 129.63 Å and c = 68.42 Å. The asymmetric unit contains 1 subunit of β-amylase, with a crystal volume per protein mass (VM) of 2.57 Å3/Da and a solvent content of 52% by volume. The three-dimensional structure of the tetrameric β-amylase from sweet potato has been determined by molecular replacement methods using the monomeric structure of soybean enzyme as the starting model. The refined subunit model contains 3,863 nonhydrogen protein atoms (488 amino acid residues) and 319 water oxygen atoms. The current R-value is 20.3% for data in the resolution range of 8-2.3 Å (with 2 σ cut-off) with good stereochemistry. The subunit structure of sweet potato β-amylase (crystallized in the absence of α-cyclodextrin) is very similar to that of soybean β-amylase (complexed with α-cyclodextrin). The root-mean-square (RMS) difference for 487 equivalent Cα atoms of the two β-amylases is 0.96 Å. Each subunit of sweet potato β-amylase is composed of a large (α/β)8 core domain, a small one made up of three long loops [L3 (residues 91-150), LA (residues 183-258), and L5 (residues 300-327)], and a long C-terminal loop formed by residues 445-493. Conserved Glu 187, believed to play an important role in catalysis, is located at the cleft between the (α/β)8 barrel core and a small domain made up of three long loops (L3, L4, and L5). Conserved Cys 96, important in the inactivation of enzyme activity by sulfhydryl reagents, is located at the entrance of the (α/β)8 barrel. © 1995 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
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  • 88
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 127-129 
    ISSN: 0887-3585
    Keywords: inverse folding ; polar fraction ; potential of mean force ; Boltzmann device ; sequence-structure alignment ; conformation recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: On the study of protein inverse folding problem, one goal is to find simple and efficient potential to evaluate the compatibility between structure and a given sequence. We present here a novo empirical mean force potential to address the importance of electrostatic interactions in protein inverse folding study. It is based on protein main chain polar fraction and constructed in a way similar with Sippl's from a database of 64 known independent three-dimensional protein structures. This potential was applied to recognize the protein native conformations among a conformation pool. Calculated results show that this potential is powerful in picking out native conformations, in addition it can also find structure similarity between proteins with low sequence similarity. The success of this new potential clearly shows the importance of electrostatic factors in protein inverse folding studies. © 1995 Wiley-Liss, Inc.
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  • 89
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 73-82 
    ISSN: 0887-3585
    Keywords: protein folding ; protein structure ; genetic algorithms ; Monte Carlo simulations ; ring closure ; dihedral angles ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have enhanced genetic algorithms and Monte Carlo methods for simulation of protein folding by introducing “local moves” in dihedral space. A local move consists of changes in backbone dihedral angles in a sequential window while the positions of all atoms outside the window remain unchanged. We find three advantages of local moves: (1) For some energy functions, protein conformations of lower energy are found; (2) these low energy conformations are found in fewer steps; and (3) the simulations are less sensitive to the details of the annealing protocol. To distinguish the effectiveness of local move algorithm from the complexity of the energy function, we have used several different energy functions. These energy functions include the Profile score (Bowie et al., Science 253:164-170, 1991), the knowledge-based energy function used by Bowie and Eisenberg 1994 (Proc. Natl. Acad. Sci. U.S.A. 91:4434-4440, 1994), two energy terms developed as suggested by Sippl and coworkers (Hendlich et al., J. Mol. Biol. 216:167180, 1990), and AMBER (Weiner and Kollman, J. Comp. Chem. 2:287-303, 1981). Besides these energy functions we have used three energy functions that include knowledge of the native structures: the RMSD from the native structure, the distance matrix error, and an energy term based on the distance between different residue types called DBIN. In some of these simulations the main advantage of local moves is the reduced dependence on the details of the annealing schedule. In other simulations, local moves are superior to other algorithms as structures with lower energy are found. © 1995 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 90
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 83-96 
    ISSN: 0887-3585
    Keywords: ROP protein ; 4-α-helix-bundle ; protein stability ; cavity mutations ; heat capacity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structural and energetic perturbations caused by cavity-creating mutations (Leu-41 → Val and Leu-41 → Ala) in the dimeric 4-α-helical-bundle protein ROP have been characterized by CD spectroscopy and differential scanning calorimetry (DSC). Deconvolution of the CD spectra showed a decrease in α -helicity as a result of the amino acid exchanges that follows qualitatively the overall decrease in conformational stability. Transition enthalpies are sensitive probes of the energetic change associated with point mutations. ΔH0 values at the respective transition temperatures, T1/2 (71.0, 65.3, and 52.9°C at 0.5 mg/ml) decrease from 580 ± 20 to 461 ± 20 kJ/(mol of dimmer) and 335 ± 20 kJ/(mol of dimmer) for wildtype ROP (Steif, C., Weber, P., Hinz, H.-J., Flossdorf, J., Cesareni, G., Kokkinidis, M. Biochemistry 32:3867-3876, 1993), L41V, and L41A, respectively. The conformational stabilities at 25°C expressed by the standard Gibbs energies of denaturation, ΔGD0, are 71.7, 61.1, and 46.1 kJ/(mol of dimmer). The corresponding transition enthalpies have been obtained from extrapolation using the cpD(T)and cpN(T) functions. Their values at 25°C are 176.3, 101.9, and 141.7 kJ/(mol of dimmer) for wild-type ROP, L41V, and L41A, respectively. When the stability perturbation resulting from the cavity creating mutations is referred to the exchange of 1 mol of CH2 group, the average ΔΔGD0 value is -5.0 ± 1 kJ/(mol of CH2 group). This decrease in conformation stability suggests that dimeric ROP exhibits the same susceptibility to Leu → Yal and Leu → Ala exchanges as small monomeric proteins. Careful determinations of the partial specific heat capacities of wild-type and mutated protein solutions suggest that the mutational effects are predominantly manifested in the native rather than the unfolded state. © 1995 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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  • 91
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 111-114 
    ISSN: 0887-3585
    Keywords: replication ; amplification ; PCR ; enzyme ; thermostability ; x-ray ; diffraction ; synchrotron ; three-dimensional ; structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thermus aquaticus DNA polymerase I is an enzyme that is of both physiological and technological interest. It carries out template-directed polymerization of DNA at elevated temperatures and is widely used in polymerase chain reaction (PCR). We have obtained crystals of the enzyme that diffracts X-rays to at least 3.0 Å resolution in a cubic space group. Determination of the three-dimensional structure of the native enzyme along with those of relevant complexes will greatly enhance our knowledge of molecular events involved in DNA replication, will permit improvements in PCR, and will add to our knowledge of the structural bases of thermo stability in proteins. © 1995 Wiley-Liss, Inc.
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  • 92
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 237-243 
    ISSN: 0887-3585
    Keywords: domain motions ; crystal packing effects ; protein dynamics ; induced-fit ; enzyme dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3. Each simulation was 200 ps in length and included a 10 Å layer of explicit solvent. The simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-averaged structures are to each other. In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations. The mouth of the substrate binding pocket is significantly more mobile in the simulation of molecule 2 than in the simulation of molecule 1. For molecule 1, the width of the mouth is only slightly larger than its X-ray value of 8.7 Å and undergoes fluctuations of about 1 Å. However, in molecule 2, the mouth of the substrate binding pocket is dramatically more open in the time-average molecular dynamics structure (14.7 Å) than in the X-ray structure (10.9 Å). Furthermore, this region of the protein undergoes large amplitude motions during the trajectory that are not seen in the trajectory of molecule 1, repeatedly opening and closing up to 7 Å. Presumably, the binding of different substrates will induce the mouth region to adopt different conformations from within the wide range of structures that are accessible. © 1995 Wiley-Liss, Inc.
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  • 93
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    Proteins: Structure, Function, and Genetics 21 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 94
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 95
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 118-121 
    ISSN: 0887-3585
    Keywords: protein crystals ; X-ray crystallography ; cleaved serpins ; plasminogen activator inhibitor-1 ; PAI-1 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To characterize the structural requirements for the conformational flexibility in plasminogen activator inhibitor-1 (Pal-1) we have crystallized human PAI-1, carrying a mutation which stabilizes PAI-1 in its substrate form. Crystallization was performed by the hanging drop diffusion method at pH 8.5 in the presence of 19% (w/v) polyethyleneglycol 4000 as a precipitant. The crystals appear after 3 days at 23°C and belong to the monoclinic space group C2 with cell dimensions of a=151.8 Å, b=47.5 Å, c=62.7 Å, and β=113.9°, and one molecule in the asymmetric unit. The X-ray diffraction data set contains data with a limiting resolution of 2.5 Å. Biochemical analysis of the redissolved crystals indicated that during the crystallization process, cleavage had occurred in the active site loop at the P1-P1′ position. The availability of good-quality crystals of the cleaved form of this serpin will allow its three-dimensional structure to be solved and will provide detailed information on the structure-function relationship in PAI-1. © 1995 Wiley-Liss, Inc.
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  • 96
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 126-127 
    ISSN: 0887-3585
    Keywords: abrin ; ribosome inactivating protein ; sparse matrix method ; synchrotron radiation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals have been obtained for a recombinant abrin-a A-chain produced by E. coli. The crystals were grown using PEG6000 as the precipitating agent. The crystals belong to an orthrhombic space group P 212121 and diffract to 1.7 Å. © 1995 Wiley-Liss, Inc.
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  • 97
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 273-281 
    ISSN: 0887-3585
    Keywords: prediction contests ; α-β barrel ; protein sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two separate unrefined models for the secondary structure of two subfamilies of the 6-phospho-β-D-galactosidase superfamily were independently constructed by examining patterns of variation and conservation within homologous protein sequences, assigning surface, interior, parsing, and active site residues to positions in the alignment, and identifying periodicities in these. A consensus model for the secondary structure of the entire superfamily was then built. The prediction tests the limits of an unrefined prediction made using this approach in a large protein with substantial functional and sequence divergence within the family. The protein belongs to the (α-β class), with the core β strands aligned parallel. The supersecondary structural elements that are readily identified in this model is a parallel β sheet built by strands C, D, and E, with helices 2 and 3 connecting strands (C + D) and (D + E), respectively, and an analogous α-β unit (strand G and helix 7) toward the end of the sequence. The resemblance of the supersecondary model to the tertiary structure formed by 8-fold α-β barrel proteins is almost certainly not coincidental. © 1995 Wiley-Liss, Inc.
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  • 98
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 303-306 
    ISSN: 0887-3585
    Keywords: lipoamide dehydrogenase ; lipoyl domain ; binding protein-dependent transport ; dehydrogenase complex ; sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A protein of molecular weight of 64 kDa (p64k) found in the outer membrane of Neisseria meningitidis shows a high degree of homology with both the lipoyl domain of the acetyltransferase and the entire sequence of the lipoamide dehydrogenase, the E2 and E3 components of the dehydrogenase multienzyme complexes, respectively. The alignment of the p64k with lipoyl domains and lipoamide dehydrogenases from different species is presented. The possible implications of this protein in binding protein-dependent transport are discussed. This is the first lipoamide dehydrogenase reported to have a lipoyl domain. © 1995 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 99
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 307-318 
    ISSN: 0887-3585
    Keywords: Lactobacillus bulgaricus ; D-2-hydroxy acid dehydrogenase ; formate dehydrogenase ; structure prediction ; L-lactate dehydrogenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A three-dimensional structure of the NAD-dependent D-lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge-based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D-LDH subunit shows, as for the formate dehydrogenase, an α/β structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His-296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg-235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe-299, a candidate for stabilizing the methyl group of the substrate. © 1995 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 100
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 282-302 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; configurational sampling ; glycine ; alanine ; valine and threonine dipeptides ; isobutyryl-(Ala)3-NH-methyl ; oligoalanine ; unfolding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5-20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full αR-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix-coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc.
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