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  • 2010-2014
  • 1990-1994  (1,196)
  • 1994  (1,196)
  • Biochemistry and Biotechnology  (1,044)
  • crystal structure  (154)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Il nuovo cimento della Società Italiana di Fisica 16 (1994), S. 1671-1678 
    ISSN: 0392-6737
    Keywords: Effects of material synthesis ; crystal structure ; chemical composition ; Y-based compounds ; Conference proceedings
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Summary YBCO with high granulometric perfection and low dispersion can be obtained by a low-temperature reaction (≈800°C) of atomic-scale dispersed powders, produced through the thermal decomposition of liquid precursors. As reacted such powders are tetragonal and not superconducting, but they transform into the high-T c phase after optimized annealing treatments. We describe the method we developed and the characteristics of the materials we achieved, and we discuss the main features of the process in the light of the current know-how.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 24 (1994), S. 759-762 
    ISSN: 1572-8854
    Keywords: Sulfonamide ; methanesulfonanilide ; crystal structure ; molecular structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound, crystallizes in the triclinic space group $$P\bar 1$$ witha=8.232(4),b=9.159(2),c=10.230(3)Å. α=74.07(3)°, β=72.50(4)°, γ=63.65(3)° andZ=2. The structure was solved by direct methods and refined by full matrix least squares methods toR=0.054 for 1817 observed reflections. The plane containing the nitrogen and sulfur atoms is perpendicular to the aromatic plane. One of the S−O bonds in each methanesulfonyl group is in nearly eclipsed conformation with the N−C bond.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 24 (1994), S. 437-440 
    ISSN: 1572-8854
    Keywords: Ca(C4H4O4)·H2O ; pentagonal pyramid ; calcium succinate ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The crystal structure of calcium succinate monohydrate, Ca(C4H4O4)·H2O, has been determined by single crystal X-ray diffraction. The crystals are monoclinic witha=11.952(2),b=9.691(2),c=11.606(2)Å, β=108.81(1)°, space group C2/c,Z=8,V=1272.49 Å3,d m =1.80, andd c =1.818 Mg m−3. The structure was refined by full-matrix least-squares techniques toR=0.027,R w =0.040, for 829 reflections with1≥3δ(I). Ca is coordinated to seven oxygen atoms, and the coordination polyhedron is best described as a pentagonal bipyramid. One carboxylate group in the succinate ion is bonded to three different Ca ions, forming a four-membered chelate ring with one Ca ion is bonded to three different Ca ions, forming a four-membered chelate ring with one Ca ion and unidentate bridge bonds to two other Ca ions. The other carboxylate group is bonded to two Ca ions through unidentate bonds. The structure is highly polymeric. The general structural features are nearly identical to those of calcium adipate monohydrate.
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  • 4
    ISSN: 1572-8854
    Keywords: Pyrimidine ; uracil ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract A new and easy method for the preparation of 1,3,7,9-tetramethylpyrido-[2,3-d∶6,5-d′]-dipyrimidine-2,4,6,8-tetrone is described. The structure of this compound has been solved by means of X-ray diffraction methods. The chemical characterization by spectral (mass, ultraviolet, infrared, and proton nuclear magnetic resonance) and thermal (thermogravimetry and differential scanning calorimetry) method is also reported. The compound is monoclinic, space groupP21/c,a=12.720(5),b=13.688(7),c=8.079(2) Å, β=107.06(4)°,Z=4. The structure consists of discrete tricyclic molecules, stacking playing an important role in crystal packing.
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  • 5
    ISSN: 1572-8862
    Keywords: Tungsten ; isomeric forms ; crystal structure ; triple bonds ; interconversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract A thorough study of compounds with the formula W2Cl4(NHCMe3)2(PR3)2, withR 3=Me3, Et3, Prg n 3 Me2,Ph, is reported. In addition to the previously reported crystalline compounds, namely Ia,trans-W2Cl4(NHCMe3)2(PMe3)2 in space group Pmmn;3a,trans-W2Cl4(NHCM3)2(PEt3)2 in space group P21/a (or P21/c); and4,cis-W2Cl4(NHCMe3)2(PMe2Ph)2 in Pna21, we have obtained and structurally characterized the following new substances,1b,trans-W2Cl4,(NHCMe3)2(PMe2)2, space group P21/c,a= 12.233 (4) Å,b= 12.872 (4) Å,c=17.095 (5) Å,β=93.52 (2)°,Z=4,V=2687 (1) Å3 2,cis-W2Cl4(NHCMe3)2(PMe3)2, P21/c,a=9.673 (4) Å,b=17.249 (4) Å,c=16.244 (5) Å,β=99.63 (3),Z = 4 ,V=2669 (1) Å.3b,trans-W2Cl4(NHCMe3)2(PEt3)2, Pl,a=16.850 (3) Å,b=17.797 (3) Å,c= 11.459 (2)Å,α= 101.02 (1),β= 103.13°, y=84.23 (1)°,Z=4,V= 3279 (1) Å5,trans-W2Cl4(NHCM3)2(PMe2Ph)2, Fdd2,a=39.563 (8) Å at 20°C; 39.325 (10) Å at -6O°C,b = 57.543 (17) Å at 20°C; 57.186 (16) Å at -60°C,c= 8.810 (1) Å at 20°C; 8.770 (1) Å at - 60°C ,Z=24,V=20057 (7) Å3 (20°C), 19723 (8) Å3 ( - 60°C) .6,trans-W2Cl4(NHCMe3 2(PPrn 3)2, Pl,a= 17.287 (2) Å (20°C); 17.077 (5) Å (-60°C),b= 19.119 (2) Å (20°C); 18.952 (6) Å (-60°C),c= 12.713 (1) Å (20°C); 12.668 (4) Å (-60°C),Z=4,V= 3980 (1) Å3 (20°C), 3898 (2) ,Å3 ( - 60°C). In addition, the structure of3a was re-determined and refined so that the disorder ratio was a refined parameter, leading to a value of 0.520:0.480 instead of being arbitrarily fixed at 0.50:0.50. In all of the structures the molecules are held in eclipsed (but very distorted) rotational conformations and the W-W distances are all within the range of 2.305-2.330 Å. As will be shown in a later paper, for all phosphines, thecis andtrans isomers are of similar stability and an equilibrium mixture exists in solution. It is also shown that1a and3a do not contain unexpectedly short W-N bonds as previously reported.
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  • 6
    ISSN: 1572-8862
    Keywords: Mixed metal cluster ; alkyne ; diphenylacetylene ; platinum ; osmium ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstract The new platinum-osmium alkyne cluster complex Pt2Os4(CO)8(μ3-PhC2Ph)3 (μ 4-PhC2Ph),2, was obtained from the reaction of Pt2Os4(CO)18,1b, with PhC2Ph and was characterized by IR.1H NMR and single-crystal X-ray diffraction analyses. The cluster of compound2 consists of an osmium capped Pt2Os3 square pyramid. It aLso contains three triply bridging and one quadruply bridging diphenylacetylene ligands. Crystal data for2: space group PI,a = 12.530(2) Å,b = 21.565(4) Å,c = 11.284(2) Å,α = 100.31(2),β = 111.89(1),β = 76.78(2),Z = 2, 3879 reflections,R = 0.032.
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  • 7
    ISSN: 1572-8854
    Keywords: Centrosymmetric ; symmetry ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The title compound crystallizes in the centrosymmetric triclinic space group $$P\bar 1$$ (C 1 l ; No.2) witha=9.9143(10) Å,b=10.2616(11) Å,c=10.7715(10) Å, α=113.887(8)°, β=109.197(8)°, γ=90.699(9)°,V=932.78(17) Å3 andZ=1. A total of 4869 data were collected and merged to a set of 2450 independent reflections; the structure was solved and refined toR=1.42% andwR=1.94%. The molecule lies on a site of $$\bar 1$$ symmetry and is disordered, with obvious scrambling of carbonyl and chloride ligands. Resulting bond lengths include Ir−P=2.339(1) Å, Ir−Cl=2.398(4) Å and Ir−CO=1.808(15) Å.
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  • 8
    ISSN: 1572-9605
    Keywords: High-Tc superconductivity ; La1.9Bi0.1CuO4+δ ; excess oxygen ; crystal structure ; superconducting transition temperature
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Notes: Abstract We have investigated the relation between the crystal structure and superconductivity in La1.9Bi0.1CuO4+δ , in which the phase separation observed in La2CuO4+δ is suppressed. A phase diagram in theT−δ plane is given for La1.9Bi0.1CuO4+δ with excess oxygen. For very smallδ values, the crystal structure is orthorhombic, and an orthorhombic-tetragonal phase transition occurs markedly atδ ∼ 0.03 in the measured temperature range between 13 and 293 K. Superconductivity is observed in the range of 0.04〈δ〈0.11. This is clear evidence thathigh-T c superconductivity also appears in the tetragonal phase.
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  • 9
    ISSN: 1572-882X
    Keywords: cellulose I ; molecular mechanics ; crystal structure ; molecular ; modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Energies for various trial packing arrangements of unit cells for the Iα and Iβ phases of native cellulose discovered by Sugiyamaet al. were evaluated. Both a rigid-ring method, PLMR, and the full-optimization, molecular mechanics program, MM3(90), were used. For both phases the models that had the lowest PLMR energy also had the lowest MM3 energy. Both calculated models have the chains packed ‘up’, O6s intg positions, and the same sheets of hydrogen-bonded chains. The Iβ structure model is essentially identical to that proposed previously for ramie cellulose by Woodcock and Sarko. It is also the same as the best parallel model previously proposed that was based on the X-ray data of Mann, Gonzalez and Wellard, once the various unit cell conventions are considered. Also, the energies from both methods for all three celluloses, Iα, Iβ and II, are in the order that rationalizes their relative stabilites.
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  • 10
    ISSN: 1573-904X
    Keywords: ephedrine ; pseudoephedrine ; salicylate ; chirality ; salt formation ; homochiral crystal ; racemic compound ; racemic conglomerate ; crystal structure ; conformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The physicochemical properties and crystal structures of the crystalline salts formed by the interaction of an achiral anion, salicylate, with homochiral and racemic ephedrinium and pseudoephedrinium cations were determined. The interaction of ephedrinium or pseudoephedrinium with salicylate in aqueous solution yielded crystalline salts with the notable exception of homochiral ephedrinium. Evaporation of the solvent from solutions of homochiral ephedrine and salicyclic acid in various organic solvents, as well as grinding together solid homochiral ephedrine and solid salicylic acid, yielded viscous semisolids suggesting that homochiral ephedrinium salicylate has a low melting point and/or a high aqueous solubility. Mixing of the two viscous solids, obtained by grinding each of the opposite enantiomers of ephedrine with equimolar salicylic acid, resulted in the formation of racemic ephedrine and subsequently, upon heating, in the formation of racemic ephedrinium salicylate. While racemic ephedrinium salicylate exists as a crystalline compound (P21/n space group) with an equal number of opposite enantiomers in the unit cell, its diastereomer, racemic pseudoephedrinium salicylate, exists as a conglomerate, i.e. a physical mixture, of the homochiral crystals of the opposite enantiomers (each P21 space group). The inability of homochiral ephedrinium to exist as a crystalline salicylate salt at 20–25°C is attributed to its high energy conformation and/or to the poor packing of homochiral ephedrinium salicylate molecules in the crystal lattice.
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  • 11
    ISSN: 1572-9001
    Keywords: tris(pyrazol-1-yl)-s-triazine ; crystal structure ; electron diffraction ; AM1 semiempirical calculation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The conformation of the TPT molecule has been analyzed using experimental and computational techniques. The solid-state molecular structure shows similar conformational features to those in the 2-pyrimidine and phenyl derivatives although a different pattern of bond angles in the triazine ring was observed. The AM1 calculations predicted two conformations of comparable stability (ΔE=1.8 kcal/mol) differing in the orientation of one pyrazole ring. While the minimum energy conformation corresponds to a model displayingC 3h symmetry (φ 1=φ 2=φ 3=0°), the other minimum (φ 1=φ 2=0°,φ 3=180°) is close to that observed in the solid state. The electron diffraction results are consistent with a planar or nearly planar conformation in agreement with the preceding studies.
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  • 12
    ISSN: 1572-9001
    Keywords: Isocinchomeronic acid ; 2,5-pyridinedicarboxylic acid ; hydrogen isocinchomeronate ; manganese(II) complex ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The reactions between Mn(II), Co(II), Ni(II), and Zn(II) ions with isocinchomeronic acid (H2-isocin) afforded complexes of the general formula M(H-isocin)2-2H2O, whereas Fe(II) gives both red and deep red-brown products of the same formula. Various physical measurements suggest that the complexes of M = Co, Ni, Zn, and Fe (brown) are octahedrally coordinated by two aqua ligands and twotrans-N,O-bidentate H-isocin− anions with dimeric hydrogen bonding. Those for M = Mn and Fe (red) are the correspondingcis isomers. The structure of the manganese complex as determined by X-ray crystallography exhibitsC 2 molecular symmetry with Mn-N = 2.279(2), Mn-O(H-isocin)− = 2.196(2), and Mn-O(aqua) = 2.137(2) Å. Each aqua ligand forms two donor O-H ⋯ O hydrogen bonds with carboxy groups of different molecules in adjacent chains.
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Journal of chemical crystallography 24 (1994), S. 731-737 
    ISSN: 1572-8854
    Keywords: Synthesis ; crystal structure ; IR data
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The synthesis, crystal structure and IR data are reported for Na2[Zn(CMA)4]·2EtOH·7H2O, where CMA− is the 9,10-dihydro-9-oxo-10-acridinacetate ion. The complex crystallizes in the monoclinic space group P2/n, with cell dimensionsa=17.335(9),b=8.440(5),c=21.875(12) Å, β=91.94(5)°,Z=2. The structure was solved by direct methods and refined to a finalR value of 0.0363 for 3022 non-zero reflections. The Zn2+ ion occupies twofold axis and is coordinated to four carboxylate ligands, the ZnO4 tetrahedron is considerably distorted with Zn−O distances of 1.978(3) and 1.961(3)Å. Each Na+ cation interacts with two water, one ethanol, and three carboxylate O atoms comprising distorted octahedron. The Zn2+ and Na+ cations are linked through monooxygen and syn-syn carboxylate bridges forming a trinuclear, mixed-metal cluster. The Zn...Na separation is 3.267(2)Å and Na...Na distance equals 3.520(2)Å. All oxygen bonded H-atoms are utilized in hydrogen bonds. The acridone rings overlap in the crystal with the 3.5 Å interlayer separations. The compound has been characterized by IR spectroscopy.
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  • 14
    ISSN: 1572-8862
    Keywords: Mixed metal ; platinum ; ruthenium ; alkyne ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Abstarct The ten metal cluster complex Pt2Ru8(CO)23(µ3−H)2, 1 was found to react with EtC2Et to form a new ten metal tris-alkyne complex Pt2Ru8(CO)18(µ3−EtC2Et)2 (µ4−EtC2Et),2 in 35% yield. Complex 2 was characterized by IR,1H NMR , and single crystalx-ray diffraction analyses. The cluster can be viewed as a dodecahedron of eight metal atoms capped with two ruthenium carbonyl groups, two triply bridging EtC2Et ligands and one quadruply bridging EtC2Et ligand. Application of the standard electron counting procedures indicate that this is an unusual complex in which the 18 electron rule applies and the polyhedral skeletal electron pair theory does not. Crystal Data for 2 2.0.5 CH2CI2: space group = P21,a = 12.759(2) A,b=18.438(2)Å,c = 20.197(3) Å,β = 91.59(1)°, Z. = 4, 6394 reflections,R = 0.037.
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  • 15
    ISSN: 1573-1111
    Keywords: 12-Membered crown ethers ; ion-selective membrane electrodes ; complexes ; crystal structure ; X-ray analysis ; conformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Lipophilic derivatives of benzo-12-crown-4 and naphtho-12-crown-4 have been synthesized. The behavior of the parent compounds and their derivatives in membrane ion-selective electrodes have been studied. Selectivity changes have been observed with the rise in lipophilicity. Crystal structures of the NaI and KI complexes of benzo-12-crown-4 (1 and2) have been determined by X-ray analysis. The alkali metal and iodide ions are in direct contact in2 but not in1. Compound1 [Na(benzo-12-crown-4)2]·I is triclinic, witha=13.368(8),b=10.727(7),c=10.325(4) Å; α=73.56(4),β=77.73(4), γ=108.70(5)°;Z=2, space group is $$P\bar 1$$ . Compound2 [K(benzo-12-crown-4)2·I] is monoclinic, witha=15.807(8),b=12.043(4),c=15.601(6) Å,β=117.74(3)°;Z=4, space groupC2/c. In both compounds the cations interact with all oxygen atoms of two crown ether molecules. Correlation of the crystal structures and behavior of the crown ethers in ion-selective membrane electrodes is discussed.
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Journal of inclusion phenomena and macrocyclic chemistry 20 (1994), S. 53-71 
    ISSN: 1573-1111
    Keywords: Lithium ionophores ; podand ; dicyclohexylamides ; Li-complex ; crystal structure ; X-ray analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The influence of structure and lipophilicity of dicyclohexylamides on the lithium selectivity in membrane electrodes is discussed. The crystal structures of the triamide podand1 and its complex with LiBr1b has been determined by X-ray analysis. Crystal data for ligand1: C48H83O6N3, triclinic,P1,a=10.749(2),b=12.097(3),c=19.123(6)Å, α=95.76(2),β=80.06(2), γ=100.27(2)0,V=2403(1) Ã3,Z=2. Crystal data for the lithium complex1b: C48H83O6N3·LiBr·x C2H5OH, monoclinic,P2 1/c,a=21.297(6),b=16.316(8),c=19.450(4) Å,β=110.87(2)0,V=6315(3) Å3,Z=4. In the complex the ligand adopts a conformation in which oxygen binding sites surrounding the Li+ cation form a slightly distorted trigonal prism.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Journal of inclusion phenomena and macrocyclic chemistry 17 (1994), S. 137-148 
    ISSN: 1573-1111
    Keywords: Clathrate hydrate ; phase diagram ; crystal structure ; tetraisoamylammonium fluoride
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The phase diagram of the binary (i-C5H11)4NF-water system has been studied in the clathrate formation region. Three polyhydrates have been discovered, two of which (1∶38.9 and 1∶32.7) are the known orthorhombic and tetragonal phases:Pbmn,a=11.88,b=21.53,c=12.70 Å,ρ means=1.019 g cm-3 (0°C), m.p.=32.4°C andP42/m, a=23.729,c=12.466 Å,ρ means=1.062 g cm-3, (0°C), m.p.=31.2°C, respectively. A single crystal X-ray analysis of the novel clathrate hydrate (i-C5H11)4NF·27 H2O is reported. This new clathrate hydrate is tetragonal,I4I/a, witha=16.894(5),c=17.111(2) Å,Z=4, (−50°C), and m.p.=34.6°C. Each (i-C5H11)4N+ cation occupies a four-chamber cavity built of 15-hedra 71635942 (idealized description), with small vacant 5444 cavities filling the intervening space.
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Journal of inclusion phenomena and macrocyclic chemistry 17 (1994), S. 187-201 
    ISSN: 1573-1111
    Keywords: β-Cyclodextrin ; sulfathiazole ; inclusion complex ; crystal structure ; thermal analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract An inclusion complex with the formula (β-cyclodextrin) (sulfathiazole) 8.3 H2O has been crystallized and characterized by physicochemical methods including single crystal X-ray analysis. The complex crystallizes in the monoclinic system, space group P21, witha=15.264(4),b= 16.500(6),c=15.559(5) Å,β=117.29(3)o andZ=2. The structure was solved using published co-ordinates forβ-cyclodextrin in an isomorphous complex. Refinement by block-diagonal leastsquares yieldedR=0.061 for 4706 unique observed reflections. Inclusion of sulfathiazole produces a slight ellipticity in the host conformation, but the guest adopts a conformation similar to that observed in its polymorphs. The guest is held in the macrocyclic cavity predominantly by hydrophobic forces, with the phenyl ring near the host primary hydroxyl side and the thiazole ring near the secondary hydroxyl side. The complex packs in layers parallel to theac-plane. Layers are linked by hydrogen bonding to water molecules which are located outside the cyclodextrin cavity. An extensive network of hydrogen bonds mediated chiefly by water molecules stabilizes the crystal structure.
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  • 19
    ISSN: 1573-1111
    Keywords: Gossypol ; complex ; crystal structure ; single crystal ; desolvation ; polymorph
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The structures of gossypol complexes are extremely sensitive to the halogenomethane present as the guest; e.g. changing the number of Cl atoms in chloromethane derivatives changes the structure of the gossypol complex. The crystals of C30H30O8·CH2Cl2 are monoclinic, space groupC2/c,a=21.320(4),b=19.199(6),c=15.765(2)Å, β=113.05(2)o,V=5916(2)Å3,Z=8,D x=1.35 g/cm3,T=295 K. The structure has been solved by direct methods and refined to the finalR value of 0.084 for 1828 reflections. In the structure H-bonded gossypol molecules form columns, generating channels in the structure which are filled by guest molecules. After decomposition (desolvation) monocrystals of the complexes are conserved without destruction, in which there are rather wide and empty channels though slightly smaller than in the complex. An attempt is made to explain some peculiarities of the behavior of the gossypol polymorph formed on the basis of its structure with empty channels.
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  • 20
    Electronic Resource
    Electronic Resource
    Springer
    Journal of inclusion phenomena and macrocyclic chemistry 17 (1994), S. 365-376 
    ISSN: 1573-1111
    Keywords: Gossypol ; inclusion compounds ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The crystal structure of a compound obtained in a condensation reaction of (±)-gossypol with (R)-(+)-phenylethylamine has been determined by X-ray structure analysis. The crystals of C46H48O6N2·(C4H8O2)2 are monoclinic, space groupP21,a=21.243(3),b=8.666(1),c=28.651(4) Å, β=108.24(1)0,V=5009(3) β3,Z=4,D x=1.195 g cm−3, μ(CuK α)=0.66 mm−1,T=292 K. The structure has been solved by direct methods and refined to the finalR value of 0.091 for 4290 observed reflections and 1049 parameters. There are two diastereoisomeric molecules of the host and four solvent molecules in the asymmetric unit. The host molecules are H-bonded into chains with diastereoisomeric molecules alternating along the chain. The fact that the host prefers the association mode in which molecules with a different configuration of the 2,2′-binaphthyl moiety are H-bonded explains why separation of diastereoisomeric diaminogossypols by fractional crystallization has been unsuccessful. The 1,4-dioxane molecules are accommodated in infinite channels but only every second guest molecule in a channel is H-bonded to the host.
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  • 21
    ISSN: 1573-1111
    Keywords: D,L-hexapeptide ; cyclic ; crystal structure ; stacks ; tubular ; β-rings ; channels
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract An X-ray analysis of single crystals (from MeOH) of cyclo(-D-Leu-L-MeLeu-D-Leu-L-MeLeu-D-Leu-L-MeLeu-) has been carried out. The analysis reveals that the molecules of the cyclopeptide occur in the crystals with two slightly different, almost hexagonal backbone conformations of the β-type, and that pairs of molecules with the same conformation interact through their nonmethylated face, forming dimeric units (units A and B) with six interannular H-bonds. This kind of pairing reproduces well that expected for a two-ring element in a stack of antiparalleβ-rings. The X-ray analysis has also revealed the presence in the A units of two water molecules, each at one of two equivalent sites located on the 3-fold axis of the units and equidistant from the center of gravity, and the presence in the B units of one water molecule at the center of the units. This provides experimental support for the idea that stacks ofβ-rings can serve as molecular channels.
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  • 22
    ISSN: 1573-1111
    Keywords: Pentaborate ; boric acid ; clathrate ; diamond-related network ; hydrogen bonding ; tetrapropy-lammonium ; tetrabutylammonium ; crystal structure ; 11B MAS NMR ; 13C MAS NMR ; thermogravimetry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Single-crystal X-ray structure analyses of N(nPr)4[B5O6(OH)4][B(OH)3]2,1, and N(nBu)4 [B5O6(OH)4][B(OH)3]2,2, reveal that these materials are novel clathrates, the isotypic host structures of which are three-dimensional assemblies of hydrogen-bonded [B5O6(OH)4]− ionsand B(OH)3 molecules. The assembly of only the pentaborate anions is a distorted (i.e., along [102] elongated) fourconnected diamond-related network. The N(nPr) 4 + and N(nBu) 4 + ions are trapped within the complex three-dimensional channel systems of the host frameworks. Both1 and2 crystallize monoclinically with space groupP21/c andZ=4. The cell constants are:1:a=13.592(5),b=12.082(2),c=17.355(6) Å, β=106.60(2)° (298K);2:a=13.874(3),b=12.585(1),c=17.588(4) Å, β=107.04(1)° (238 K). The results obtained by both11B and13C MAS NMR spectroscopy are discussed. Thermogravimetric studies under a flowing inert-gas atmosphere suggest that water, stemming from polycondensation of the hydrous borate species, is released from the clathrates at ca. 443 K (1) and 398 K (2) before the decomposition of the organic cations starts at ca. 603 K (1) and 603 K (2).
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  • 23
    ISSN: 1573-1111
    Keywords: Calixarenes ; arenetricarbonylchromium ; crystal structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The structures of three arene-tricarbonylchromium complexes prepared from cone and 1,3-alternate-25, 26,27,28-tetrapropoxycalix[4]arene(1) and Cr(CO)6 were determined by single crystal X-ray studies. Crystal data for 1,3-alternate-1·Cr(CO)3 are space groupP21/a,a=19.496(3)Å,b=11.118(2)Å,c=19.121(2)Å, β=109.95°(1) andV=3895Å3. The structure was refined toRw=0.068. Crystal data for cone-1·Cr(CO)3 are space groupP21/a,a=21.457(4)Å,b=12.184(1)Å,c=14.816(2)Å, β=91.61°(1) andV=3872Å3. The structure was refined toRw=0.077. Crystal data for cone-1·2Cr(CO)3 are space groupP21/a,a=18.019(3)Å,b=41.347(4)Å,c=11.743(2)Å, β=97.39°(1) andV=8676Å3. The single crystal included two similar but slightly different structures but the data were successfully refined toRw=0.092. The structure of 1,3-alternate-1·Cr(CO)3 differs only slightly from that of the regular 1,3-alternate calix[4]arene. In contrast, cone-1·Cr(CO)3 and cone-1·2Cr(CO)3 show an unusual conformation with a pair of faced gablelike roofs, which is considerbly distorted from the regular cone calix[4]arene. The origin of this distortion is discussed in combination with the spectral studies.
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  • 24
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 1-3 
    ISSN: 0887-3585
    Keywords: protein folding ; protein conformation ; Paracelsus award ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 25
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 4-13 
    ISSN: 0887-3585
    Keywords: trichosanthin ; ribosome-inactivating proteins ; crystal structure ; orthorhombic ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Trichosanthin (TCS) is one of the single chain ribosome-inactivating proteins (RIPs). The crystals of the orthorhombic form of trichosanthin have been obtained from a citrate buffer (pH 5.4) with KC1 as the precipitant. The crystal belongs to the space group P212121 with a = 38.31, b = 76.22, c = 79.21 Å. The structure was solved by molecular replacement method and refined using the programs XPLOR and PROLSQ to an R-factor of 0.191 for the reflections within the 6-1.88 Å resolution range. The bond length and bond angle in the protein molecule have root-mean-square deviations from ideal value of 0.013 Å and 3.3°, respectively. The refined model includes 247 residues and 197 water molecules. The TCS molecule consists of two structural domains. The large domain contains six α-helices, a six stranded sheet, and an antiparallel β-sheet. The small domain has a largest α-helix, which shows a distinct bend. The possible active site of the molecule located on the cleft between two domains was proposed. In the active site Arg-163 and Glu-160, Glu-189 and Arg-122 form two ion pairs, Glu-189 and Gln-156 are hydrogen bonded to each other. Three water molecules are bonded to the residues in the active site region. The structures of TCS molecule and ricin A-chain (RTA) superimpose quite well, showing that the structures of the two protein molecules are homologous. Comparison of the structures of the TCS molecule in this orthorhombic crystal with that in the monoclinic crystal indicates that there are no essential differences of the structures between the two protein crystals. © 1994 Wiley-Liss, Inc.
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  • 26
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 80-83 
    ISSN: 0887-3585
    Keywords: maize protein ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Phospholipid transfer protein from maize seedlings has been crystallized using trisodium citrate as precipitant. The crystal belongs to the orthorhombic space group P212121 with unit cell dimensions of a = 24.46 Å, b = 49.97 Å, and c = 69.99 Å. The presence of one molecule in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.36 Å 3/Da and a solvent content of 48% by volume. The X-ray diffraction pattern extends at least to 1.6 Å Bragg spacing when exposed to both CuKα and synchrotron X-rays. A set of X-ray data to approximately 1.9 Å Bragg spacing has been collected from a native crystal. © 1994 Wiley-Liss, Inc.
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  • 27
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 85-97 
    ISSN: 0887-3585
    Keywords: protein conformation ; secondary structure ; protein folding ; helix stability ; helix formation ; conformational entropy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Much effort has been invested in seeking to understand the thermodynamic basis of helix stability in both peptides and proteins. Recently, several groups have measured the helix-forming propensities of individual residues (Lyu, P. C., Liff, M. I., Marky, L. A., Kallenbach, N. R. Science 250:669-673, 1990; O'Neil, K. T., DeGrado, W. F. Science 250:646-651, 1990; Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., Baldwin, R. L. Nature (London) 344:268-270, 1990). Using Monte Carlo computer simulations, we tested the hypothesis that these differences in measured helix-forming propensity are due primarily to loss of side chain conformational entropy upon helix formation (Creamer, T. P., Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992). Our previous study employed a rigid helix backbone, which is here generalized to a completely flexible helix model in order to ensure that earlier results were not a methodological artifact. Using this flexible model, side chain rotamer distributions and entropy losses are calculated and shown to agree with those obtained earlier. We note that the side chain conformational entropy calculated for Trp in our previous study was in error; a corrected value is presented. Extending earlier work, calculated entropy losses are found to correlate strongly with recent helix propensity scales derived from substitutions made within protein helices (Horovitz, A., Matthews, J. M., Fersht, A. R. J. Mol. Biol. 227:560-568, 1992; Blaber, M., Zhang, X.-J., Matthews, B. M. Science 260:1637-1640, 1993). In contrast, little correlation is found between these helix propensity scales and the accessible surface area buried upon formation of a model polyalanyl α-helix. Taken in sum, our results indicate that loss of side chain entropy is a major determinant of the helix-forming tendency of residues in both peptide and protein helices. © 1994 Wiley-Liss, Inc.
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  • 28
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 165-173 
    ISSN: 0887-3585
    Keywords: algoriths ; structure alignment ; Protein Data Bank ; protein superfamilies ; structural homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J. C., Strandberg, B. E., Hart, R. G., Davies, D. R., Phillips, D. C., Shore, V. C. Nature (London) 185:422-427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships. © 1994 Wiley-Liss, Inc.
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  • 29
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 199-221 
    ISSN: 0887-3585
    Keywords: multicopy simulation search ; rational drug design ; database search ; computer-aided design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29-34, 1991). HOOK places molecular “skeletons” from a database into the protein binding region by making bonds between sites (“hooks”) on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 105 or more skeletons for binding to 102 or more functional group minima are outlined. © 1994 Wiley-Liss, Inc.
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  • 30
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 230-243 
    ISSN: 0887-3585
    Keywords: aspartate transcarbamylase ; multienzyme complex ; comparative structure modeling ; allosteric enzymes ; molecular evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In Saccharomyces cerevisiae the first two reactions of the pyrimidine pathway are catalyzed by a multifunctional protein which possesses carbamylphosphate synthetase and aspartate transcarbamylase activities. Genetic and proteolysis studies suggested that the ATCase activity is carried out by an independently folded domain. In order to provide structural information for ongoing mutagenesis studies, a model of the three-dimensional structure of this domain was generated on the basis of the known X-ray structure of the related catalytic subunit from E. coli ATCase. First, a model of the catalytic monomer was built and refined by energy minimization. In this structure, the conserved residues between the two proteins were found to constitute the hydrophobic core whereas almost all the mutated residues are located at the surface. Then, a trimeric structure was generated in order to build the active site as it lies at the interface between adjacent chains in the E. coli catalytic trimer. After docking a bisubstrate analog into the active site, the whole structure was energy minimized to regularize the interactions at the contact areas between subunits. The resulting model is very similar to that obtained for the E. coli catalytic trimer by X-ray crystallography, with a remarkable conservation of the structure of the active site and its vicinity. Most of the interdomain and intersubunit interactions that are essential for the stability of the E. coli catalytic trimer are maintained in the yeast enzyme even though there is only 42% identity between the two sequences. Free energy calculations indicate that the trimeric assembly is more stable than the monomeric form. Moreover an insertion of four amino acids is localized in a loop which, in E. coli ATCase, is at the surface of the protein. This insertion exposes hydrophobic residues to the solvent. Interestingly, such an insertion is present in all the eukaryotic ATCase genes sequenced so far, suggesting that this region is interacting with another domain of the multifunctional protein. © 1994 Wiley-Liss, Inc.
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  • 31
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    Proteins: Structure, Function, and Genetics 19 (1994) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 32
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 273-276 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 33
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 302-309 
    ISSN: 0887-3585
    Keywords: dinuclear copper site ; hemocyanin ; oxygen binding ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 Å resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space group R32 with one subunit per asymmetric unit forming hexamers with 32 point group symmetry. Molecular oxygen is bound to a dinuclear copper center in the protein's second domain, symmetrically between and equidistant from the two copper atoms. The copper-copper distance in oxygenated Limulus hemocyanin is 3.6 ± 0.2 Å, which is surprisingly 1 Å less than that seen previously in deoxygenated Limulus polyphemus subunit II hemocyanin (Hazes et al., Protein Sci. 2:597, 1993). Away from the oxygen binding sites, the tertiary and quaternary structures of oxygenated and deoxygenated Limulus subunit II hemocyanins are quite similar. A major difference in tertiary structures is seen, however, when the Limulus structures are compared with deoxygenated Panulirus interruptus hemocyanin (Volbeda, A., Hol, W. G. J. J. Mol. Biol. 209:249, 1989) where the position of domain 1 is rotated by 8° with respect to domains 2 and 3. We postulate this rotation plays an important role in cooperativity and regulation of oxygen affinity in all arthropod hemocyanins. © 1994 Wiley-Liss, Inc.
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  • 34
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    Proteins: Structure, Function, and Genetics 20 (1994) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 35
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 197-201 
    ISSN: 0887-3585
    Keywords: cytochrome P450 ; erythromycin ; P450eryF ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cytochrome P450eryF was overexpressed in Escherichia coli and purified in high yield. Crystals of the protein in the presence of the substrate, 6-deoxyerythronolide B, have been obtained by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 54.16 Å, b = 79.67 Å, and c = 99.48 Å and one molecule per asymmetric unit. A complete native data set has been collected to a resolution of 2.1 Å, and anomalous dispersion difference Patterson maps have revealed the location of the single heme iron atom. © 1994 Wiley-Liss, Inc.
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  • 36
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 34-51 
    ISSN: 0887-3585
    Keywords: enzymology ; protein structure ; biochemical properties ; gene characterization ; bacterial diagnosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Pyrrolidone carboxyl peptidase (EC 3.4.11.8) is an exopeptidase commonly called PYRase, which hydrolytically removes the pGlu from pGlu-peptides or pGlu-proteins.pGlu also known as pyrrolidone carboxylic acid may occur naturally by an enzymatic procedure or may occur as an artifact in proteins or peptides. The enzymatic synthesis of pGlu suggests that this residue may have important biological and physiological functions. Several studies are consistent with this supposition.PYRase has been found in a variety of bacteria, and in plant, animal, and human tissues For over two decades, biochemical and enzymatic properties of PYRase have been investigated. At least two classes of PYRase have been characterized. The first one includes the bacterial and animal type I PYRases and the second one the animal type II and serum PYRases. Enzymes from these two classes present differences in their molecular weight and in their enzymatic properties.Recently, the genes of PYRases from four bacteria, have been cloned and characterized, allowing the study of the primary structure of these enzymes, and their over-expression in heterelogous organisms. Comparison of the primary structure of these enzymes revealed striking homologies.Type I PYRases and bacterial PYRases are generally soluble enzymes, whereas type II PYRases are membrane-bound enzymes. PYRase II appears to play as important a physiological role as other neuropeptide degrading enzymes. However, the role of type I and bacterial PYRases remains unclear.The primary application of PYRase has been its utilization for some protein or peptide sequencing. Development of chromogenic substrates for this enzyme has allowed its use in bacterial diagnosis. © 1994 Wiley-Liss, Inc.
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  • 37
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 52-67 
    ISSN: 0887-3585
    Keywords: nuclear magnetic resonance ; defensin ; hydrogen exchange ; antimicrobial peptides ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The exchange kinetics for the slowly exchanging amide hydrogens in three defensins, rabbit NP-2, rabbit NP-5, and human HNP-1, have been measured over a range of pH at 25°C using 1D and 2D NMR methods. These NHs have exchange rates 102 to 105 times slower than rates from unstructured model peptides. The observed distribution of exchange rates under these conditions can be rationalized by intramolecular hydrogen bonding of the individual NHs, solvent accessibility of the NHs, and local fluctuations in structure. The temperature dependencies of NH chemical shifts (NH temperature coefficients) were measured for the defensins and these values are consistent with the defensin structure. A comparison is made between NH exchange kinetics, NH solvent accessibility, and NH temperature coefficients of the defensins and other globular proteins. Titration of the histidine side chain in NP-2 was examined and the results are mapped to the three-dimensional structure. © 1994 Wiley-Liss, Inc.
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  • 38
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 133-147 
    ISSN: 0887-3585
    Keywords: myoglobin ; simulation ; hydration ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of a molecular dynamics simulation of metmyoglobin in an explicit solvent environment of 3,128 water molecules has been performed. Both statics and dynamics of the protein-solvent interface are addressed in a comparison with experiment. Three-dimensional density distributions, temperature factors, and occupancy weights are computed for the solvent by using the trajectory coordinates. Analysis of the hydration leads to the localization of more than 500 hydration sites distributed into multiple layers of solvation located between 2.6 and 6.8 Å from the atomic protein surface. After locating the local solvent density maxima or hydration sites we conclude that water molecules of hydration positions and hydration sites are distinct concepts. Both global and detailed properties of the hydration cluster around myoglobin are compared with recent neutron and X-ray data on myoglobin. Questions arising from differences between X-ray and neutron data concerning the locations of the protein-bound water are investigated. Analysis of water site differences found from X-ray and neutron experiments compared with our simulation shows that the simulation gives a way to unify the hydration picture given by the two experiments. © 1994 John Wiley & Sons, Inc.
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  • 39
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 119-132 
    ISSN: 0887-3585
    Keywords: electrostatics ; protein conformation ; DelPhi ; hydrophobicity ; RNase H ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper we discuss the problem of including solvation free energies in evaluating the relative stabilities of loops in proteins. A conformational search based on a gas-phase potential function is used to generate a large number of trial conformations. As has been found previously, the energy minimization step in this process tends to pack charged and polar side chains against the protein surface, resulting in conformations which are unstable in the aqueous phase. Various solvation models can easily identify such structures. In order to provide a more severe test of solvation models, gas phase conformations were generated in which side chains were kept extended so as to maximize their interaction with the solvent. The free energies of these conformations were compared to that calculated for the crystal structure in three loops of the protein E. coli RNase H, with lengths of 7, 8, and 9 residues. Free energies were evaluated with a finite difference Poisson-Boltzmann (FDPB) calculation for electrostatics and a surface area-based term for nonpolar contributions. These were added to a gas-phase potential function. A free energy function based on atomic solvation parameters was also tested. Both functions were quite successful in selecting, based on a free energy criterion, conformations quite close to the crystal structure for two of the three loops. For one loop, which is involved in crystal contacts, conformations that are quite different from the crystal structure were also selected. A method to avoid precision problems associated with using the FDPB method to evaluate conformational free energies in proteins is described. © 1994 John Wiley & Sons, Inc.
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  • 40
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 107-118 
    ISSN: 0887-3585
    Keywords: protein crystallography ; four helix bundle ; iron ; macromolecular assembly ; regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ferritin is a 24 subunit protein that controls biomineralization of iron in animals, bacteria, and plants. Rates of mineralization vary among members of the ferritin family, particularly between L and H type subunits of animal ferritins which are differentially expressed in various cell types. To examine ferritin from a highly differentiated cell type and to clarify the relationship between ferritin structure and function, bullfrog red cell L ferritin has been cloned, overexpressed in E. coli, and crystallized under two conditions. Crystals were obtained at high ionic strength in the presence of MnCl2 at a concentration comparable to that of the protein and in the presence of MgCl2 at a concentration much higher than that of the protein. Under both crystallization conditions, the crystals are tetragonal bipyramids in the space group F432 with unit cell dimensions a=b=c= 182 ± 0.5 Å. Crystals obtained in the presence of manganese and ammonium sulfate diffract to 1.9 Å, while those obtained in the presence of magnesium and sodium tartrate diffract to 1.6 Å. Isomorphous crystals have been obtained under similar conditions for a site-directed mutant with a reduced mineralization rate in which Glu-57, -58, -59, and -61 are all replaced by Ala. The structure of wild type L-subunit with magnesium has been solved by molecular replacement using the calcium salt of human liver H subunit (Lawson et al., Nature (London) 349:541-544, 1991) as the model. The crystallographic R factor for the 6-2.2 Å shell is 0.21. The overall fold of human H and bullfrog L ferritins is similar with an rms difference in backbone atomic positions of 0.97 Å. The largest structural differences occur in the D helix and the loop connecting the D and E helices of the four helix bundle. Because red cell L ferritin and liver H ferritin show differences in both rates of mineralization and three-dimensional structure, more detailed comparisons of these structures are likely to shed new light on the relationship between conformation and function. © 1994 John Wiley & Sons, Inc.
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  • 41
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 148-160 
    ISSN: 0887-3585
    Keywords: myoglobin ; solvation ; dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The dynamics of water at the protein-solvent interface is investigated through the analysis of a molecular dynamics simulation of metmyoglobin in explicit aqueous environment. Distribution implied dynamics, harmonic and quasiharmonic, are compared with the simulated macroscopic dynamics. The distinction between distinguishable solvent molecules and hydration sites developed in the previous paper is used. The simulated hydration region within 7 Å from the protein surface is analyzed using a set of 551 hydration sites characterized by occupancy weights and temperature B-factors determined from the simulation trajectory. The precision of the isotropic harmonic and anisotropic harmonic models for the description of proximal solvent fluctuations is examined. Residence times and dipole reorientation times of water around the protein surface are compared with NMR and ESR results. A correlation between diffraction experiment quantities such as the occupancy weights and temperature factors and the residence and correlation times resulting from magnetic resonance experiments is found via comparison with simulation. © 1994 John Wiley & Sons, Inc.
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  • 42
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 198-200 
    ISSN: 0887-3585
    Keywords: catalytic antibody ; chorismate mutase ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Fab′ fragment of a catalytic antibody with chorismate mutase activity has been crystallized as a complex with the transition-state analog hapten. The complex was crystallized by the vapor diffusion method using ammonium sulfate as the precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions a = 37.1 Å, b = 63.3 Å, c = 178.5 Å, and there is one Fab' molecule per asymmetric unit. The crystals diffract X-rays to at least 3.0 Å and are suitable for X-ray crystallographic studies. © 1994 John Wiley & Sons, Inc.
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  • 43
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 330-346 
    ISSN: 0887-3585
    Keywords: lentil lectin ; legume lectin ; lectin ; side chain clusters ; sugar-protein interactions ; phosphate binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structures of two crystal forms of lentil lectin are determined and refined at high resolution. Orthorhombic lentil lectin is refined at 1.80 Å resolution to anR-factor of 0.184 and monoclinic lentil lectin at 1.75 Å resolution to anR-factor of 0.175. These two structures are compared to each other and to the other available legume lectin structures. The monosaccharide binding pocket of each lectin monomer contains a tightly bound phosphate ion. This phosphate makes hydrogen bonding contacts with Asp-81β, Gly-99β, and Asn-125β, three residues that are highly conserved in most of the known legume lectin sequences and essential for monosaccharide recognition in all legume lectin crystal structures described thus far. A detailed analysis of the composition and properties of the hydrophobic contact network and hydrophobic nuclei in lentil lectin is presented. Contact map calculations reveal that dense clusters of nonpolar as well as polar side chains playa major role in secondary structure packing. This is illustrated by a large cluster of 24 mainly hydrophobic amino acids that is responsible for the majority of packing interactions between the two β-sheets. Another series of four smaller and less hydrophobic clusters is found to mediate the packing of a number of loop structures upon the front sheet. A very dense, but not very conserved cluster is found to stabilize the transition metal binding site. The highly conserved and invariant nonpolar residues are distributed asymmetrically over the protein. © 1994 Wiley-Liss, Inc.
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  • 44
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 105-123 
    ISSN: 0887-3585
    Keywords: structure prediction ; helix to helix packing ; coiled coils ; leucine zippers ; heptad repeats ; molecular dynamics ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simulated annealing method for atomic resolution structure prediction of α-helical coiled coil proteins is described which draws upon knowledge of the oligomerization state, the helix directionality, and the properties of heptad repeat sequences. Unknown structural parameters, such as the coiled coil twist angle and the side chain conformations, are heavily sampled while allowing for flexibility in the helix backbone geometry. Structures of the wild-type GCN4 dimer [O'Shea et al., Science 254:539-544, 1991] and a mutant tetramer [Harbury et al., Science 292:1401-1407, 1993] have been generated and compared with the X-ray crystal structures. The wild-type dimer model has a root mean square coordinate deviation from the crystal structure of 0.73 Å for nonhydrogen atoms in the dimerization interface. Structures of a mutant dimer and a mutant trimer have been predicted. Packing energetics were analyzed for core leucine and isoleucine side chains in dimeric and tetrameric coiled coils. Strong packing preferences were found in the dimers but not in the tetramers. Thus, packing in the dimer may be responsible for the switch from a two-stranded to a four-stranded coiled coil caused by the GCN4 leucine zipper mutations. © 1994 Wiley-Liss, Inc.
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  • 45
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 139-148 
    ISSN: 0887-3585
    Keywords: hardware ; molecular dynamics ; simulation ; special-purpose computer ; supercomputing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been extensively used in research of proteins. Since these simulations are quite computer intensive, their acceleration is of main interest of the research. In molecular dynamics simulations, almost all computing time is consumed in calculating the forces between particles, e.g., Coulomb and van der Waals forces. We have designed and built GRAPE-2A (GRAvity PipE 2A), a special-purpose computer for use in simulations of classical many-body systems. GRAPE-2A calculates forces exerted on a particle from the other particles. GRAPE-2A can calculate force of an arbitrary functional form of a central force. The host computer, which is connected to GRAPE-2A through the VME bus, performs other calculations such as time integration. The peak speed of GRAPE-2A is 180 Mflops. We can also stimulate systems with periodic boundary conditions by the Ewald method, using GRAPE-2A and another special-purpose computer, WINE (Wave space INtegrator for the Ewald method). © 1994 Wiley-Liss, Inc.
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  • 46
    ISSN: 0887-3585
    Keywords: triglyceride lipase ; proenzyme ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.
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  • 47
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 309-317 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; predicted contact maps ; correlated mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information. © 1994 John Wiley & Sons, Inc.
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  • 48
    ISSN: 0887-3585
    Keywords: endonuclease overexpression ; crystallization ; X-ray diffraction ; protein-DNA complex ; Type II restriction enzyme ; vapor diffusion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have overexpressed the type II restriction endonuclease PvuII (R.PvuII) in E. coli, prepared large amounts of the homogeneous enzyme, and crystallized it with an oligonucleotide carrying a PvuII recognition site. The cocrystals are orthorhombic space group P212121 with cell constants a = 95.8 Å, b = 86.3 Å, c = 48.5 Å, and diffract X-rays to at least 2.7 Å. There is a complex of two protein subunits and one oligonucleotide duplex in the asymmetric unit. © 1994 Wiley-Liss, Inc.
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  • 49
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 318-323 
    ISSN: 0887-3585
    Keywords: ribonuclease T1 ; functional cooperativity ; double mutant cycle ; subsite ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We report on the functional cooperativity of the primary site and the sub-site of ribonuclease T1 (RNase T1; EC 3.1.27.3). The kinetic properties of the single Tyr-38-Phe and Asn-98-Ala mutants have been compared with those of the corresponding double mutant. The Tyr-38-Phe mutation has been used to probe enzyme-substrate interactions at the primary site; the Asn-98-Ala mutation monitors subsite interactions.1 In addition to the dinucleoside phosphate substrate GpC, we measured the kinetics for GpMe, a synthetic substrate in which the leaving nucleoside cytosine has been replaced by methanol. All data were combined in a triple mutant box to analyze the interplay between Tyr-38, Asn-98, and the leaving group. The free energy barriers to kcat, introduced by the single Tyr-38-Phe and Asn-98-Ala mutations are not additive in the corresponding double mutant. The energetic coupling between both mutations is independent of the binding of the leaving cytosine at the subsite. We conclude that the coupling of the Tyr-38-Phe and Asn-98-Ala mutations arises through distortion or reorientation of the 3′-guanylic acid moiety bound at the primary site. The experimental data indicate that the enzyme-substrate interactions beyond the scissile phosphodiester bond contribute to catalysis through the formation of new or improved contacts in going from ground state to transition state, which are functionally independent of primary site interactions. © 1994 John Wiley & Sons, Inc.
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  • 50
    ISSN: 0887-3585
    Keywords: crystallography ; hydroxamate ; high resolution ; metalloproteinase ; zinc ; X-ray ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β-sheet and three α-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley-Liss, Inc.
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  • 51
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 110-119 
    ISSN: 0887-3585
    Keywords: folding intermediate ; urea denaturation ; stopped-flow circular dichroism ; molten globule ; hemindicyanide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped-flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of 〉 1 × 102 s-1, (4.5-9.3) S-1, and (2-5) × 10-3 s-1. In the fastest phase, a substantial amount of secondary structure (40%) is formed within the dead time of the CD stopped-flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a “heme pocket precursor” recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand-exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group. © 1994 Wiley-Liss, Inc.
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  • 52
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 120-131 
    ISSN: 0887-3585
    Keywords: enzymes ; protein immobilization ; microcalorimetry ; protein melting domains ; protein DSC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ribonuclease A has been immobilized on silica beads through glutaraldeyde-mediated chemical coupling in order to improve the stability of the protein against thermal denaturation. The thermodynamic and binding properties of the immobilized enzyme have been studied and compared with those of the free enzyme. The parameters describing the binding of the inhibitor 3′ -CMP (Ka and ΔH) as monitored by spectrophotometry and calorimetry were not significantly affected after immobilization. Conversely both the stability and unfolding mechanism drastically changed. Thermodynamic analysis of the DSC data suggests that uncoupling of protein domains has occurred as a consequence of the immobilization. The two state approximation of the protein unfolding process is not longer valid for the immobilized RNase. Protein stability strongly depends on the hydrophobicity properties of the support surface as well as on the presence of the inhibitor and pH. For example, after immobilization on a highly hydrophobic surface, the enzyme is partially in the unfolded state. The binding of a ligand is able to reorganize the protein structure into a native-like conformation. The refolding rates are different for the two protein domains and vary as a function of pH and presence of the inhibitor 3′-CMP. © 1994 Wiley-Liss, Inc.
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  • 53
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 132-140 
    ISSN: 0887-3585
    Keywords: distant protein folds ; sequence homology ; database searching ; profile analysis ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new method to detect remote relationships between protein sequences and known three-dimensional structures based on direct energy calculations and without reliance on statistics has been developed. The likelihood of a residue to occupy a given position on the structural template was represented by an estimate of the stabilization free energy made after explicit prediction of the substituted side chain conformation. The profile matrix derived from these energy values and modified by increasing the residue self-exchange values successfully predicted compatibility of heatshock protein and globin sequences with the three-dimensional structures of actin and phycocyanin, respectively, from a full protein sequence databank search. The high sensitivity of the method makes it a unique tool for predicting the three-dimensional fold for the rapidly growing number of protein sequences. © 1994 Wiley-Liss, Inc.
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  • 54
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 158-160 
    ISSN: 0887-3585
    Keywords: crystallization ; cellulases ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Endoglucanase CelC from Clostridium thermocellum expressed in Escherichia coli has been crystallized in two different crystal forms by the hanging drop method. Crystals of form I were grown with polyethylene glycol as a precipitant. They are orthorhombic, space group P212121, with cell dimensions a =51.4 Å, b =84.3 Å, and c =87.5 Å. Crystals of form II, obtained in ammonium sulfate solutions, belong to the tetragonal space group P41212 (or P43212) with cell dimensions of a = b = 130.7 Å and c = 69.6 Å. Diffraction data to 2.8 Å resolution were observed for both crystal forms with a rotating anode generator. Preliminary oscillation images of the orthorhombic form I crystals using a synchrotron radiation source show diffraction to 2.2 Å resolution, indicating that these crystals are suitable for high resolution crystallographic analysis. © 1994 Wiley-Liss, Inc.
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  • 55
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    Proteins: Structure, Function, and Genetics 19 (1994) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 56
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; Rfree ; ATP and AMP binding sites ; Mg2+ coordination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of E. coli adenylate kinase with bound AMP and AMPPNP at 2.0 Å resolution is presented. The protein crystallizes in space group C2 with two molecules in the asymmetric unit, and has been refined to an R factor of 20.1% and an Rfree of 31.6%. In the present structure, the protein is in the closed (globular) form with the large flexible lid domain covering the AMPPNP molecule. Within the protein, AMP and AMPPNP, an ATP analog, occupy the AMP and ATP sites respectively, which had been suggested by the most recent crystal structure of E. coli adenylate kinase with AP5A bound (Müller and Schulz, 1992, ref. 1) and prior fluorescence studies (Liang et al., 1991, ref. 2). The binding of substrates and the positions of the active site residues are compared between the present structure and the E. coli adenylate kinase/Ap5A structure. We failed to detect a peak in the density map corresponding to the Mg2+ ion which is required for catalysis, and its absence has been attributed to the use of ammonium sulfate in the crystallization solution. Finally, a comparison is made between the present structure and the structure of the heavy chain of muscle myosin. © 1994 Wiley-Liss, Inc.
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  • 57
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 185-190 
    ISSN: 0887-3585
    Keywords: heme ; secondary structure ; conformation ; hemopexin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hemopexin is a serum glyco-protein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptormediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% β-structure, 15% α-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme-hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the hemeprotein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis. © 1994 Wiley-Liss, Inc.
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  • 58
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 340-342 
    ISSN: 0887-3585
    Keywords: protein ; ribosome ; inactivation ; toxin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single crystals of the protein gelonin isolated from the seeds of Gelonium multiforum have been grown at room temperature by vapor diffusion method. The crystals are monclinic with a = 49.4 Å, b = 44.9 Å, c = 137.4 Å, and β = 98.3°. The space group is P21, with two molecules in the asymmetric unit which are related by a noncrystallographic 2-fold axis along ψ =13° and φ =88°. The crystals diffract X-rays to high resolution, making it possible to obtain an accurate structure of this single chain ribosome inactivating protein. © 1994 Wiley-Liss, Inc.
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  • 59
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 81-93 
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
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  • 60
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 248-258 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; trp-repressor ; ligand ; domain ; dynamic cross-correlation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations of the apo- and holo-forms of thetrp-repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand-protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X-ray temperature factors. Distance, distance fluctuation, and dynamic cross-correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three-domain format has been proposed for the crystal structure (Zhang et at., Nature 327:591-597, 1987) namely, helices A-C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three-domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix-turn-helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA-binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments. © 1994 Wiley-Liss, Inc.
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  • 61
    ISSN: 0887-3585
    Keywords: cell multipole method ; Newton-Euler inverse mass operator ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two new methods developed for molecular dynamics simulations of very large proteins are applied to a series of proteins ranging up to the protein capsid of tomato bushy stunt virus (TBSV).For molecular dynamics of very large proteins and polymers, it is useful to carry out the dynamics using internal coordinates (say, torsions only) rather than Cartesian coordinates. This allows larger time steps, eliminates problems with the classical description of high energy modes, and focuses on the important degrees of freedom. The resulting equation of motion has the form where for T is the vector of generalized forces, M(θ) is the moments of inertia tensor, is the vector of torsions, and C is a vector containing Coriolis forces and nonbond forces. The problem is that to calculate the acceleration vector from M, C, and Trequires inverting. M(θ), an order N3calculation. Since the number of degrees of freedom might be 300,000 for a million atom system, solving these equations every time step is impractical, restricting internal coordinate methods to small systems. The new method, Newton-Euler Inverse Mass Operator (NEIMO) dynamics, constructs the torsional accelerations vector directly by an order N process, allowing internal-coordinate dynamics to be solved for super larger (million atom) systems, The first use of the NEIMO method for molecular dynamics of proteins is presented here.A second serious difficulty for large proteins is calculation of the nonbond forces. We report here the first application to proteins of the new Cell Multipole Method (CMM) to evaluate the Coulomb and van der Waals interactions. The cost of CMM scales linearly with the number of particles while retaining an accuracy significantly better than standard non bond methods (involving cutoffs).Results for NEIMO and CMM are given for simulations of a wide range of peptide and protein systems, including the protein capsid of TBSV with 488,000 atoms. The computational times for NEIMO and CMM are demonstrated to scale linearly with size. With NEIMO the dynamics time steps can be as large as 20 fs (for small peptides), much larger than possible with standard Cartesian coordinate dynamics.For TBSV we considered both the normal form and the high pH form, in which the Ca2+ ions are removed. These calculations lead to a contraction of the protein for both forms (probably because of ignoring the RNA core not observed in the X-ray). © 1994 Wiley-Liss, Inc.
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  • 62
    ISSN: 0887-3585
    Keywords: glutathione S. transferase ; temperature-sensitive protein ; chimeric protein ; mutant protein ; X-ray analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A chimeric enzyme (GST121) of the human α-glutathione S-transferases GST1-1 and GST2-2, which has improved catalytic efficiency and thermostability from its wild-type parent proteins, has been crystallized in a space group that is isomorphous with that reported for crystals of GST1-1. However, a single-site (G82R) mutant of GST121, which exhibits a significant reduction both in vitro and in vivo in protein thermostability, forms crystals that are not isomorphous with GST1-1. The mutant protein crystallizes in space group P212121, with cell dimensions a = 49.5, b = 92.9, c = 115.9 Å, and one dimer per asymmetric unit. Preliminary crystallographic results show that a mutation of the surface residue Gly 82 from a neutral to a charged residue causes new salt bridges to be formed among the GST dimers, suggesting that the G82R mutant might aggregate more readily than does GST121 in solution resulting in a change of its solution properties. © 1994 Wiley-Liss, Inc.
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  • 63
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 264-278 
    ISSN: 0887-3585
    Keywords: hydrophobic interactions ; protein stability ; hydrophobicity scale ; protein mutant stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic interactions are believed to play an important role in protein folding and stability. Semi-empirical attempts to estimate these interactions are usually based on a model of solvation, whose contribution to the stability of proteins is assumed to be proportional to the surface area buried upon folding. Here we propose an extension of this idea by defining an environment free energy that characterizes the environment of each atom of the protein, including solvent, polar or nonpolar atoms of the same protein or of another molecule that interacts with the protein. In our model, the difference of this environment free energy between the folded state and the unfolded (extended) state of a protein is shown to be proportional to the area buried by nonpolar atoms upon folding. General properties of this environment free energy are derived from statistical studies on a database of 82 well-refined protein structures. This free energy is shown to be able to discriminate misfolded from correct structural models, to provide an estimate of the stabilization due to oligomerization, and to predict the stability of mutants in which hydrophobic residues have been substituted by site-directed mutagenesis, provided that no large structural modifications occur. © 1994 Wiley-Liss, Inc.
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  • 64
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 19-33 
    ISSN: 0887-3585
    Keywords: Discover program ; protein dynamics ; computer simulation ; protein motions ; counterions ; dielectric ; protein electrostatics ; aqueous simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance-dependent dielectric or a constant dielectric. Use of a linear distance-dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 Å) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 Å was needed in order to properly couple solvent and solute. Distances shorter than 15.0 Å resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 Å and an inner cutoff distance of 11.5 worked well. While a 10 Å shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost. © 1994 John Wiley & Sons, Inc.
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  • 65
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 34-48 
    ISSN: 0887-3585
    Keywords: normal mode refinement ; correlation function ; intra- and intermolecular correlation ; higher order scattering ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.
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  • 66
    ISSN: 0887-3585
    Keywords: protein ; mutation ; Fab ; Fv ; complementarity determining region ; hypervariability ; integrin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray crystal structures of fragments from two different humanized antiCD18 antibodies are reported. The Fv fragment of the nonbinding version has been refined in space group C2 with a=64.2 Å, b=61.3 Å, c=51.8 Å, and β=99° to an R-value of 18.0% at 1.9 Å, and the Fab fragment of the tight-binding version has been refined in space group P3 with a=101. Å and c=45.5 Å to an R-value of 17.8% at 3.0 Å resolution. The very large difference in their binding affinity (〉1000-fold) is attributed to large and local structural differences in the C-terminal part of CDR-H2, and from this we conclude there is direct contact between this region and antigen when they combine. X-ray structures of antibody-antigen complexes available in the literature have yet to show this part of CDR-H2 in contact with antigen, despite its hypervariable sequence. Implications of this result for antibody humanization are discussed. © 1994 John Wiley & Sons, Inc.
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  • 67
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 63-67 
    ISSN: 0887-3585
    Keywords: entropy ; thermodynamics ; binding energetics ; translational entropy ; macromolecular interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The loss of translational degrees of freedom makes an important, unfavorable contribution to the free energy of binding. Examination of experimental values suggest that calculation of this entropy using the Sackur-Tetrode equation produces largely overestimated values. Better agreement is obtained using the cratic entropy. Theoretical considerations suggest that the volumes available for the movement of a ligand in solution and in a complex are rather similar, suggesting also that the cratic entropy provides the best estimate of the loss of translational entropy. © 1994 John Wiley & Sons, Inc.
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  • 68
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    Proteins: Structure, Function, and Genetics 18 (1994) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 69
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 94-101 
    ISSN: 0887-3585
    Keywords: surface representation ; molecular recognition ; protein docking ; surface triangulation ; molecular graphics ; molecular visualization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have defined a molecular surface representation that describes precisely and concisely the complete molecular surface. The representation consists of a limited number of critical points disposed at key locations over the surface. These points adequately represent the shape and the important characteristics of the surface, despite the fact that they are modest in number. We expect the representation to be useful in areas such as molecular recognition and visualization. In particular, using this representation, we are able to achieve accurate and efficient protein-protein and protein-small molecule docking. © 1994 John Wiley & Sons, Inc.
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  • 70
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    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 71
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 150-157 
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; membrane protein ; ion channels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the channel-forming domain of colicin E1 from E. coli were grown by vapor diffusion at pH 6.4 and higher pH values. Cleavage of the colicin molecule with trypsin or thermolysin produced two of the pore-forming polypeptides used in these experiments. The third polypeptide was purified from a constructed plasmid that overexpresses only the C-terminal domain of colicin E1. Polypeptide crystals are tetragonal with space group I4, have one monomer in the asymmetric unit, and diffract to 2.2-2.4 Å. Unit cell parameters for the tryptic and thermolytic polypeptides are a = 102.9 Å and c = 35.6 Å. Crystals of the overexpressed polypeptide have unit cell parameters of a =87.2 Å and c =59.1 Å. The crystals were characterized by precession photography, and native data sets of each channel-forming fragment were collected on a Siemens-Nicolet area detector. The crystallization and characterization of these polypeptides are the first steps in the structure determination of the channel-forming domain of colicin E1. © 1994 Wiley-Liss, Inc.
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  • 72
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 141-149 
    ISSN: 0887-3585
    Keywords: dynamics ; flexibility index ; protein stability ; antigenic regions ; epitopes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Schulz (Naturwissenschaften 72:212-213, 1985). The accuracy of four flexibility prediction techniques was studied by comparing atomic temperature factors of known three-dimensional protein structures to predictions by using correlation coefficients. The size of the prediction window was optimized for each method. Predictions made with our new parameters, using an optimized window size of 9 residues in the prediction window, were giving the best results. The difference from another previously used technique was small, whereas two other methods were much poorer. Applicability of the predictions was also tested by searching for known epitopes from amino acid sequences. The best techniques predicted correctly 20 of 31 continuous epitopes in seven proteins. Flexibility parameters have previously been used for calculating protein average flexibility indices which are inversely correlated to protein stability. Indices with the new parameters showed better correlation to protein stability than those used previously; furthermore they had relationship even when the old parameters failed. © 1994 Wiley-Liss, Inc.
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  • 73
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 161-162 
    ISSN: 0887-3585
    Keywords: Proteinase K ; naturally occurring inhibitor ; enzyme-inhibitor complex ; microdialysis ; crystal ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of a complex of proteinase K (molecular mass, 28,790 Da) with its naturally occurring protein inhibitor PK13 (19,641 Da), have been prepared by a microdialysis technique and modified by hanging drop vapor diffusion against 25% ammonium sulfate in 50 mM Tris-HCl, pH 7.8. The crystals are long prisms with diamond-shaped cross sections of 0.2 × 0.4 × 1.5 mm3 and they diffract X-rays to a resolution of 2.5 Å. They belong to the orthorhombic space group P212121 with cell dimensions a = 64.1 Å, b = 66.8 Å, and c = 133.8 Å. Assuming one whole complex in the asymmetric unit, one obtains VM = 2.95 Å3/Da and the solvent content, Vsolv = 58.3%. © 1994 Wiley-Liss, Inc.
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  • 74
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 174-182 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; docking ; computer simulation ; substrate docking ; immunoglobulin ; rational drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using transrational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search (“helicopter view”) is obtained, which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed. © 1994 Wiley-Liss, Inc.
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  • 75
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 222-229 
    ISSN: 0887-3585
    Keywords: protein electrostatics ; energy calculations ; ion pairs ; Monte-Carlo simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge-charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley-Liss, Inc.
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  • 76
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 244-255 
    ISSN: 0887-3585
    Keywords: energy minimization ; rotamers ; automaton ; de novo design ; sequence prediction ; side-chain conformation prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globular proteins have high packing densities as a result of residue side chains in the core achieving a tight, complementary packing. The internal packing is considered the main determinant of native protein structure. From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side-chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side-chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side-chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. © 1994 Wiley-Liss, Inc.
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  • 77
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 256-268 
    ISSN: 0887-3585
    Keywords: unfolding ; solvation ; contact maps ; protein design ; structural domains ; normal modes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X-ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3-D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one-dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering. © 1994 Wiley-Liss, Inc.
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  • 78
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 324-329 
    ISSN: 0887-3585
    Keywords: multiple copy conformational sampling ; protein flexibility ; sampling convergence ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Effects of protein flexibility on multiple copy conformational sampling were systematically evaluated by studying the side-chain placement of Phe-14 in protein Zif268. The multiple copy sampling is shown to be significantly more efficient when a flexible but harmonically constrained protein is used instead of a rigid protein. A range of constraint force from 1 to 25 kcal/mol. Å per atom is determined to be sufficient to prevent the protein from distortion while allowing the protein to fluctuate for enhanced sampling. The protein fluctuations are essential in smoothing the effective energy surface as shown by the opening-closing of a protein hydrophobic pocket during a multiple copy energy minimization, a phenomenon that has been previously observed only in molecular dynamics. These results provide a practical guidance for applying the multiple copy techniques to molecular modeling and computer-aided drug design. © 1994 Wiley-Liss, Inc.
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  • 79
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 343-347 
    ISSN: 0887-3585
    Keywords: hydroxynitrile lyase ; flavoenzyme ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single crystals of three different isoenzymes of (R)-(+) mandelonitrile lyase (hydroxynitrile lyase) from almonds (Prunus amygdalus) have been obtained by hanging drop vapor diffusion using polyethylene glycol 4000 and isopropanol as co-precipitants. The crystals belong to the monoclinic space group P2l with unit cell parameters a = 69.9, b = 95.1, c = 95.6 Å, and β = 118.5°. A complete set of diffraction data has been collected to 2.6 Å resolution on native crystals of isoenzyme III. © 1994 Wiley-Liss, Inc.
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  • 80
    ISSN: 0887-3585
    Keywords: phospholipase A2 ; n-dodecylphosphorylcholine ; complex ; inhibitor ; X-ray crystal analysis ; molecular dynamics simulation ; interaction ; calcium-binding ; catalytic network ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of n-dodecylphosphorylcholine (n-C12PC)-bovine pancreas phospholipase A2 (PLA2) complex provided the following structural.characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N -terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (β-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a cholinereceiving pocket of n-C12PC and (3) the N-termillal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 Å resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (M D) simulation, assuming a system in aqueous solution at 310K. The M D simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the M D simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain. © 1994 Wiley-Liss, Inc. © 1994 Wiley-Liss, Inc.
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  • 81
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; extracellular matrix ; multiwavelength anomalous diffraction (MAD) ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of a fragment of human fibronectin encompassing the 7th through the RGD-containing 10th type III repeats (FN7-10) have been produced with protein expressed in E. coli. The crystals are monoclinic with one molecule in the asymmetric unit and diffract to beyond 2.0 Å Bragg spacings. A mutant FN7-10 was produced in which three methionines, in addition to the single native methionine already present, have been introduced by site-directed mutagenesis. Diffraction-quality crystals of this mutant protein have been grown in which methionine was replaced with selenomethionine. The introduction of methionine by site-directed mutagenesis to allow phasing from selenomethionyl-substituted crystals is shown to be feasible by this example and is proposed as a general approach to solving the crystallographic phase problem. Strategies for selecting propitious sites for methionine mutations are discussed. © 1994 Wiley-Liss, Inc.
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  • 82
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 55-72 
    ISSN: 0887-3585
    Keywords: secondary structure prediction ; prediction of secondary structure class ; prediction of secondary structure content ; evolutionary information ; multiple alignment profiles ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three-level system of neural networks by using additional input information derived from multiple alignments. Using a position-specific conservation weight as part of the input increases performance. Using the number of insertions and deletions reduces the tendency for overprediction and increases overall accuracy. Addition of the global amino acid content yields a further improvement, mainly in predicting structural class. The final network system has a sustained overall accuracy of 71.6% in a multiple cross-validation test on 126 unique protein chains. A test on a new set of 124 recently solved protein structures that have no significant sequence similarity to the learning set confirms the high level of accuracy. The average cross-validated accuracy for all 250 sequence-unique chains is above 72%. Using various data sets, the method is compared to alternative prediction methods, some of which also use multiple alignments: the performance advantage of the network system is at least 6 percentage points in three-state accuracy. In addition, the network estimates secondary structure content from multiple sequence alignments about as well as circular dichroism spectroscopy on a single protein and classifies 75% of the 250 proteins correctly into one of four protein structural classes. Of particular practical importance is the definition of a position-specific reliability index. For 40% of all residues the method has a sustained three-state accuracy of 88%, as high as the overall average for homology modelling. A further strength of the method is greatly increased accuracy in predicting the placement of secondary structure segments. © 1994 Wiley-Liss, Inc.
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  • 83
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 390-393 
    ISSN: 0887-3585
    Keywords: protein crystallization ; enzyme copurification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An unknown protein crystallized from a lobster muscle preparation in which arginine kinase was the majority component. It was identified as enolase by peptide sequencing and activity testing, and a SIRAS electron density map showed its three-dimensional structure to be very similar to that of yeast enolase. © 1994 John Wiley & Sons, Inc.
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  • 84
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 381-389 
    ISSN: 0887-3585
    Keywords: ab initio calculations ; semiempirical calculations ; solvent reaction field ; trimethyllysine ; dimethyllysine ; monomethyllysine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lysine residues with one, two, or three methyl groups substituted on the ∊-nitrogen atom are found in many proteins. To evaluate the effect of the posttranslational methylation on ion-pair formation we have performed semiempirical and ab initio molecular orbital calculations, using the AMI method and the 6-31G* basis set, respectively. Combinations of various methylated forms of methylamine and ethylamine with formate, acetate, and dimethyl phosphate were studied as model compounds. This approach allowed us to obtain information relevant to the interaction of the modified Lys residues with carboxylate groups of proteins, and the backbone of nucleic acids. We have found that the interaction energy decreases with an increasing number of methyl groups. Inclusion of a solvent reaction field in the semiempirical calculations gave reasonable values for the interaction energy in aqueous solution, when formate and acetate were the counterions. These studies suggest that, in addition to other factors, a weakening of ionic interactions contributes to the various physiological effects of lysine methylation. © 1994 John Wiley & Sons, Inc.
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  • 85
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 353-366 
    ISSN: 0887-3585
    Keywords: tertiary structure prediction ; protein folding pathways ; molten globule state ; protein A ; crambin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The hierarchy of lattice Monte Carlo models described in the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352, 1994) is applied to the simulation of protein folding and the prediction of 3-dimensional structure. Using sequence information alone, three proteins have been successfully folded: the B domain of staphylococcal protein A, a 120 residue, monomeric version of ROP dimer, and crambin. Starting from a random expanded conformation, the model proteins fold along relatively well-defined folding pathways. These involve a collection of early intermediates, which are followed by the final (and rate-determining) transition from compact intermediates closely resembling the molten globule state to the native-like state. The predicted structures are rather unique, with native-like packing of the side chains. The accuracy of the predicted native conformations is better than those obtained in previous folding simulations. The best (but by no means atypical) folds of protein A have a coordinate rms of 2.25 Å from the native Cα trace, and the best coordinate rms from crambin is 3.18 Å. For ROP monomer, the lowest coordinate rms from equivalent Cαs of ROP dimer is 3.65 Å. Thus, for two simple helical proteins and a small α/β protein, the ability to predict protein structure from sequence has been demonstrated. © 1994 John Wiley & Sons, Inc.
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  • 86
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    Proteins: Structure, Function, and Genetics 19 (1994), S. 73-76 
    ISSN: 0887-3585
    Keywords: molecular recognition ; protein assembly ; protein folding ; protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent advances in the measurement and theory of “hydration” interactions between biomolecules provide a basis on which to formulate mechanisms of biomolecular recognition. In this paper we have developed a mathematical formalism for analyzing specificity encoded in dynamic distributions of surface polar groups, a formalism that incorporates newly recognized properties of directly measured “hydration” forces. As expected, attraction between surfaces requires complementary patterns of surface polar groups. In contrast to usual expectations, thermal motion can create these complementary surface configurations. We have demonstrated that assembly can occur with an increase in conformational entropy of polar residues. Elevated temperature then facilitates recognition rather than hinders it. This mechanism might underlie some temperature-favored assembly reactions common in biological systems that are usually associated with the “hydrophobic effect” only. © 1994 Wiley-Liss, Inc.
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  • 87
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 174-184 
    ISSN: 0887-3585
    Keywords: coiled-coils ; keratin ; intermediate filament proteins ; link segments ; heptad phasing ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure. © 1994 Wiley-Liss, Inc.
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  • 88
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 191-196 
    ISSN: 0887-3585
    Keywords: human Clara cell 10-kDa protein ; X-ray diffraction ; phospholipase A2 inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of recombinant human Clara cell 10-kDa protein were grown both from ammonium sulfate and polyethylene glycol (PEG) solutions. Crystals grown from ammonium sulfate solution have been characterized by X-ray diffraction studies as monoclinic with the space group C2 and lattice constants a = 69.2 Å, b = 83.0 Å, c = 58.3 Å, and β = 99.7°. The monoclinic crystals diffract to beyond 2.5 Å. Some of the crystals grown from PEG were of a similar habit to those grown from ammonium sulfate, but others were triclinic with the space group P1 and cell constants a = 40.3 Å, b = 46.3 Å, c = 51.3 Å, α = 117.7°, β = 102.3°, and γ = 71.4°. These crystals diffract to beyond 3.2 Å. © 1994 Wiley-Liss, Inc.
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  • 89
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 1-3 
    ISSN: 0887-3585
    Keywords: protein secondary structure prediction ; pleckstrin homology domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A consensus prediction for the secondary structure of the pleckstrin homology (PH) domain is presented. The prediction is based on an analysis of patterns of conservation and variation of homologous protein sequences. The structure is predicted to be formed largely from beta strands with a single alpha helix. © 1994 Wiley-Liss, Inc.
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  • 90
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 15-24 
    ISSN: 0887-3585
    Keywords: Monte Carlo docking ; antibody/antigen recognition ; antibody binding ; induced fit ; substrate binding ; drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Antibody-antigen interactions are representative of a broad class of receptor-ligand interactions involving both specificity and potential inducible complementarity. To test possible mechanisms of antigenantibody recognition and specificity computationally, we have used a Metropolis Monte Carlo algorithm to dock fragments of the epitope Glu-Val-Val-Pro-His-Lys-Lys to the X-ray structures of both the free and the complexed Fab of the antibody B13I2 (raised against the C-helix of myohemerythri). The fragments Pro-His and Val-Pro-His, which contain residues experimentally identified as important for binding, docked correctly to both structures, but all tetrapeptide and larger fragments docked correctly only to the complexed Fab, even when torsional flexibility was added to the ligand. However, only tetrapeptide and larger fragments showed significantly more favorable energies when docked to the complexed Fab coordinates than when docked to either the free Fab or a non-specific site remote from the combining site. Comparison of the free and complexed B13I2 structures revealed that atoms within 5 Å of Val-Pro-His showed little movement upon peptide binding, but atoms within 5 Å of the other four epitope residues showed greater movements. These results computationally distinguish recognition and binding processes with practical implications for drug design strategies. Overall, this new fragment docking approach establishes distinct roles for the “lock-and-key” (recognition) and the “handshake” (binding) paradigms in antibody-antigen interaction, suggests an incremental approach to incorporating flexibility in computational docking, and identifies critical regions within receptor binding sites for ligand recognition. © 1994 Wiley-Liss, Inc.
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  • 91
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    Proteins: Structure, Function, and Genetics 18 (1994) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 92
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    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 93
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 8-18 
    ISSN: 0887-3585
    Keywords: docking algorithm ; antigen-antibody complex ; epitope ; influenza virus hemagglutinin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An automatic docking algorithm has been applied to the modeling of the complex between hemagglutinin from influenza virus and the Fab fragment of a monoclonal antibody raised against this antigen. We have introduced here the use of biochemical information provided by mutants of hemagglutinin. The docking procedure finds a small number of candidate solutions where three sites of escape mutations are buried and form hydrogen bonds in the interface. The localization of the epitope is improved by additional biochemical data about mutants that do not affect antibody binding. Five candidate solutions with low energy, reasonably well-packed interfaces, and six to ten hydrogen bonds are compatible with mutant information. One of the five stands out as generally better than the others from these points of views. © 1994 John Wiley & Sons, Inc.
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  • 94
    ISSN: 0887-3585
    Keywords: α-helix capping ; α-helix initiation ; α-helix termination ; synthetic peptides ; protein folding ; circular dichroism ; 1H nmr ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain-main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser-Glu-Asp-Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain-main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.
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  • 95
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 279-282 
    ISSN: 0887-3585
    Keywords: protein tertiary structure ; enzyme DNA complex ; cleavage pattern ; active site ; DNA recognition sequence ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five-stranded β-sheet and two α-helices packed against it and could be described as α-β sandwich in which helices and β-strands lie in two stacked layers. While the spatial structure of this α-β sandwich is conserved in both enzymes, there are no detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used. © 1994 Wiley-Liss, Inc.
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  • 96
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    Proteins: Structure, Function, and Genetics 20 (1994), S. 283-286 
    ISSN: 0887-3585
    Keywords: membrane protein ; protein structure ; photosynthesis ; detergent ; pigment-protein complexes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The reaction center from the nonsulfur purple bacteriumRhodobacter sphaeroideshas been crystallized in a new form. The crystals grew in the presence of polyethylene glycol 4000, the detergent β-octyl glucoside, and the amphiphiles heptane triol and benzamidine hydrochloride, using the sitting drop method. The space group of these crystals is tetragonal, P41(43)212, and the cell constants are a = b = 141.5 Å and c = 276.7 Å with probably 2 proteins per asymmetric unit. A native data set has been set collected to a resolution of 2.8 Å consisting of 56,332 unique reflections (50,731 with F 〉 2σ) with anRsym of 9.5%. Analysis of the diffraction data is underway using molecular and isomorphous replacement. © 1994 Wiley-Liss, Inc.
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  • 97
    ISSN: 0887-3585
    Keywords: crystallization ; X-ray crystallography ; cell adhesion molecule ; immunoglobulin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A molecular fragment comprising the first two domains of the human vascular cell adhesion molecule-l (VCAM-l) has been crystallized by the vapor diffusion method. Two crystal forms have been examined by X-ray analysis: One crystal form belongs to the space group C2 with two molecules in the asymmetric unit and cell parameters: a = 122.1 Å, b = 48.9 Å, c = 73.4 Å, and β = 117.4°. The other crystal form belongs to the space group P21 with one molecule in the asymmetric unit and cell parameters: a = 40.4 Å, b = 45.7 Å, c = 54.7 Å, and β = 100.5°. Diffraction data up to 1.9 Å resolution have been collected for the C2 crystal form. © 1994 Wiley-Liss, Inc.
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  • 98
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    Proteins: Structure, Function, and Genetics 20 (1994) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 99
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 174-185 
    ISSN: 0887-3585
    Keywords: computer modeling ; protein structure prediction ; α-carbons ; structure evaluation ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD-based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X-ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5-0.7 Å, and all-atom RMS values of 1.5-1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.
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  • 100
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    Proteins: Structure, Function, and Genetics 18 (1994), S. 161-173 
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; disulfide oxidoreductases ; FAD ; NADPH ; drug target ; Chagas' disease ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of trypanothione reductase (TR) (EC 1.6.4.8) from Trypanosoma cruzi has been solved at 0.33 nm resolution by molecular replacement using the structure of C. fasciculata TR as a starting model. Elucidation of the T. cruzi TR structure represents the first step in the rational design of a drug against Chagas' disease. The structure of T. cruzi TR is compared with those of C. fasciculata TR as well as human and E. coli glutathione reductase (GR). In the FAD-binding domain, TR has two insertions, each about 10 residues long, which do not occur in GR. The first one is a rigid loop stabilizing the position of helix 91-117 which is responsible for the wider active site of TR as compared to GR. The second insertion does not occur where it is predicted by sequence alignment; rather the residues extend three strands of the 4-stranded β-sheet by one or two residues each. This increases the number of hydrogen bonds within the sheet structure. The structure of the NADPH.TR complex has been solved at 0.33 nm resolution. The nicotinamide ring is sandwiched between the flavin ring and the side chain of Phe-198 which undergoes the same conformational change upon coenzyme binding as Tyr-197 in GR. In addition to Arg-222 and Arg-228, which are conserved in TR and GR, Tyr-221 - the last residue of the second β-sheet strand of the βαβ dinucleotide binding fold - is in hydrogen bonding distance to the 2′ phosphate group of NADPH. © 1994 John Wiley & Sons, Inc.
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