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  • 1995-1999  (11,016)
  • 1880-1889
  • 1996  (11,016)
  • Chemistry  (11,016)
  • Polymer and Materials Science  (4,900)
  • Nuclear reactions
  • 1
    Electronic Resource
    Electronic Resource
    Perceptions of chemistry: Why is the common perception of chemistry, the most visual of sciences, so distorted? (1996)
    Springer
    Journal of science education and technology 5 (1996), S. 193-201 
    Details
    ISSN: 1573-1839
    Keywords: Chemistry ; chemistry education ; multiple intelligences ; imagery ; visual-spatial thinking
    Source: Springer Online Journal Archives 1860-2000
    Topics: Natural Sciences in General , Technology
    Notes: Abstract Chemistry has evolved from a science dominated by mathematics into a science highly dependent on spatial-visual intelligence. Yet the chemical content of introductory courses remains taught essentially the same as 40–50 years ago. Chemistry, today, is recognized by chemists as the molecular science. Yet, school chemistry is alienated from that perception. Thanks to the computer, young people are more comfortable with visual imaging than their instructors were at the same age. Thus the time is rife to reinvigorate chemistry education by means of the visual-spatial approach, an approach wholly in conformance with the way modern chemistry is thought about and practiced.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01575303
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular dynamics study of glucocorticoid receptor-DNA binding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 115-133 
    Details
    ISSN: 0887-3585
    Keywords: receptor proteins ; estrogen receptor ; DNA bending ; DNA unwinding ; DNA recognition ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to investigate the binding of the glucocorticoid receptor (GR) dimer to DNA. For this purpose simulations of the complex formed by a DNA segment and a dimer of GR-DNA binding domains (GR-DBD) have been carried out, employing an available X-ray structure. A second set of simulations was based on this structure as well, except that the DNA segment was altered to the consensus glucocorticoid response element (GRE). Simulations of a single GR-DBD and of the uncomplexed GRE served as controls. For the simulations, each system was encapsulated in an ellipsoid of water. Protein-DNA interactions, dimer interactions, and DNA structural parameters were analyzed for each system and compared. The consensus GRE is found to yield more favorable and symmetric interactions between the GR-DBDs and the GRE, explaining the ability of the GR dimer to recognize this DNA segment. Further analysis focused on deformations of the DNA that are induced by the binding of GR. The deformations observed involve a 35° bend of the DNA, an unwinding, and a displacement of the helical axis. These deformations are consistent with a mechanism for transcriptional regulation that involves a change of nucleosome packing upon GR binding. Significant protein-protein and protein-DNA interactions, both direct and water mediated, develop due to the deformations of the GRE and are indicative of an increased recognition achieved through DNA deformation. The interactions include direct interactions between the GRE and glycine-458 and serine-459, side groups which differentiate GR from other members of the nuclear hormone receptor family.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 92-114 
    Details
    ISSN: 0887-3585
    Keywords: phospholipid membranes ; permeation ; antibiotics ; computer simulations ; tryptophan ; water ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The microscopic details of lipid-protein interactions are examined using molecular dynamics simulations of the gramicidin A channel embedded in a fully hydrated dimyristoyl phosphatidylcholine (DMPC) bilayer. A novel construction protocol was used to assemble the initial configurations of the membrane protein complex for the simulations. Three hundreds systems were constructed with different initial lipid placement and conformations. Seven systems were simulated with molecular dynamics. One system was simulated for a total of 600 psec, four were simulated for 300 psec, and two for 100 psec. Analysis of the resulting trajectories shows that the bulk solvent-membrane interface region is much broader than traditionally pictured in simplified continuum theories: its width is almost 15 Å. In addition, lipid-protein interactions are far more varied, both structurally and energetically, than is usually assumed: the total interaction energy between the gramicidin A and the individual lipids varies from 0 to -50 kcal/mol. The deuterium quadrupolar splittings of the lipid acyl chains calculated from the trajectories are in good agreement with experimental data. The lipid chains in direct contact with the GA are ordered but the effect is not uniform due to the irregular surface of the protein. Energy decompositions shows that the most energetically favorable interactions between lipid and protein involve nearly equal contributions from van der Waals and electrostatic interactions. The tryptophans, located near the bulk-membrane interface, appear to be particularly important in mediating both hydrogen bonding interactions with the lipid glycerol backbone and water and also in forming favorable van der Waals contacts with the hydrocarbon chains. In contrast, the interactions of the leucine residues with the lipids, also located near the interface, are dominated by van der Waals interactions with the hydrocarbon lipid chains.
    Additional Material: 16 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240101
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  • 5
    Electronic Resource
    Electronic Resource
    Neutron scattering redux? (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. iii 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240102
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  • 6
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray analysis of volvatoxin A2 from Volvariella volvacea (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 141-142 
    Details
    ISSN: 0887-3585
    Keywords: cardiotoxin ; hemolysis ; ion channel toxicology ; mushroom ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Volvatoxin A2, an ion channel disturbed cardiotoxic and hemolytic protein from the edible mushroom, Volvarilla volvacea, has been crystallized by the vapor diffusion method using polyethylene glycol 4000 and ammonium sulfate in sodium acetate buffer pH 4.6. The best crystals belong to the monoclinic space group C2 with unit cell dimensions a = 155.25 Å, b = 58.06 Å, c = 116.92 Å, and β = 119.5°. These crystals diffract to at least 2.2 Å and there are four molecules of molecular weight 24 kDa per asymmetric unit with a solvent content of 48%.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Future directions in folding: The multi-state nature of protein structure (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 145-151 
    Details
    ISSN: 0887-3585
    Keywords: protein stability ; protein dynamics ; hydrogen exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: All possible protein folding intermediates exist in equilibrium with the native protein at native as well as non-native conditions, with occupation determined by their free energy level. The study of these forms can illuminate the fundamental principles of protein structure and folding. Hydrogen exchange methods can be used to detect and characterize these partially unfolded forms at native conditions and as a function of mild denaturant and temperature. This information illuminates the requirements that govern the ability of kinetic and equilibrium methods to study folding intermediates.
    Additional Material: 4 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    Comparison of an antibody model with an X-ray structure: The variable fragment of BR96 (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 152-157 
    Details
    ISSN: 0887-3585
    Keywords: antibody X-ray crystallography ; antibody modeling ; protein structure prediction ; structure comparison ; model evaluation ; prediction accuracy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the BR96 antibody variable regions is compared to two X-ray structures of a BR96-carbohydrate complex, independently determined after the model was built and analyzed. The comparison illustrates the opportunities and limitations of antibody modeling. Encouraging results were obtained for the prediction of single CDR loop conformations and for the outline of the BR96 antigen binding site. The comparison of CDR loop conformations in the two X-ray structures provides a realistic reference frame for the CDR loop predictions. CDR loop prediction accuracy is lower when not only conformational, but also positional criteria are taken into account.
    Additional Material: 3 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 165-177 
    Details
    ISSN: 0887-3585
    Keywords: sequence data sets ; similarity screening ; redundancy reduction ; signal peptides ; database errors ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: When preparing data sets of amino acid or nucleotide sequences it is necessary to exclude redundant or homologous sequences in order to avoid overestimating the predictive performance of an algorithm. For some time methods for doing this have been available in the area of protein structure prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary threshold value for excluding redundant sequences. The impact of the choice of scoring matrix used in the alignments is examined. We demonstrate that the parameter determining the quality of the correlation is the relative entropy of the matrix, rather than the assumed (PAM or identity) substitution model. Results are presented for the case of prediction of cleavage sites in signal peptides. By inspection of the false positives, several errors in the database were found. The procedure presented may be used as a general outline for finding a problem-specific similarity measure and threshold value for analysis of other functional amino acid or nucleotide sequence patterns.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    A complete relaxation matrix refinement of the solution structure of a paramagnetic metalloprotein: Reduced HiPIP I from Ectothiorhodospira halophila (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 158-164 
    Details
    ISSN: 0887-3585
    Keywords: NMR ; iron-sulfur proteins ; nuclear Overhauser effect ; paramagnetic relaxation ; relaxation matrix analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have accounted for the effect of paramagnetism on the intensities of NOEs in a 73-residue paramagnetic metalloprotein, the reduced high-potential iron sulfur protein ISO I from Ectothiorhodospira halophila, whose solution structure had been recently solved by us. The paramagnetic effects were dealt with through a suitably modified complete relaxation matrix approach. We have then recalculated the structure through a distance geometry program by minimizing the difference between the sixth roots of the calculated and experimental NOEs.The average RMSD, calculated on residues 4-71, within the structures constituting the two families decreased from 0.67 to 0.46 Å for backbone atoms and from 1.23 to 1.06 Å for all heavy atoms. The structures in the new family are for the most part within the indetermination of the previous, less resolved, family. A few specific differences are detected and related to the presence of non-negligible paramagnetic effects, which are now properly evaluated.
    Additional Material: 5 Ill.
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  • 11
    Electronic Resource
    Electronic Resource
    Cysteine-191 in aspartate aminotransferases appears to be conserved due to the lack of a neutral mutation pathway to the functional equivalent, alanine-191 (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 195-208 
    Details
    ISSN: 0887-3585
    Keywords: protein evolution ; conserved cysteine ; pyridoxal phosphate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: It was previously suggested that the conserved Cys-191 of aspartate aminotransferases (AATases) is conserved, not because it is essential, but because it is frozen in the sequence, with no neutral corridor to traverse to the similar phenotype of Ala-191 (Gloss et al., Biochemistry 31:32-39, 1992). This hypothesis has now been tested by additional mutations. All possible one-base mutations from Cys were made at position 191. All of these variants display kinetic parameters (kcat and kcat/KM values) that differ from the wild-type enzyme by 30% or more. The non-conserved cysteines that are predominantly Ala in other AATase sequences (Cys-82, Cys-192, and Cys-401) were mutated to Ser to test the corollary that a neutral Cys → Ala corridor does exist for these positions. These Cys → Ser mutations yielded enzymes with wild-type-like kinetic parameters. The pKa values of the internal aldimines of the mutants, Cys-191 → Ser, Phe, Tyr, and Trp are higher than that of wild type by 0.6-0.8 pH units. The stabilities to urea denaturation of the Cys-191 mutants are similar to that of wild type, while those of the non-conserved cysteines show greater variation. Examination of the three-dimensional environment of the five cysteines showed that the van der Waals contacts of Cys-191 are more conserved than are those of the non-conserved cysteines. These data provide further support for the above hypothesis.
    Additional Material: 5 Ill.
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  • 12
    Electronic Resource
    Electronic Resource
    Solution structure of P01, a natural scorpion peptide structurally analogous to scorpion toxins specific for apamin-sensitive potassium channel (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 359-369 
    Details
    ISSN: 0887-3585
    Keywords: scorpion venom ; neurotoxin ; NMR ; structure-activity relationships ; calcium activated-potassium channel ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The venom of the North African scorpion Androctonus mauretanicus mauretanicus possesses numerous highly active neurotoxins that specifically bind to various ion channels. One of these, P05, has been found to bind specifically to calcium-activated potassium channels and also to compete with apamin, a toxin extracted from bee venom. Besides the highly potent ones, several of these peptides (including that of P01) have been purified and been found to possess only a very weak, although significant, activity in competition with apamin. The amino acid sequence of P01 shows that it is shorter than P05 by two residues. This deletion occurs within an α-helix stretch (residues 5-12). This α-helix has been shown to be involved in the interaction of P05 with its receptor via two arginine residues. These two arginines are absent in the P01 sequence. Furthermore, a proline residue in position 7 of the P01 sequence may act as an α-helix breaker. We have determined the solution structure of P01 by conventional two-dimensional 1H nuclear magnetic resonance and show that 1) the proline residue does not disturb the α-helix running from residues 5 to 12; 2) the two arginines are topologically replaced by two acidic residues, which explains the drop in activity; 3) the residual binding activity may be due to the histidine residue in position 9; and 4) the overall secondary structure is conserved, i.e., an α-helix running from residues 5 to 12, two antiparallel stretches of β-sheet (residues 15-20 and 23-27) connected by a type I′ β-turn, and three disulfide bridges connecting the α-helix to the β-sheet.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Thermally induced hydrogen exchange processes in small proteins as seen by FTIR spectroscopy (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 379-387 
    Details
    ISSN: 0887-3585
    Keywords: infrared spectroscopy ; protein structure ; unfolding ; RNase T1 ; RNase A ; histone-like protein HBsu ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fourier-transform infrared (FTIR) spectroscopy has been used to study the thermally induced exchange characteristics of those backbone amide protons which persist H-D exchange at ambient conditions in ribonuclease A, in wild type ribonuclease T1 and some of its variants, and in the histone-like protein HBsu. The H-D exchange processes were induced by increasing the thermal energy of the protein solutions in two ways: (i) by linearly increasing the temperature, and (ii) by a temperature jump. To trace the H-D exchange in the proteins, various infrared absorption bands known to be sensitive to H-D exchange were used as specific monitors. Characteristic H-D exchange curves were obtained from which the endpoints (TH/D) of H-D exchange could be determined. The H-D exchange curves, the TH/D-values and the phase transition temperatures Tm were used to estimate the structural flexibility and stability of the given proteins. It is suggested that time-resolved FTIR spectroscopy can be used to determine global stability parameters of proteins.
    Additional Material: 9 Ill.
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  • 14
    Electronic Resource
    Electronic Resource
    A partial model of the erythropoietin receptor complex (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 394-401 
    Details
    ISSN: 0887-3585
    Keywords: cytokines ; homology modeling ; erythropoietin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the structure of erythropoietin (Epo) is presented based on structural homology to other hemopoietic cytokines. A model of the erythropoietin receptor complex was made based on evidence that this includes a homodimer of the receptor chain with known sequence. Key interactions are noted which explain data from mutation experiments, although at not all residues believed to be important to binding of Epo are at the interface. This is consistent with the hypothesis that the Epo receptor complex includes proteins in addition to the cloned receptor chain that have been cross-linked to Epo (Todokoro et al., Proc. Natl. Acad. Sci. USA 84:4126-4130, 1987; Mayeux et al., J. Biol. Chem. 266:23380-23385, 1991) but not isolated.
    Additional Material: 5 Ill.
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  • 15
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray analysis of the Escherichia coli replication terminator protein complexed with DNA (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 402-403 
    Details
    ISSN: 0887-3585
    Keywords: Tus ; terminus site ; protein-DNA interaction ; replication arrest ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the Escherichia coli replication terminator protein (Tus) complexed with its binding site DNA were obtained by a microdialysis method using PEG 4000. They belong to the tetragonal space group P41212 or P43212 with the unit cell parameter: a = 68.1 Å, c = 230.7 Å and contain one protein-DNA complex in an asymmetric unit. The native data set has been collected to 2.7 Å resolution.
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  • 16
    Electronic Resource
    Electronic Resource
    Purification, crystallization, and preliminary crystallographic analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 404-406 
    Details
    ISSN: 0887-3585
    Keywords: DAHP synthase ; metalloenzyme ; shikimate pathway ; KDOP synthase ; affinity chromatography ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The phenylalanine-regulated isozyme of 3-deoxy-D-arabino-heptulosonate-7-phosphate- synthase (DAHPS) from Escherichia coli, its binary complexes with either substrate, phosphoenolpyruvate (PEP), or feedback inhibitor, Phe, and its ternary complexes with either PEP or Phe plus metal cofactor (either Mn2+, Cd2+, or Pb2+) were crystallized from polyethylglycol (PEG) solutions. All crystals of the DAHPS without Phe belong to space group C2, with cell parameters a = 213.5 Å, b = 54.3 Å, c = 149.0 Å, β = 116.6°. All crystals of the enzyme with Phe also belong to space group C2, but with cell parameters a = 297.1 Å, b = 91.4 Å, c = 256.5 Å, and β = 148.2°.
    Additional Material: 1 Tab.
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  • 17
    Electronic Resource
    Electronic Resource
    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240301
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  • 18
    Electronic Resource
    Electronic Resource
    Federal support for protein engineering (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 1-1 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240302
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  • 19
    Electronic Resource
    Electronic Resource
    Current protocols in protein science, edited by J.E. Coligan, B.M. Dunn, H.L. Ploegh, D.W. Speicher, and P.T. Wingfield. New York: Wiley, 1995, 864 pages (core) + 576 pages (4 supplements)/year (updated looseleaf), print and CD-ROM (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 409-409 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240303
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  • 20
    Electronic Resource
    Electronic Resource
    Errata (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 410-410 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240304
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  • 21
    Electronic Resource
    Electronic Resource
    The role of helix formation in the folding of a fully α-helical coiled coil (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 427-432 
    Details
    ISSN: 0887-3585
    Keywords: GCN4 ; protein folding ; folding kinetics ; helix formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To determine when secondary structure forms as two chains coalesce to form an α-helical dimer, the folding rates of variants of the coiled coil region of GCN4 were compared. Residues at non-perturbing positions along the exterior length of the helices were substituted one at a time with alanine and glycine to vary helix propensity and therefore dimer stability. For all variants, the bimolecular folding rate remains largely unchanged; the unfolding rate changes to largely account for the change in stability. Thus, contrary to most folding models, widespread helix is not yet formed at the rate-limiting step in the folding pathway. The high-energy transition state is a collapsed form that contains little if any secondary structure, as suggested for the globular protein cytochrome c (Sosnick et al., Proteins 24:413-426, 1996).
    Additional Material: 4 Ill.
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  • 22
    Electronic Resource
    Electronic Resource
    Hydrophilicity of cavities in proteins (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 433-438 
    Details
    ISSN: 0887-3585
    Keywords: structure refinement ; buried water ; free energy calculation ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at -12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.
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  • 23
    Electronic Resource
    Electronic Resource
    Molecular collapse: The rate-limiting step in two-state cytochrome c folding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 413-426 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; folding kinetics ; folding barriers ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Experiments with cytochrome c (cyt c) show that an initial folding event, molecular collapse, is not an energetically downhill continuum as commonly presumed but represents a large-scale, time-consuming, cooperative barrier-crossing process. In the absence of later misfold-reorganization barriers, the early collapse barrier limits cyt c folding to a time scale of milliseconds. The collapse process itself appears to be limited by an uphill search for some coarsely determined transition state structure that can nucleate subsequent energetically downhill folding events. An earlier “burst phase” event at strongly native conditions appears to be a non-specific response of the unfolded chain to reduced denaturant concentration. The molecular collapse process may or may not require the co-formation of the amino- and carboxyl-terminal helices, which are present in an initial metastable intermediate directly following the rate-limiting collapse. After the collapse-nucleation event, folding can proceed rapidly in an apparent two-state manner, probably by way of a predetermined sequence of metastable intermediates that leads to the native protein structure (Bai et al., Science 269:192-197, 1995).
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  • 24
    Electronic Resource
    Electronic Resource
    For Guldberg and Waage, with love and cratic entropy (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240402
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    Molecular dynamics study of phospholipase A2 on a membrane surface (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 12-27 
    Details
    ISSN: 0887-3585
    Keywords: protein-membrane interaction ; free energy perturbation ; lipid desolvation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The desolvation of lipid molecules in a complex of the enzyme human synovial phospholipase A2 with a lipid membrane is investigated as a mechanism that enhances the overall activity of the enzyme. For this purpose the interaction of the enzyme phospholipase A2 with a dilauryl-phosphatityl-ethanolamin (DLPE) membrane monolayer surface has been studied by means of molecular dynamics simulations. Two enzyme-membrane complexes, a loose and a tight complex, are considered. For comparison, simulations are also carried out for the enzyme in aqueous solution. The conformation, dynamics, and energetics of the three systems are compared, and the interactions between the protein and lipid molecules are analyzed. Free energies of solvation are calculated for the lipid molecules in the enzyme-membrane interface. Along with the calculated dielectric susceptibility at this interface, the results show the desolvation of lipids in a tightly bound, but not in a loosely bound protein-membrane complex. The desolvated lipids are found to interact mainly with hydrophobic protein residues, Including Leu-2, Val-3, Ala-18, Leu-19, Phe-24, Val-31, and Phe-70. The results also explain why the turnover rate of phospholipase A2 complexed to a membrane is enhanced after a critical amount of negatively charged reaction product is accumulated. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.2
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    Predicting solvent accessibility: Higher accuracy using Bayesian statistics and optimized residue substitution classes (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 38-47 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; Bayesian statistics ; amino acid substitution ; information theory ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We introduce a novel Bayesian probabilistic method for predicting the solvent accessibilities of amino acid residues in globular proteins. Using single sequence data, this method achieves prediction accuracies higher than previously published methods. Substantially improved predictions - comparable to the highest accuracies reported in the literature to date - are obtained by representing alignments of the example proteins and their homologs as strings of residue substitution classes, depending on the side chain types observed at each alignment position. These results demonstrate the applicability of this relatively simple Bayesian approach to structure prediction and illustrate the utility of the classification methodology previously developed to extract information from aligned sets of structurally related proteins. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.4
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    On the sensitivity of MD trajectories to changes in water-protein interaction parameters: The potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 89-103 
    Details
    ISSN: 0887-3585
    Keywords: computer simulation ; force-field analysis ; molecular dynamics of proteins ; water solvation properties ; van der Waals interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A critical evaluation is presented of the sensitivity of the results of molecular dynamics simulations of proteins to changes in the parameters describing water-protein and protein-protein van der Waals interactions in the GROMOS force field. The origin of the van der Waals and electrostatic parameters of the GROMOS standard force field is reviewed, and possible weaknesses are discussed. Four alternate sets of van der Waals parameters for the oxygen types of the GROMOS force field that have been suggested by different authors are then tested against the original force field. Six 500 ps molecular dynamics simulations of the potato carboxypeptidase inhibitor (PCI) in solution using the different parameter sets are analyzed and the results compared with the available X-ray and NMR data. It is shown that the behavior of the molecular system is very sensitive to changes in the van der Waals parameters of the oxygens, especially when affecting the interactions between water and aliphatic or aromatic groups. It is also shown that correction of just the repulsive van der Waals parameter of the water oxygen for its interactions with nonpolar groups is sufficient to correct the main deficiency of the original GROMOS parameter set. Nevertheless, the present study suggests that further refinement of the current parameters is still needed for a proper representation of nonbonded interactions. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.7
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    Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 502-513 
    Details
    ISSN: 0887-3585
    Keywords: de novo design ; protein structure ; inverse folding ; genetic algorithms ; 1H NMR ; CD ; peptide ; protein folding ; methanol ; ethylene glycol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1-3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all-β protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to “fit” the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence-structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.
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    Crystallization and preliminary X-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 520-522 
    Details
    ISSN: 0887-3585
    Keywords: dehalogenase ; hydrolase ; Pseudomonas ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The dimeric L-2-haloacid dehalogenase from Pseudomonas sp. YL, (subunit mass, 26179 Da), has been crystallized by vapor diffusion, supplemented by repetitive seeding, against a 50 mM potassium dihydrogenphosphate solution (pH 4.5) containing 15% (w/v) polyethylene glycol 8,000 and 1% (v/v) n-propanol. The crystals belong to the monoclinic space group C2 with unit cell dimensions of a = 92.21 Å, b = 62.78 Angst; c = 50.84 Å, and β = 122.4°, and contain two dehalogenase dimers in the unit cell. They are of good quality and diffract up to 1.5 Å resolution.
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    The magnitude of the backbone conformational entropy change in protein folding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 143-156 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The magnitude of the conformational entropy change experienced by the peptide backbone upon protein folding was investigated experimentally and by computational analysis. Experimentally, two different pairs of mutants of a 33 amino acid peptide corresponding to the leucine zipper region of GCN4 were used for high-sensitivity microcalorimetric analysis. Each pair of mutants differed only by having alanine or glycine at a specific solvent-exposed position under conditions in which the differences in stability could be attributed to differences in the conformational entropy of the unfolded state. The mutants studied were characterized by different stabilities but had identical heat capacity changes of unfolding (ΔCp), identical solvent-related entropies of unfolding (ΔSsolv), and identical enthalpies of unfolding (ΔH) at equivalent temperatures. Accordingly, the differences in stability between the different mutants could be attributed to differences in conformational entropy. The computational studies were aimed at generating the energy profile of backbone conformations as a function of the main chain dihedral angles φ and ϱ. The energy profiles permit a direct calculation of the probability distribution of different conformers and therefore of the conformational entropy of the backbone. The experimental results presented in this paper indicate that the presence of the methyl group in alanine reduces the conformational entropy of the peptide backbone by 2.46 ± 0.2 cal/K · mol with respect to that of glycine, consistent with a 3.4-fold reduction in the number of allowed conformations in the alanine-containing peptides. Similar results were obtained from the energy profiles. The computational analysis also indicates that the addition of further carbon atoms to the side chain had only a small effect as long as the side chains were unbranched at position β. A further reduction with respect to Ala of only 0.61 and 0.81 cal/K · mol in the backbone entropy was obtained for leucine and lysine, respectively. β-branching (Val) produces the largest decrease in conformational entropy (1.92 cal/K · mol less than Ala). Finally, the backbone entropy change associated with the unfolding of an α-helix is 6.51 cal/K · mol for glycine. These and previous results have allowed a complete estimation of the conformational entropy changes associated with protein folding. © 1996 Wiley-Liss, Inc.
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    Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 169-179 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; prediction of secondary structural class ; prediction of folding type ; amino acid composition ; jackknife analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The success rates reported for secondary structural class prediction with different methods are contradictory. On one side, the problem of recognizing the secondary structural class of a protein knowing only its amino acid composition appears completely solved by simply applying jury decision with an elliptically scaled distance function. Chou and coworkers repeatedly (see Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995) published prediction accuracies near 100%. On the other hand, traditional secondary structure prediction techniques achieve success rates of about 70% for the secondary structural state per residue and about 75% for structural class only with extensive input information (full sequence of the query protein, its amino acid composition and length, multiple alignments with homologous sequences).In this article, we resolve the paradox and consider (1) the question of the secondary structural class definition, (2) the role of the representativity of the test set of protein tertiary structure for the current state of the Protein Data Bank (PDB); and (3) we estimate the real impact of amino acid composition on secondary structural class. We formulate three objective criteria for a reasonable definition of secondary structural classes and show that only the criterion of Nakashima et al. (J. Biochem. 99:153-162, 1986) complies with all of them. Only this definition matches the distribution of secondary structural content in representative PDB subsets, whereas other criteria leave many proteins (up to 65% of all PDB entries) simply unassigned.We review critically specialized secondary-structural class prediction methods, especially those of Chou and coworkers, which claim almost 100% accuracy using only amino acid composition, and resolve the paradox that these prediction accuracies are better than those from secondary structure predictions from multiple alignments. We show (i) that these techniques rely on a preselection of test sets which removes irregular proteins and other proteins without any class assignment (about 35% of all PDB entries); and (ii) that even for preselected representative test sets, the success rate drops to 60% and lower for a 4-type classification (α, β, α + β, α/β). The prediction accuracies fall to about 50% if the secondary structural class definition of Nakashima et al. is applied and only few irregular proteins are preselected and removed from automatically generated, representative subsets of the PDB.We have applied two new vector decomposition methods for secondary structural content prediction from amino acid composition alone, with and without consideration of amino acid compositional coupling in the learning set of tertiary structures respectively, to the problem of class prediction and achieve about 60% correct assignment among four classes (α, β, mixed, irregular) as well as single sequence-based secondary structure prediction methods like GORIII and COMBI. Our results demonstrate that 60% correctness is the upper limit for a 4-type class prediction from amino acid composition alone for an unknown query protein and that consideration of compositional coupling does not improve the prediction success. The prediction program SSCP offering secondary structural class assignment for query compositions and sequences has been made available as a World Wide Web and E-mail service. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.3
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    Structure of a ternary complex of proteinase K, mercury, and a substrate-analogue hexa-peptide at 2.2 Å resolution (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 195-201 
    Details
    ISSN: 0887-3585
    Keywords: proteinase K ; complex ; hexapeptide ; mercury ; ternary complex ; inhibitor ; structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a ternary complex of proteinase K, Hg(II) and a hexapeptide N-Ac-Pro-Ala-Pro-Phe-Pro-Ala-NH2 has been determined at 2.2 Å resolution and refined to an R factor of 0.172 for 12,910 reflections. The mercury atom occupies two alternate sites, each of which was assigned an occupancy of 0.45. These two sites are bridged by Cys-73 Sγ which forms covalent bonds to both. Both mercury sites form regular polyhedrons involving atoms from residues Asp-39, His-69, Cys-73, His-72, Met-225, and Wat-324. The complex formation with mercury seems to disturb the stereochemistry of the residues of the catalytic triad Asp-39, His-69, and Ser-224 appreciably, thus reducing the enzymatic activity of proteinase K to 15%. The electron density in the difference Fourier map shows that the hexapeptide occupies the S1 subsite predominantly and the standard recognition site constituted by Ser-132 to Gly-136 and Gly-100 to Tyr-104 segments is virtually empty. The hexapeptide is held firmly through a series of hydrogen bonds involving protein atoms and water molecules. As a result of complex formation, Asp-39, His-69, Met-225, Ile-220, Ser-219, Thr-223, and Ser-224 residues move appreciably to accommodate the mercury atoms and the hexapeptide. The largest movement is observed for Met-225 which is involved in multiple interactions with both mercury and the hexapeptide. The activity results indicate an inhibition rate of 95%, as a result of the combined effect of mercury and hexapeptide. © 1996 Wiley-Liss, Inc.
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    Ab initio models for receptor-ligand interactions in proteins. 4. Model assembly study of the catalytic mechanism of triosephosphate isomerase (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 225-236 
    Details
    ISSN: 0887-3585
    Keywords: enzyme reaction ; ab initio quantum mechanical ; semiempirical quantum mechanical ; continuum electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The catalytic mechanism of triosephosphate isomerase (TIM) was investigated with ab initio quantum mechanical calculations. Electrostatic interactions between the quantum mechanical active site and the protein and solvent environment were modeled using the finite difference Poission-Boltzman method. The complexes of TIM with the substrate dihydroxyacetone phosphate (DHAP), five possible intermediates and the product glyceraldehyde-3-phosphate (GAP) were optimized in the active-site model at the 3-21G(*) level and energy profile for the proton abstraction from DHAP by the active-site Glu167 was calculated at the MP2/3-21G(*)//3-21G(*) level. Calculated energetics of the enzyme reaction were found to be in reasonable agreement with the experimental findings. Calculations revealed that an enediol of the substrate is a probable intermediate in the enzyme reaction. It was suggested that the proton abstracted from the substrate by the active-site glutamate goes to the carbonyl oxygen of the substrate producing enediol intermediate either directly or after it is exchanged with solvent. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.8
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    The surface of β-sheet proteins contains amphiphilic regions which may provide clues about protein folding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 253-260 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; protein folding ; chaperone ; folding path ; amphiphilic sequences ; β-sheet proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A major bottleneck in the field of biochemistry is our limited understanding of the processes by which a protein folds into its native conformation. Much of the work on this issue has focused on the conserved core of the folded protein. However, one might imagine that a ubiquitous motif for unaided folding or for the recognition of chaperones may involve regions on the surface of the native structure. We explore this possibility by an analysis of the spatial distribution of regions with amphiphilic α-helical potential on the surface of β-sheet proteins.All proteins, Including β-sheet proteins, contain regions with amphiphilic α-helical potential. That is, any α-helix formed by that region would be amphiphilic, having both hydrophobic and hydrophilic surfaces. In the three-dimensional structure of all β-sheet proteins analyzed, we have found a distinct pattern in the spatial distribution of sequences with amphiphilic α-helical potential. The amphiphilic regions occur in ring shaped clusters approximately 20 to 30 Å in diameter on the surface of the protein. In addition, these regions have a strong preference for positively charged amino acids and a lower preference for residues not favorable to α-helix formation. Although the purpose of these amphiphilic regions which are not associated with naturally occurring α-helix is unknown, they may play a critical role in highly conserved processes such as protein folding. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.10
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    The native state of apomyoglobin described by proton NMR spectroscopy: The A-B-G-H interface of wild-type sperm whale apomyoglobin (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 267-285 
    Details
    ISSN: 0887-3585
    Keywords: myoglobin ; histidine ; hydrophobic core ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proton nuclear magnetic resonance spectroscopy was applied to sperm whale apomyoglobin to describe the conformation adopted by the protein under native conditions. The study focused on the A-B-G-H interface, a region known to form a compact subdomain in the apoprotein (Hughson and Baldwin, Biochemistry 28:4415-4422, 1989). Two histidine residues located in this subdomain, His24 and His119, interact and are thought to play a role in the acid denaturation process (Barrick et al., J. Mol. Biol. 237:588-601, 1994). A stable double mutant at these positions (His24Va1/His119Phe sperm whale apomyoglobin) was compared with wild-type apomyoglobin. The amino acid replacements result in chemical shift perturbations near the mutations, in particular in the AB interhelical region, and in a deceleration of backbone amide hydrogen exchange in the B helix from position 27 to position 33. The double mutant data were used to expand and confirm the wild-type spectral analysis. Signals from the D helix were identified that demonstrate the formation of holoprotein-like structure. The assigned wild-type nuclear Overhauser effects, although in small number, were sufficient to construct a model of the compact subdomain of the apoprotein. This was achieved by using the structure of the holoprotein and restraining it with the geometrical information on the apoprotein in a simulated annealing procedure. The experimental restraints define a low-resolution model of the A-B-G-H interface in apomyoglobin. © 1996 Wiley-Liss, Inc.
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    Identification and analysis of long-range electrostatic effects in proteins by computer modeling:Aspartate transcarbamylase (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 300-314 
    Details
    ISSN: 0887-3585
    Keywords: electrostatic modeling ; Poisson-Boltzmann equation ; finite difference ; multigrid ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three-dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site-site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson-Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK1/2 values. Most of the residues with pK1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site-site interaction free energies on distance is complex, with a steep dependence at distances less than 5 Å and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 Å require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long-range structural effects and allosteric signals. © 1996 Wiley-Liss, Inc.
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    The linker of calmodulin lacking Glu84 is elongated in solution, although it is bent in the crystal (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 335-341 
    Details
    ISSN: 0887-3585
    Keywords: solution X-ray scattering ; calcium-dependent conformational change ; calmodulin-melittin complex ; deviation from crystal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution structure of a mutant calmodulin (des84) lacking Glu84 in the central helix linking the two calmodulin lobes is substantially different from its crystal structure. As determined by small-angle X-ray scattering, the radius of gyration and the maximum linear dimension of des84 in the presence of 0.1 mM calcium are 20.8 Å and 62.5 Å, respectively. These respective dimensions are larger than those expected from the crystal structure of des84, 18.5 Å and 55.0 Å, and smaller than those expected from the crystal structure of wild type, 22.8 Å and 67.5 Å. The distance distribution function of des84 indicates that it assumes an elongated, dumbbell shape in solution. The solution scattering profile of des84 is indistinguishable from that of wild-type calmodulin. The calcium-dependent binding of melittin to des84 causes a change in its shape from elongated to spherical, as seen with other calmodulins. In comparison with calcium-saturated des84, calcium-free des84 is slightly elongated; a slight compaction is observed with native calmodulin. The observed differences between the averaged solution structure and the crystal structure of des84 suggests that an ensemble of structures is available to calmodulin in solution and that its target need not induce a change in its conformation. These results support the theory that the linker region of the central helix of calmodulin functions as a flexible tether. © 1996 Wiley-Liss, Inc.
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    Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 354-365 
    Details
    ISSN: 0887-3585
    Keywords: classification of protein structures ; method for structural comparison ; porin ; bacteriochlorophyll α protein ; sequence-structure relationship ; WWW ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have developed a new method and program, SARF2, for fast comparison of protein structures, which can detect topological as well as nontopological similarities. The method searches for large ensembles of secondary structure elements, which are mutually compatible in two proteins. These ensembles consist of small fragments of Cα-trace, similarly arranged in three-dimensional space in two proteins, but not necessarily equally-ordered along the polypeptide chains. The program SARF2 is available for everyone through the World-Wide Web (WWW). We have performed an exhaustive pairwise comparison of all the entries from a recent issue of the Protein Data Bank (PDB) and report here on the results of an automated hierarchical cluster analysis. In addition, we report on several new cases of significant structural resemblance between proteins. To this end, a new definition of the significance of structural similarity is introduced, which effectively distinguishes the biologically meaningful equivalences from those occurring by chance. Analyzing the distribution of sequence similarity in significant structural matches, we show that sequence similarity as low as 20% in structurally-prealigned proteins can be a strong indication for the biological relevance of structural similarity. © 1996 Wiley-Liss, Inc.
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    Crystallization and preliminary x-ray diffraction studies of human procathepsin L (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 398-400 
    Details
    ISSN: 0887-3585
    Keywords: procathepsin L ; proenzyme ; cysteine protease ; crystallization ; purification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human procathepsin L has been expressed in the yeast Pichia pastoris and its inactive (Cys25Ser) and unglycosylated (Thr110Ala) mutant purified, concentrated to 4 mg/ml, and crystallized by vapor diffusion against solution containing 1.4 M (Na, K)PO4 buffer, pH 7.8. Crystal size was Increased by multiple macroseeding. The crystals are orthorhombic, of space group P212121, with cell dimensions of a = 40.2 Å, b = 88.4 Å, and c = 94.9 Å. A 2.2 Å native data set was collected using synchrotron radiation. Although molecular replacement solution for the mature portion of the enzyme was easily found, the resulting maps could not be interpreted in the proregion. Heavy-atom derivative search is in progress. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.11
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    Hydrophobic patches on the surfaces of protein structures (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 389-397 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; molecular surface ; lipophilicity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A survey of hydrophobic patches on the surface of 112 soluble, monomeric proteins is presented. The largest patch on each individual protein averages around 400 Å2 but can range from 200 to 1,200 Å2. These areas are not correlated to the sizes of the proteins and only weakly to their apolar surface fraction. Ala, Lys, and Pro have dominating contributions to the apolar surface for smaller patches, while those of the hydrophobic amino acids become more important as the patch size Increases. The hydrophilic amino acids expose an approximately constant fraction of their apolar area independent of patch size; the hydrophobic residue types reach similar exposure only in the larger patches. Though the mobility of residues on the surface is generally higher, it decreases for hydrophilic residues with Increasing patch size. Several characteristics of hydrophobic patches catalogued here should prove useful in the design and engineering of proteins. © 1996 Wiley-Liss, Inc.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.10
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    Electronic Resource
    Molecular systematics in 3D: The classification of protein structures, Paris, april 9-11, 1996 (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340250302
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  • 42
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    Electronic Resource
    Docking enzyme-inhibitor complexes using a preference-based free-energy surface (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 403-419 
    Details
    ISSN: 0887-3585
    Keywords: surface complementarity ; macro-molecular interactions ; HIV-1 protease inhibitor binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present a docking scheme that utilizes both a surface complementarity screen as well as an energetic criterion based on surface area burial. Twenty rigid enzyme/inhibitor complexes with known coordinate sets are arbitrarily separated and reassembled to an average all-atom rms (root mean square) deviation of 1.0 Å from the native complexes. Docking is accomplished by a hierarchical search of geometrically compatible triplets of surface normals on each molecule. A pruned tree of possible bound configurations is built up using successive consideration of larger and larger triplets. The best scoring configurations are then passed through a free-energy screen where the lowest energy member is selected as the predicted native state. The free energy approximation is derived from observations of surface burial by atom pairs across the interface of known enzyme/inhibitor complexes. The occurrence of specific atom-atom surface burial, for a set of complexes with well-defined secondary structure both in the bound and unbound states, is parameterized to mimic the free energy of binding. The docking procedure guides the inhibitor into its native state using orientation and distance-dependent functions that reproduce the ideal model of free energies with an average rms deviation of 0.9 kcal/mol. For all systems studied, this docking procedure identifies a single, unique minimum energy configuration that is highly compatible with the native state. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.1
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  • 43
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    Oxygen binding by single crystals of hemoglobin: The problem of cooperativity and inequivalence of alpha and beta subunits (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 425-437 
    Details
    ISSN: 0887-3585
    Keywords: nickel-iron hybrid hemoglobins ; two-state allosteric model ; single crystal absorption spectra ; Bohr effect ; multisubunit proteins ; quaternary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Oxygen binding by the human hemoglobin tetramer in the T quaternary structure is apparently noncooperative in the crystalline state (Hill n = 1.0), as predicted by the two-state allosteric model of Monod, Wyman, and Changeux (MWC) (Mozzarelli et al., Nature 351:416-419, 1991; Rivetti et al., Biochemistry 32:2888-2906, 1993). However, cooperativity within the tetramer can be masked by a difference in affinity between the α and β subunits. Indeed, analysis of the binding curves derived from absorption of light polarized along two different crystal directions, for which the projections of the α and β hemes are slightly different, revealed an inequivalence in the intrinsic oxygen affinity of the α and β subunits (p50(α) ≅ 80 torr, p50(β) ≅ 370 torr at 15°C) that compensates a small amount of cooperativity (Rivetti et al., Biochemistry 32:2888-2906, 1993). To further investigate this problem, we have measured oxygen binding curves of single crystals of hemoglobin (in a different lattice) in which the iron in the α subunits has been replaced by the non-oxygen-binding nickel(II). The Hill n is 0.90 ± 0.06, and the p50 is slightly different for light polarized parallel to different crystal directions, indicating a very small difference in affinity between the two crystallographically inequivalent β subunits. The average crystal p50 is 110 ± 20 torr at 15°C, close to the p50 of 80 torr observed in solution, but about threefold less than the p50 calculated by Rivetti et al. (Biochemistry 32:2888-2906, 1993) for the β subunits of the unsubstituted tetramer. These results suggest that Rivetti et al., if anything, overestimated the α/β inequivalence. They therefore did not underestimate the cooperativity within the T quaternary structure, when they concluded that it represents a small deviation from the perfectly noncooperative binding of an MWC allosteric model. Our conclusion of nearly perfect MWC behavior for binding to the T state of unmodified hemoglobin raises the question of the relevance of the large T-state cooperativity inferred for cyanide binding to partially oxidized hemoglobin (Ackers et al., Science 255:54-63, 1992). © 1996 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.3
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  • 44
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    Evolution of β-amylase: Patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 456-472 
    Details
    ISSN: 0887-3585
    Keywords: protein database ; DNA database ; PROSITE ; fingerprints ; PRINTS ; α/β-barrel ; protein evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Soybean and sweet potato β-amylases are structured as α/β barrels and the same kind of folding may account for all known β-amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of β-amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known β-amylases. Our approach combines the identification of the putative eightfold structural core formed by β-strands with a complete multi-alignment analysis of all known sequences. Comparing putative β-amylase (α/β)8 cores from plants and microorganisms, two differentiated versions of residues at the packing sites, and a unique set of eight identical residues at the C-terminal catalytical site are observed, indicating early evolutionary divergence and absence of localized three-dimensional evolution, respectively. A new analytical approach has been developed in order to work out conserved motifs for β-amylases, mostly related with the enzyme activity. This approach appears useful as a new routine to find sets of motifs (each set being known as a fingerprint) in protein families. We demonstrate that the evolutionary mechanism for β-amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and α-helix-containing loops. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.6
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  • 45
    Electronic Resource
    Electronic Resource
    In vivo association of protein fragments giving active AraC (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 501-505 
    Details
    ISSN: 0887-3585
    Keywords: protein-protein interaction ; translational reinitiation ; intracistronic complementation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Frameshift mutations in a restricted portion of the arabinose operon regulatory gene araC from Escherichia coli give rise to active AraC protein, likely from the in vivo synthesis of two Incomplete fragments that are active together. Synthesis of corresponding fragments, each separately inactive, from two plasmids within cells also resulted in complementation. © 1996 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.9
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  • 46
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    Production and crystallization of a selenomethionyl variant of UmuD′, an Echerichia coli SOS response protein (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 506-509 
    Details
    ISSN: 0887-3585
    Keywords: MAD phasing ; mutagenesis ; auto-digestion ; replication ; dimerization ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of both native and mutant Escherichia coli UmuD′ protein were obtained using the hanging drop method. Soaking the native crystals in solutions of heavy metal ions failed to produce good isomorphous derivatives, and selenomethionine substituted wild-type protein did not crystallize under conditions that gave native crystals. Site-directed mutagenesis was used to change the penultimate residue, a methionine amino acid, to either a valine or a threonine amino acid. Crystals were subsequently obtained from these mutant proteins with and without selenomethionine Incorporation. Crystals of the native, the mutant, and the selenomethionine Incorporated protein were all similar, crystallizing in the P41212 space group. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.10
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  • 47
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    Electronic Resource
    Expression, purification, and crystallization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 514-516 
    Details
    ISSN: 0887-3585
    Keywords: D-amino acid ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The gene encoding the meso-diaminopimelate dehydrogenase (DAPDH) from Corynebacterium glutamicum was overexpressed and purified to homogeneity. Crystals of the binary DAPDH-NADP+ complex were obtained from solutions of polyethylene glycol 8000, 100 mM sodium cacodylate, pH 6.5, and 150-300 mM Mg(OAc)2. The crystals diffract to 2.2 Å, belong to the orthorhombic space group P21, and contain two molecules per asymmetric unit. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.12
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  • 48
    Electronic Resource
    Electronic Resource
    1996 Johns Hopkins protein folding meeting (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340250402
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  • 49
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    Building self-avoiding lattice models of proteins using a self-consistent field optimization (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 1-8 
    Details
    ISSN: 0887-3585
    Keywords: lattice models of proteins ; self-consistent field optimization ; self-avoiding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present an algorithm to build self-avoiding lattice models of chain molecules with low RMS deviation from their actual 3D structures. To find the optimal coordinates for the lattice chain model, we minimize a function that consists of three terms: (1) the sum of squared deviations of link coordinates on a lattice from their off-lattice values, (2) the sum of “short-range” terms, penalizing violation of chain connectivity, and (3) the sum of “long-range” repulsive terms, penalizing chain self-intersections. We treat this function as a chain molecule “energy” and minimize it using self-consistent field (SCF) theory to represent the pairwise link repulsions as 3D fields acting on the links. The statistical mechanics of chain molecules enables computation of the chain distribution in this field on the lattice. The field is refined by iteration to become self-consistent with the chain distribution, then dynamic programming is used to find the optimal lattice model as the “lowest-energy” chain pathway in this SCF. We have tested the method on one of the coarsest (and most difficult) lattices used for model building on proteins of all structural types and show that the method is adequate for building self-avoiding models of proteins with low RMS deviations from the actual structures. © 1996 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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  • 50
    Electronic Resource
    Electronic Resource
    Computational simulations of stem-cell factor/c-Kit receptor interaction (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 42-54 
    Details
    ISSN: 0887-3585
    Keywords: cell surface receptors ; hematopoietic factors ; cytokines ; structure prediction ; homology modeling ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Stem-cell factor (SCF) is a noncovalent homodimeric cytokine that exhibits profound biological function in the early stages of hematopoiesis by binding to a cell surface tyrosine kinase receptor that is encoded by the c-Kit proto-oncogene. The results obtained from a combined implementation of homology-based molecular modeling and computational simulations in the study of species-specific SCF/c-Kit interactions are reported. The structural models of the human and rat SCF ligands are based on the close structural similarity to the cytokine M-CSF, whose Cα structure has recently become available. The constant domains of the human Fc fragment are used as a template for the ligand binding domains of the c-Kit receptor. The factors responsible for the stabilization of the SCF quaternary structure and the molecular determinants for ligand recognition and ligand specificity have been identified by assessing the conformational, topographical, and dynamic features of the isolated ligands and of the ligand-receptor complexes. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 51
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    Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: Pyridine nucleotide-binding and interaction with an electron-transfer partner (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 32-41 
    Details
    ISSN: 0887-3585
    Keywords: α/β structure ; β barrel ; electrostatic potential ; flavin adenine dinucleotide ; flavin mononucleotide ; pyridine nucleotide ; structure refinement ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic properties on the protein surface were examined on the basis of the crystal structure of NADH-cytochrome b5 reductase refined to a crystallographic R factor of 0.223 at 2.1 Å resolution and of the other three flavin-dependent reductases. A structural comparison of NADH-cytochrome b5 reductase with the other flavin-dependent reductases, ferredoxin-NADP+ reductase, phthalate dioxygenase reductase, and nitrate reductase, showed that the α/β structure is the common motif for binding pyridine nucleotide. Although the amino acid residues associated with pyridine nucleotide-binding are not conserved, the electrostatic properties and the location of the pyridine nucleotide-binding pockets of NADH-requiring reductases were similar to each other. The electrostatic potential of the surface near the flavin-protruding side (dimethylbenzene end of the flavin ring) of NADH-cytochrome b5 reductase was positive over a wide area while that of the surface near the heme-binding site of cytochrome b5 was negative. This implied that the flavin-protruding side of NADH-cytochrome b5 reductase is suitable for interacting with its electron-transfer partner, cytochrome b5. This positive potential area is conserved among four flavin-dependent reductases. A comparison of the electron-transfer partners of four flavin-dependent reductases showed that there are significant differences in the distribution of electrostatic potential between inter-molecular and inter-domain electron-transfer reactions. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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  • 52
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    Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: A molecular dynamics study (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 66-71 
    Details
    ISSN: 0887-3585
    Keywords: BPTI ; folding ; unfolding ; disulfide ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure and folding of basic pancreatic trypsin inhibitor (BPTI) has been studied extensively by experimental means. We report a computer simulation study of the structural stability of various disulfide mutants of BPTI, involving eight 250-psec molecular dynamics simulations of the proteins in water, with and without a phosphate counterion. The presence of the latter alters the relative stability of the single disulfide species [5-55] and [30-51]. This conclusion can explain results of mutational studies and the conservation of residues in homologues of BPTI, and suggests a possible role of ions in stabilizing one intermediate over another in unfolding or folding processes. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 53
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    Electronic Resource
    A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 81-94 
    Details
    ISSN: 0887-3585
    Keywords: Site-directed mutagenesis ; G protein-coupled receptors ; database ; information storage and retrieval ; software ; World-Wide Web ; Internet ; ligand-receptor interactions ; signal transduction ; sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A database system and computer programs for storage and retrieval of information about guanine nucleotide-binding protein (G protein) -coupled receptor mutants and associated biological effects have been developed. Mutation data on the receptors were collected from the literature and a database of mutants and effects of mutations was developed. The G protein-coupled receptor, family A, point mutation database (GRAP) provides detailed information on ligand-binding and signal transduction properties of more than 2130 receptor mutants. The amino acid sequences of receptors for which mutation experiments have been reported were aligned, and from this alignment mutation data may be retrieved. Alternatively, a search form allowing detailed specification of which mutants to retrieve may be used, for example, to search for specific amino acid substitutions, substitutions in specific protein domains or reported biological effects. Furthermore, ligand and bibliographic oriented queries may be performed. GRAP is available on the Internet (URL: http://www-grap.fagmed.uit.no/GRAP/homepage.html) using the World-Wide Web system. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 72-80 
    Details
    ISSN: 0887-3585
    Keywords: phage 434 Cro protein ; phage 434 repressor protein ; helix-turn-helix motif ; normal mode analysis ; molecular mechanics ; protein conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two DNA binding proteins, Cro and the amino-terminal domain of the repressor of bacteriophage 434 (434 Cro and 434 repressor) that regulate gene expression and contain a helix-turn-helix (HTH) motif responsible for their site-specific DNA recognition adopt very similar three-dimensional structures when compared to each other. To reveal structural differences between these two similar proteins, their dynamic structures, as examined by normal mode analysis, are compared in this paper. Two kinds of structural data, one for the monomer and the other for a complex with DNA, for each protein, are used in the analyses. From a comparison between the monomers it is found that the interactions of Ala-24 in 434 Cro or Val-24 in 434 repressor, both located in the HTH motif, with residues 44, 47, 48, and 51 located in the domain facing the motif, and the interactions between residues 17, 18, 28, and 32, located in the HTH motif, cause significant differences in the correlative motions of these residues. From the comparison between the monomer and the complex with DNA for each protein, it was found that the first helix in the HTH motif is distorted in the complex form. While the residues in the HTH motif in 434 Cro have relatively larger positive correlation coefficients of motions with other residues within the HTH motif, such correlations are not large in the HTH motif of 434 repressor. It is suggestive to their specificity because the 434 repressor is less specific than 434 Cro. Although a structural comparison of proteins has been performed mainly from a static or geometrical point of view, this study demonstrates that the comparison from a dynamic point of view, using the normal mode analysis, is useful and convenient to explore a difference that is difficult to find only from a geometrical point of view, especially for proteins very similar in structure. © 1996 Wiley-Liss, Inc.
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  • 55
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    Electronic Resource
    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260101
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  • 56
    Electronic Resource
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    No crystals no grant (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No Abstracts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260102
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  • 57
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    Structure model of a complex between the factor for inversion stimulation (FIS) and DNA: Modeling protein-DNA complexes with dyad symmetry and known protein structures (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 486-500 
    Details
    ISSN: 0887-3585
    Keywords: protein-DNA interaction ; DNA bending ; helix-turn-helix ; Poisson-Boltzmann electrostatics ; docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method is presented to predict overall conformations of protein-DNA complexes on the basis of the known three-dimensional structures of the proteins. The method is restricted to proteins with a common twofold symmetry axis, which show only minor conformational changes upon binding to DNA. The method uses a numerical finite difference solution of the linearized Poisson-Boltzmann equation and subsequent energy minimization cycles. Structural parameters - the rotation angle of the DNA relative to the protein around the common symmetry axis, the protein-DNA distance, and intermolecular hydrogen-bonding contacts - are presented for two test cases, DNA bound to CAP (catabolite gene activator protein) and to the Cro-repressor of bacteriophage 434. The DNA curvature in the starting model of the docking procedure was chosen as a smoothed approximation of the conformation found in the X-ray structures of these complexes. The method is further used to predict the unknown structure of the complex between the factor for inversion stimulation (FIS) and DNA, which is bent upon binding to FIS. In contrast to the test cases, the unknown curvature of the starting model is derived from a calibration of electrostatic precalculations for different proteins according to crystallographically observed DNA bending. The results of the modeling are in good accordance with the experimentally observed overall structure of protein-DNA complexes for the two test cases; for FIS, they correspond to several of the experimentally proposed protein-DNA contacts. © 1996 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/prot.8
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  • 58
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    Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 157-166 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; enzyme-substrate interaction ; binding free energy difference ; electrostatic screening ; dielectric constant ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The numerical quadrature thermodynamic integration method is used to investigate enzyme-substrate interaction of D-xylose isomerase. A screening function for the coulombic interaction is introduced into the simulation to correct the effect of finite cutoff radius for the non-bonded interaction. The binding free energy difference for D-xylose with D-xylose isomerase and its N184D mutant has been calculated, and the result 3.9 ± 1.2 kJ/mol agrees well with experimental data of 4.38 kJ/mol. In addition, the structure and dynamics of enzyme-substrate complex were simulated for mutant and wild-type enzyme, respectively. Analysis of the structures and intramolecular interactions of the complexes were found to be valuable for understanding the reaction mechanism of the enzyme D-xylose isomerase. © Wiley-Liss, Inc.
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  • 59
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    Evaluation of threading specificity and accuracy (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 172-185 
    Details
    ISSN: 0887-3585
    Keywords: contact potentials ; fold recognition ; protein threading ; Gibbs sampling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Threading experiments with proteins from the globin family provide an indication of the nature of the structural similarity required for successful fold recognition and accurate sequence-structure alignment. Threading scores are found to rise above the noise of false positives whenever roughly 60% of residues from a sequence can be aligned with analogous sites in the structure of a remote homolog. Fold recognition specificity thus appears to be limited by the extent of structural similarity, regardless of the degree of sequence similarity. Threading alignment accuracy is found to depend more critically on the degree of structural similarity. Alignments are accurate, placing the majority of residues exactly as in structural alignment, only when superposition residuals are less than 2.5 Å. These criteria for successful recognition and sequence-structure alignment appear to be consistent with the successes and failures of threading methods in blind structure prediction. They also suggest a direct assay for improved threading methods: Potentials and alignment models should be tested for their ability to detect less extensive structural similarities, and to produce accurate alignments when superposition residuals for this conserved “core” fall in the range characteristic of remote homologs. © 1996 Wiley-Liss, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.
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  • 60
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    Structural aspects of the functional modules in human protein kinase-Cα deduced from comparative analyses (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 217-235 
    Details
    ISSN: 0887-3585
    Keywords: catalytic region ; comparative modeling ; cysteine-rich domain ; phosphorylation ; pseudo-substrate specificity ; synaptotagmin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three-dimensional models of the five functional modules in human protein kinase Cα (PKCα) have been generated on the basis of known related structures. The catalytic region at the C-terminus of the sequence and the N-terminal auto-inhibitory pseudo-substrate have been modeled using the crystal structure complex of cAMP-dependent protein kinese (cAPK) and PKI peptide. While the N-terminal helix of the catalytic region of PKCα is predicted to be in a different location compared with cAPK, the C-terminal extension is modeled like that in the cAPK. The predicted permissive phosphorylation site of PKCα, Thr 497, is found to be entirely consistent with the mutagenesis studies. Basic Lys and Arg residues in the pseudo-substrate make several specific interactions with acidic residues in the catalytic region and may interact with the permissive phosphorylation site. Models of the two zinc-binding modules of PKCα are based on nuclear magnetic resonance and crystal structures of such modules in other PKC isoforms while the calcium phospholipid binding module (C2) is based on the crystal structure of a repeating unit in synaptotagmin I. Phorbol ester binding regions in zinc-binding modules and the calcium binding region in the C2 domain are similar to those in the basis structures. A hypothetical model of the relative positions of all five modules has the putative lipid binding ends of the C2 and the two zinc-binding domains pointing in the same direction and may serve as a basis for further experiments. © 1996 Wiley-Liss, Inc.
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260201
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    Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 257-261 
    Details
    ISSN: 0887-3585
    Keywords: membrane proteins ; α-helices ; packing ; two-stage model ; computational searching ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A more global search method, using fewer assumptions, has been used to predict the structure of the dimeric transmembrane region of the protein glycophorin A. The resulting model significantly differs from that previously determined. In particular, the arrangement between the two transmembrane helices is now more symmetric resulting in improved interaction energies and an increased buried surface area. An increase in the van der Waals interaction energy due to tighter packing compensates for the loss of the interhelical hydrogen bond observed between Thr-87 of each helix in the previous model. © 1996 Wiley-Liss, Inc.
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    Modeling of serpin-protease complexes: Antithrombin-thrombin, α1-antitrypsin (358Met→Arg)-thrombin, α1-antitrypsin (358Met→Arg)-trypsin, and antitrypsin-elastase (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 288-303 
    Details
    ISSN: 0887-3585
    Keywords: serine-protease inhibitor ; protease complex ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Based on the most recent available crystal structures and biochemical studies of protease complexes of normal and mutant serine protease inhibitors (serpins), we have built models of the complexes: α1-antitrypsin + human neutrophil elastase; α1-antitrypsin Pittsburgh (358Met→Arg) (Scott et al., J. Clin. Invest. 77:631-634, 1986) + trypsin; α1-antitrypsin Pittsburgh (358Met→Arg) + thrombin; and antithrombin + thrombin. All serpin sequences correspond to human molecules.The models show correct stereochemistry and no steric clashes between protease and inhibitor. The main structural differences in the serpins from the parent structures are: (1) the reactive center loop is inserted into the A-sheet as far as P12; (2) strand s1C is removed from the C-sheet; and (3) the C-terminus has changed conformation and interacts with the protease.In the absence of an X-ray structure determination of a serpin-protease complex, the demonstration that insertion of the reactive center loop into the A-sheet as far as P12 is stereo-chemically feasible provides structures of a protease-bound conformation of intact serpins with which to rationalize the properties of mutants, guide the design of experiments, and form a basis for further modeling studies, such as the investigation of the interaction of heparin with serpin-protease complexes. © 1996 Wiley-Liss, Inc.
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    Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 304-313 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of recombinant human granulocyte-macrophage colony stimulating factor (rhGM-CSF) has been refined against data extending to a resolution of ∼2.4 Å along a* and ∼1.9 Å along b* and c*. Anisotropic scale factors of B11 = -20.8 Å2, B22 = 7.4 Å2, B33 = 13.3 Å2 corrected for the more rapid fall of diffraction in the a* direction. The anisotropy correlates with the weak crystal packing interactions along the a axis. In addition to apolar side chains in the protein core, there are 10 buried hydrogen bonding residues. Those residues involved in intramolecular hydrogen bonding to main chain atoms are better conserved than those hydrogen bonding to other side chain atoms; 24 solvation sites are observed at equivalent positions in the two molecules in the asymmetric unit, and the strongest among these are located in clefts between secondary structural elements. No buried water sites are seen. Two surface clusters of hydrophobic side chains are located near the expected receptor binding regions. Mutagenesis of 11 residues on the helix A/helix C face confirms the importance of Glu-21 and shows that Gly-75 and Gln-86, located on helix C, each cause a greater than fourfold drop in activity. Glu-21 and Gly-75, but not Gln-86, are structurally equivalent to residues involved in the growth hormone binding to its receptor. © 1996 Wiley-Liss, Inc.
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    An extended sampling of the configurational space of HPr from E. coli (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 314-322 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; molecular dynamics ; essential dynamics ; nuclear magnetic resonance ; nuclear Overhauser effect ; distance restraints ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) to obtain an extended sampling of the configurational space of proteins, using an adapted form of molecular dynamics (MD) simulations, based on the essential dynamics (ED) (Amadei et al., Proteins 17:412-425, 1993) method. In the present study, this ED sampling technique is applied to the histidine-containing phosphocarrier protein HPr from Escherichia coli. We find a cluster of conformations that is an order of magnitude larger than that found for a usual MD simulation of comparable length. The structures in this cluster are geometrically and energetically comparable to NMR structures. Moreover, on average, this large cluster satisfies nearly all NMR-derived distance restraints. © 1996 Wiley-Liss, Inc.
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260301
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    Editorial Announcement (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. fmii 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260302
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    Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 363-376 
    Details
    ISSN: 0887-3585
    Keywords: hydrogen bond ; network ; force field ; protein structure ; validation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy. For this goal, an empirical hydrogen bond force field was derived from small molecule crystal structures. Bifurcated hydrogen bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, sidechain conformations of His, Gln, and Asn residues are allowed to change their last χ angle by 180° to compensate for crystallographic misassignments. Crystal structure symmetry is taken into account where appropriate. The results can have significant implications for molecular dynamics simulations, protein engineering, and docking studies. The largest impact, however, is in protein structure verification: over 85% of protein structures tested can be improved by using our procedure. Proteins 26:363-376 © 1996 Wiley-Liss, Inc.
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    Spectroscopic evidence for preexisting T- and R-state insulin hexamer conformations (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 377-390 
    Details
    ISSN: 0887-3585
    Keywords: allostery ; hexameric insulin ; positive and negative cooperativity ; half-site reactivity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The insulin hexamer is an allosteric protein exhibiting both positive and negative cooperative homotropic interactions and positive cooperative heterotropic interactions (C. R. Bloom et al., J. Mol. Biol. 245, 324-330, 1995). In this study, detailed spectroscopic analyses of the UV/Vis absorbance spectra of the Co(II)-substituted human insulin hexamer and the 1H NMR spectra of the Zn(II)-substituted hexamer have been carried out under a variety of ligation conditions to test the applicability of the sequential (KNF) and the half-site reactivity (SMB) models for allostery. Through spectral decomposition of the characteristic d → d transitions of the octahedral Co(II)-T-state and tetrahedral Co(II)-R-state species, and analysis of the 1H NMR spectra of T- and R-state species, these studies establish the presence of preexisting T- and R-state protein conformations in the absence of ligands for the phenolic pockets. The demonstration of preexisting R-state species with unoccupied sites is incompatible with the principles upon which the KNF model is based. However, the SMB model requires preexisting T- and R-states. This feature, and the symmetry constraints of the SMB model make it appropriate for describing the allosteric properties of the insulin hexamer. Proteins 26:377-390 © 1996 Wiley-Liss, Inc.
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    Computational design of a substrate specificity mutant of a protein (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 459-464 
    Details
    ISSN: 0887-3585
    Keywords: trp repressor ; ligand ; free energy ; molecular dynamics ; protein design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The wild-type trp repressor of E. coli bound 5-methoxytryptophan, a Trp analogue, less tightly than Trp. A mutant repressor (Val58→Ala) that should bind 5-methoxytryptophan preferentially to Trp was computationally designed by free-energy calculations accompanied by free-energy decomposition. The designed mutant was demonstrated by experiments to bind 5-methoxytryptophan more tightly than Trp, consistent with the computational prediction. This success indicates the usefulness of free energy decomposition in protein design. Proteins 26:459-464 © 1996 Wiley-Liss, Inc.
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    Factors governing the foldability of proteins (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 411-441 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; lattice Monte Carlo simulations ; kinetic accessibility and stability ; kinetic partitioning mechanism ; native conformation nucleation collapse ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We use a three-dimensional lattice model of proteins to investigate systematically the global properties of the polypeptide chains that determine the folding to the native conformation starting from an ensemble of denatured conformations. In the coarse-grained description, the polypeptide chain is modeled as a heteropolymer consisting of N beads confined to the vertices of a simple cubic lattice. The interactions between the beads are taken from a random gaussian distribution of energies, with a mean value Bo 〈 0 that corresponds to the overall average hydrophobic interaction energy. We studied 56 sequences all with a unique ground state (native conformation) covering two values of N (15 and 27) and two values of Bo. The smaller value of |Bo| was chosen so that the average fraction of hydrophobic residues corresponds to that found in natural proteins. The higher value of |Bo| was selected with the expectation that only the fully compact conformations would contribute to the thermodynamic behavior. For N = 15 the entire conformation space (compact as well as noncompact structures) can be exhaustively enumerated so that the thermodynamic properties can be exactly computed at all temperatures. The thermodynamic properties for the 27-mer chain were calculated using the slow cooling technique together with standard Monte Carlo simulations. The kinetics of approach to the native state for all the sequences was obtained using Monte Carlo simulations. For all sequences we find that there are two intrinsic characteristic temperatures, namely, Tθ and Tf. At the temperature Tθ the polypeptide chain makes a transition to a collapsed structure, while at Tf the chain undergoes a transition to the native conformation. We show that foldability of sequences can be characterized entirely in terms of these two temperatures. It is shown that fast folding sequences have small values of σ = (Tθ - Tf)/Tθ whereas slow folders have larger values of σ (the range of σ is 0 〈 σ 〈 1). The calculated values of the folding times correlate extremely well with σ. An increase in σ from 0.1 to 0.7 can result in an increase of 5-6 orders of magnitudes in folding times. In contrast, we demonstrate that there is no useful correlation between folding times and the energy gap between the native conformation and the first excited state at any N for any value of Bo. In particular, in the parameter space of the model, many sequences with varying energy gaps, all with roughly the same folding time, can be easily engineered. Folding sequences in this model, therefore, can be classified based solely on the value of σ. Fast folders have small values of σ (typically less than about 0.1), moderate folders have values of σ in the approximate range between 0.1 and 0.6, while for slow folders σ exceeds 0.6. The precise boundary between these categories depends crucially on N and on the model. The range of σ for fast folders decreases with the length of the chain. At temperatures close to Tf fast folders reach the native conformation via a native conformation nucleation collapse mechanism without forming any detectable intermediates, whereas only a fraction of molecule φ(T) reaches the native conformation by this process for moderate folders. The remaining fraction reaches the native state via three-stage multipathway process. For slow folders φ(T) is close to zero at all temperatures. The simultaneous requirement of native state stability and kinetic accessibility can be achieved at high enough temperatures for those sequences with small values of σ. The utility of these results for de novo design of proteins is briefly discussed. Proteins 26:411-441 © 1996 Wiley-Liss, Inc.
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    Molecular modeling of vimentin filament assembly (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 472-478 
    Details
    ISSN: 0887-3585
    Keywords: vimentin ; desmin ; keratin ; α helix ; β helix ; β strand ; coiled coil ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Intermediate-filament forming proteins are known to form rod-shaped dimers that are calculated to be 45 nm in length. Molecular modeling indicates that the dimerization is promoted by interchain hydrophobic interactions between sections of α helix β and helix. Further aggregation involves the formation of tetramers in which two dimers are anti-parallel and staggered to two characteristic degrees of overlap. Modeling indicated that the degrees of stagger are dictated by the association of sections of α helix in 4-chain bundles, in which hydrophobic side chains are sequestered from contact with water. The staggered arrangement of two dimers produces a tetramer having sections of 2-chain rod in which hydrophobic side chains are exposed to water. Extension of the tetramer to form protofilaments may be driven by associations with the 2-chain regions that reduce aqueous exposure of the hydrophobic side chains. Exposure of hydrophobic groups may be reduced by the 2-chain regions folding back upon themselves so that the entire tetramer becomes a 4-chain conformation. This prediction is in line with electron microscope data showing that mixtures of the lower oligomers contain rods of uniform thickness ranging upwards from 45 nm in a series having incremental increases in length. Data from previous chemical crosslinking studies support this model and also the idea that the completed intermediate filaments each consist of seven 4-chain protofilaments. Proteins 26:472-478 © 1996 Wiley-Liss, Inc.
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    Changes at Proteins (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260402
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    Crystallization of the bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domain of the human trifunctional enzymeThis is NRCC publication No. 39937. (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 479-480 
    Details
    ISSN: 0887-3585
    Keywords: crystallization ; folate ; multifunctional ; twinning ; dehydrogenase ; cyclohydrolase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Methylenetetrahydrofolate([H4] folate) dehydrogenase (D) and methenyl[H4] folate cyclohydrolase (C) coexist as a bifunctional enzyme (DC) or as the amino-terminal domain of a trifunctional enzyme (DCS) where the third activity is 10-formyl[H4]lfolate synthetase (S). Two crystal forms of the DC domain of the human cytosolic DCS enzyme have been grown from polyethyleneglycol solution. The monoclinic P21 crystals diffract to 2.8 Å with a = 72.5 Å, b = 68.5 Å, c = 125.2 Å, and β = 91.8° but were found to be twinned. The orthorhombic P212121 crystals diffract to 2.5 Å with a = 67.7 Å, b = 135.9 Å, c = 61.6 Å, and contain two molecules per asymmetric unit. Proteins 26:479-480 © 1996 Wiley-Liss, Inc.
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    Comonomer sequence determination of vinyl acetate-glycidyl methacrylate copolymers by NMR spectroscopy (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 333-339 
    Details
    ISSN: 0887-624X
    Keywords: reactivity ratios ; microstructure ; 13C-NMR spectroscopy ; (vinyl acetate)/(glycidyl methacrylate) copolymers ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (Vinyl acetate)/(glycidyl methacrylate) (V/G) copolymers were prepared by free radical solution polymerization in benzene. Copolymer composition was determined by 1H-NMR spectroscopy. Comonomer reactivity ratios were calculated by Kelen-Tüdos (KT) and error-in-variables (EVM) methods. The values reactivity ratios calculated by these methods are rV = 0.03 ± 0.01; rG = 38.9 ± 6.20 (KT) and rV = 0.03 ± 0.002; rG = 39.5 ± 1.97 (EVM). The microstructure of V/G copolymers in terms of the distribution of V and G centered was obtained from 13C{1H}-NMR spectra using the carbonyl carbon resonance signals of V as well as G units. © 1996 John Wiley & Sons, Inc.
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    Preparation and properties of polyamides and polyimides derived from 1,3-diaminoadamantane (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 117-124 
    Details
    ISSN: 0887-624X
    Keywords: polyimide ; polyamide ; adamantane ; thermal properties ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1,3-Diaminoadamantane (I) was used as a monomer with various aromatic dicarboxylic acyl chlorides and dianhydrides to synthesize polyamides and polyimides, respectively. Polyamides having inherent viscosities of 0.10-0.27 dL/g were prepared by low-temperature solution polycondensation. The polyamides were soluble in a variety of solvents such as N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMAc), N-methyl-2-pyrrolidone (NMP), pyridine, dioxane, and nitrobenzene. These polyamides had glass transition temperatures in the 179-187°C range and 5% weight loss temperatures occurred at up to 354°C. Polyimides based on diamine I and various aromatic dianhydrides were synthesized by the two-stage procedure that included ring-opening to form polyamic acids, followed by thermal conversion to polyimides. The polyamic acids had inherent viscosities of 0.14-0.38 dL/g. The glass transition temperature of these polyimides were in the 245-303°C range and showed almost no weight loss up to 350°C under air and nitrogen atmosphere. © 1996 John Wiley & Sons, Inc.
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    Preparation and characterization of a homobifunctional silicone rubber membrane grafted with acrylic acid via plasma-induced graft copolymerization (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 141-148 
    Details
    ISSN: 0887-624X
    Keywords: polyacrylic acid ; silicone rubber membrane ; plasma-induced graft polymerization ; homobifunctional membrane ; 1,1-diphenyl-2-picryhydrazyl ; surface modification ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polyacrylic acid (PAA) was grafted onto the surface of silicone rubber membrane (SR) by plasma-induced graft copolymerization (PIP). Ar-plasma was used to activate the surface of SR. Also, a determination was made of the influences of plasma treatment power, pressure, time, grafted copolymerization reaction time, and monomer concentration on polymerization yield. The surface properties of SR were measured by ATR-FTIR, ESCA, and SIMS. In those analyses, the elemental composition and different carbon bindings on the surface of SR were examined by ESCA with the amount of O1s/C1s being approximately 0.7 at 60 s by Ar-plasma treatment (60 W, 200 mtorr). The peroxide group introduced on SR was measured via 1,1-diphenyl-2-picryhydrazyl (DPPH). The optimum amount of peroxide groups was 6.85 × 10-8 mol/cm2 at 60 s of Ar-plasma treatment. The peroxide group (33D peak) was introduced onto the surface of SR by negative spectra of SIMS analysis after SR treatment by Ar-plasma. An increase was obtained in grafted polymerization yield with a region of 5 to 50% (v/v) of acrylic acid aqueous solution. Both sites of polyacrylic acid were detected after staining by toluidine blue O. That is, a homobifunctional membrane was developed via this surface modification method. © 1996 John Wiley & Sons, Inc.
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    Reactions on polymers with amine groups. III. Description of the addition reaction of pyridine and imidazole compounds with α,β-unsaturated monocarboxylic acids (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 261-270 
    Details
    ISSN: 0887-624X
    Keywords: chemically modified polymers ; addition reactions ; carboxybetaines ; reaction mechanisms and kinetics ; pyridines ; imidazoles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A detailed study of the synthesis of betaine products that result from addition reactions of poly (4-vinylpyridine) and poly (N-vinylimidazole) as well as of their model compounds, with α,β-unsaturated monocarboxylic acids is presented. A reaction mechanism based on experimental observations and proved by kinetic analysis is proposed. It consists of two reactions: the addition, which involves two molecules of acid and leads to X+B--like structures, where the cation X+ results from the addition of the amino nitrogen to the double bond of acid and B- is the carboxyl anion, and an equilibrium reaction between X+B- and the betaine structure X±. The latter occurs only in protic solvents and is coupled with the addition reaction. The process was especially investigated in methanol, because this solvent allows determination of the kinetic parameters. Some values of the addition rate constants are given. The study is based on 1H-NMR measurements and observations. © 1996 John Wiley & Sons, Inc.
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    Synthesis of poly(N-vinylisobutyramide) from poly(N-vinylacetamide) and its thermosensitive property (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 301-303 
    Details
    ISSN: 0887-624X
    Keywords: thermosensitive polymer ; water soluble polymer ; polymer modification reaction ; poly(vinylamine) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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    Relative reactivities in vinyl copolymerization (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 157-163 
    Details
    ISSN: 0887-624X
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: From data in the literature on relative rates of copolymerization it has been possible to evaluate two constants, Q and e, characteristic of an individual monomer, which appear to account satisfactorily for its behavior in copolymerization. The constant Q describes the “general monomer reactivity” and is apparently related to possibilities for stabilization in a radical adduct. The constant e takes account of polar factors influencing copolymerization.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/pola.1996.807
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    Synthesis and characterization of polyimides from imidazole-blocked 2,5-bis[(n-alkyloxy)methyl]-1,4-benzene diisocyanates and pyromellitic dianhydride (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 357-365 
    Details
    ISSN: 0887-624X
    Keywords: processable polyimides ; poly(pyromellitimide)s ; rigid-rod polyimides ; polyimides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: From imidazole-blocked 2,5-bis[(n-alkyloxy)methyl]-1,4-benzene diisocyanates and pyromellitic dianhydride a series of new rigid-rod polyimides (Cn-PY-PI; n = 4, 6, 8) having linear and flexible (alkyloxy)methyl ((SINGLE BOND)CH2OCnH2n + 1; n = 4, 6, 8) side chains were prepared and characterized and their properties were measured and discussed with regard to effects of side chains. Incorporation of the side chains onto the rigid main chain greatly enhanced the solubility and fusibility of the polymers, and melting point of C8-PY-PI was determined to be 277°C. The UV-VIS absorption behavior was independent of side-chain length. TGA thermograms revealed a two-step pyrolysis behavior, in which the side chains split off separately at lower temperatures. X-ray diffractograms showed that all the polyimides are crystalline at room temperature. Sharp reflections in small-angle region obviously indicated the presence of a layered crystal structure. © 1996 John Wiley & Sons, Inc.
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    Aromatic and rigid rod polyelectrolytes based on sulfonated poly(benzobisthiazoles) (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 481-492 
    Details
    ISSN: 0887-624X
    Keywords: poly(benzobisthiazoles) ; sulfonated poly(benzobisthiazoles) ; rigid rod polymers ; polyelectrolytes ; thermally stable polymers ; conducting polymers ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Aromatic polyelectrolytes based on sulfonated poly(benzobisthiazoles) (PBTs) have been synthesized by a polycondensation reaction of sulfo-containing aromatic dicarboxylic acids with 2,5-diamino-1,4-benzenedithiol dihydrochloride (DABDT) in freshly prepared polyphosphoric acid (PPA). Several sulfonated PBTs, poly[(benzo[1,2-d:4,5-d′]bisthiazole-2,6-diyl)-2-sulfo-1,4-phenylene] sodium salt (p-sulfo PBT), poly[(benzo[1,2-d:4,5-d′]bisthiazole-2,6-diyl)-5-sulfo-1,3-phenylene] sodium salt (m-sulfo PBT), their copolymers, and poly[(benzo[1,2-d:4,5-d′]bisthiazole-2,6-diyl)-4,6-disulfo-1,3-phenylene] potassium salt (m-disulfo PBT), have been targeted and the polymers obtained characterized by 13C-NMR, FT-IR, elemental analysis, thermal analysis, and solution viscosity measurements. Structural analyses confirm the structures of p-sulfo PBT and m-disulfo PBT, but suggest that the sulfonate is cleaved from the chain during synthesis of m-sulfo PBT. m-Disulfo PBT dissolves in water as well as strong acids, while p-sulfo PBT dissolves well in strong acids, certain solvent mixtures containing strong acids, and hot DMSO. TGA indicates that these sulfonated PBTs are thermally stable to over 500°C. Free-standing films of p-sulfo PBT, cast from dilute neutral DMSO solutions, are transparent, tough, and orange in color. Films cast from basic DMSO are also free standing, while being opaque and yellow-green. p-Sulfo PBT was incorporated as the dopant ion in polypyrrole, producing conductive films with conductivities as high as 3 S/cm and electrical anisotropies as high as 10. © 1996 John Wiley & Sons, Inc.
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    Commentary: Reflections on “interfacial polycondensation. II. Fundamentals of polymer formation at liquid interfaces,” by Paul W. Morgan and Stephanie L. Kwolek, J. Polym. Sci., XL, 299 (1959) (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 517-518 
    Details
    ISSN: 0887-624X
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/pola.1996.813
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    Liquid crystalline polyurethanes with novel organometallic complexes (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 721-728 
    Details
    ISSN: 0887-624X
    Keywords: polyurethane ; metal ions ; synthesis ; coordination ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of polyurethane organometallic complexes based on novel diols, bis[N-[[2-hydroxyphenyl]methylene]hydroxylethyleneamino]-copper(II) (DBSICu), were synthesized successfully. The products are elastomeric glassy materials or powders. Similar to other polyurethane elastomers, these coordination block copolymers exhibit 2-phase microstructure and thermoplastic properties. It is interesting to note that some of these polyurethanes show a Schlieren pattern under the polarizing optical microscope. The liquid crystalline properties of DBSICu and the coordination polymers are studied in detail in this study. © 1996 John Wiley & Sons, Inc.
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    New poly(amide-imide)s syntheses. XVII. Preparation and properties of poly(amide-imide)s derived from 3,3-Bis[4-(4-aminophenoxy)phenyl]phthalimidine and various bis(trimellitimide)s (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 747-754 
    Details
    ISSN: 0887-624X
    Keywords: poly(amide-imide)s ; bis(trimellitimide)s ; 3,3-bis[4-(4-aminophenoxy)phenyl]-phthalimidine ; triphenyl phosphite John Wiley & Sons, Inc. ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of novel bis(phenoxy)phthalimidine-containing poly(amide-imide)s III were synthesized by the direct polycondensation of 3,3-bis[4-(4-aminophenoxy)phenyl]phthalimidine (BAPP) with various aromatic bis(trimellitimide)s in N-methyl-2-pyrrolidone (NMP) using triphenyl phosphite and pyridine as condensing agents. Poly(amide-imide)s III, having inherent viscosities up to 1.36 dL/g, were obtained in quantitative yields. All resulting polymers showed an amorphous nature and were readily soluble in polar solvents such as NMP and N,N-dimethylacetamide. All the soluble poly(amide-imide)s afforded transparent, flexible, and tough films. The glass transition temperatures of these polymers were in the range of 267-322°C and the 10% weight loss temperatures were above 490°C in nitrogen. Some properties of poly(amide-imide)s III were compared with those of the corresponding isomeric poly(amide-imide)s III′ prepared from 3,3-[4-(4-trimellitimidophenoxy)phenyl]-phthalimidine and various aromatic diamines. © 1996 John Wiley & Sons, Inc.
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    Zwitterionic polymerization of 1-[4-[(4-hydroxy-1-naphthyl)thio]butyl]quinuclidinium hydroxide inner salt (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 801-809 
    Details
    ISSN: 0887-624X
    Keywords: zwitterion ; hydroxide inner salt ; polymerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The zwitterion, 1-[4-[(4-hydroxy-1-naphthyl)thio]butyl]quinuclidinium hydroxide inner salt, was synthesized from tetrahydro-1-(4-hydroxy-1-naphthyl)thiophenium hydrochloride and quinuclidine and characterized by NMR and IR spectroscopy. Polymerization of the zwitterion was studied over the temperature range 175-225°C. The polymer was identified as poly(1,4-piperidinediylethyleneoxy-1,4-naphthylenethiotetramethylene) based on NMR and IR spectroscopy. The polymer was found to contain 3-butenylthio and 4-hydroxy-1-naphthyl end groups. Based on the signal area of the olefinic end group, the polymer M⊼n varied between 8500 and 13,000. The highest molecular weight was achieved at the lowest temperature, indicating that termination became more favored at higher temperature. A mechanism is proposed to describe the polymerization. © 1996 John Wiley & Sons, Inc.
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    The copolymerization of allyl glycidyl ether with acrylonitrile initiated by gamma-rays (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 833-838 
    Details
    ISSN: 0887-624X
    Keywords: allyl glycidyl ether ; acrylonitrile ; copolymerization ; gamma-rays ; reactivity ratios ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Copolymers of allyl glycidyl ether (AGE) with acrylonitrile (AN) have been prepared by bulk polymerization of their monomers with gamma rays. Copolymers thus obtained were characterized by Fourier transform infrared (FTIR), and ultraviolet (UV) spectroscopic techniques. The composition of the copolymers is determined indirectly by FTIR, UV, and directly by elemental analysis. The results obtained by different methods are compared. The reactivity ratios of monomer pairs (AGE + AN) which copolymerized heterogeneously were calculated by using different methods of determination. Among the three experimental methods used for the analysis of compositions and two theoretical methods of computations, the elemental analysis technique and the application of nonlinear least-squares method gave the most reliable reactivity ratios. These are found to be 1.86 and 0.21 for acrylonitrile and allyl glycidyl ether, respectively. © 1996 John Wiley & Sons, Inc.
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    Preparation and structural determination of siloxane-modified sulfone-containing epoxy resins (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 869-884 
    Details
    ISSN: 0887-624X
    Keywords: hot-melt polycondensation ; siloxane-modified sulfone-containing epoxy resin ; PMPS ; PDMS ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Siloxane-modified sulfone-containing epoxy resins (ESBS) were prepared by polycondensation of PMPS and/or PDMS siloxane oligomers with EBS, the sulfone-containing epoxy resin. Structures were analyzed by IR, 1H-, and 13C-NMR. The siloxane content in the copolymers was determined by 1H-NMR with an integration technique. Epoxy equivalent weight (EEW) determination indicated that the oxirane ring of EBS was intact with this hot-melt procedure. The GPC measurement of these ESBS copolymers showed that molecular weight (MW) increased with increasing siloxane content in PMPS-modified copolymers. Evidence of siloxane incorporation in the copolymer was discussed. © 1996 John Wiley & Sons, Inc.
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    Chain transfer by addition-fragmentation mechanism. VII.For Part VI, see Reference 1. Radical polymerization of vinyl monomers in the presence of ethyl 2-[1-(trimethylsilylperoxy)ethyl]propenoateSystematic name: 1, ethyl 2-methylene-3-trimethylsilyl-dioxybutanoate. and related compounds (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 893-902 
    Details
    ISSN: 0887-624X
    Keywords: chain transfer ; addition-fragmentation ; peroxysilane ; radical polymerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ethyl 2-[1-(trimethylsilylperoxy)ethyl]propenoate 1, ethyl 2-[1-(dimethylvinylsilylperoxy)-ethyl]propenoate 2, ethyl 2-[1-(1-(2-ethoxycarbonyl-1-methyl-2-propenylperoxysilyl)-1-methylethylperoxy)ethyl]propenoate 3, and 2-phenyl-2-trimethylsilylperoxypropane 4 were synthesized and added to the free radical polymerization of vinylic monomers. 1 and 2 were found to show no homopolymerizability but act as effective chain transfer reagents in radical polymerizations of methyl methacrylate (MMA), styrene (St), and n-butyl acrylate (BA). The estimated chain transfer constants (Ctr) are as follows: Ctr (1) = 0.15 for MMA, 0.90 for St, and 2.03 for BA at 60°C; Ctr (2) = 0.12 for MMA, 1.16 for St, and 1.9 for BA at 60°C. 1H-NMR spectra of poly(St) formed in the presence of 1 is consistent with the view that the polymers bear an oxirane at one terminal and an trimethylsilyloxy fragment at the other end. Moreover, peroxysilane 4 showed very low transfer properties by direct homolytic substitution (SH2). These findings indicate that the ethyl 2-[1-(substituted dimethylsilylperoxy)ethyl]-propenoates 1-3 undergo chain transfer reaction via a intramolecular homolytic substitution (SHi) following an addition process. Preparation of poly(styrene) up to high conversion in the presence of 3 yielded to the formation of the corresponding polymeric structures bearing hydrolysable C(SINGLE BOND)O(SINGLE BOND)Si(SINGLE BOND)O(SINGLE BOND)C bonds. © 1996 John Wiley & Sons, Inc.
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    Emulsion co- and terpolymerization of styrene, methyl methacrylate and methyl acrylate. II. Control of emulsion terpolymer microstructure with optimal addition profiles (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 949-955 
    Details
    ISSN: 0887-624X
    Keywords: emulsion terpolymerization ; control of microstructure ; monomer addition profile ; chemical composition distribution ; gradient polmer elution chromatography ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An optimal addition profile for the preparation of a chemically homogeneous emulsion terpolymer of styrene, methyl methacrylate, and methyl acrylate was determined using a recently developed model for describing composition drift in emulsion co- and terpolymerizations. TRISEPS, described in Part I of this series. The model uses recently published simplified equations to describe monomer partitioning and the terminal model for describing terpolymer composition. The optimal addition rate profile was determined from the calculated optimal addition profile with a purely empirical and iterative method. With gradient polymer elution chromatography (GPEC®) the homogeneity and/or heterogeneity of the terpolymers prepared in the iterative series of experiments could be determined and compared to the heterogeneity of the corresponding batch terpolymer described in Part I. It was shown that a homogeneous terpolymer could be obtained indicating that the simplified equations for monomer partitioning and the terminal model for terpolymer composition describe the system adequately. It was also shown that GPEC® was useful in the determination of the optimal addition rate profile. © 1996 John Wiley & Sons, Inc.
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    “Titration” polymerization of monovinylacetylene (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 985-990 
    Details
    ISSN: 0887-624X
    Keywords: monovinylacetylene ; poly(vinylacetylene) ; anionic polymerization ; titration ; tertiary butyllithium ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A polymer consisting of a saturated carbon backbone with pendent acetylenic groups was prepared from monovinylacetylene. A titration was performed between the monomer and tertiary butyllithium, its lithiating agent. The charge transfer complex formed between the solvent THF and the tertiary butyllithium was used as an indicator of the unreacted butyllithium. Hence, a stoichiometric quantity of tertiary butyllithium was added dropwise to a solution of monovinylacetylene in THF to form lithiovinylacetylene. The addition of a slight excess of butyllithium led to the polymerization of the lithiated monomer. The obtained polymer was reprotonated and characterized. This polymerization was evaluated as a possible route to synthesize poly(vinylacetylene) with processable molecular weights, for its application as a potential carbon fiber precursor. © 1996 John Wiley & Sons, Inc.
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    Mechanism of radiation degradation of polyisobutylene (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 971-984 
    Details
    ISSN: 0887-624X
    Keywords: radiation ; polyisobutylene ; NMR ; GC/MS ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: GC, GC/MS, GPC, and Solution NMR spectra were used to study the γ radiolysis of polyisobutylene (PIB) in vacuum to different total doses (0-900 kGy) and at different temperatures (77-423 K). NMR spectra show a large number of new resonances with relatively narrow line widths, and a variety of NMR techniques have been employed to determine and quantify the structures associated with these new resonances. Chemical shift assignments were made by comparison with those for small molecule model compounds and predictions based upon calculations according to several different schemes. Chain-end structures have been proposed that account well for the majority of the new resonances, all being the result of an initial chain scission reaction initiated by the radiation. These assignments support some previous proposals for the mechanism of radiation degradation of polyisobutylene and exclude others. For example, NMR provides no evidence for the formation of ethyl chain ends and some of the main chain unsaturated structures previously proposed. NMR also indicate that at higher doses the chain end products formed during initial stages undergo secondary reactions. GC/MS data show the formation of oligomers during irradiation, which may be due to a backbitting mechanism. © 1996 John Wiley & Sons, Inc.
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    The synthesis and cationic polymerization behavior of ambifunctional monomers (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1015-1024 
    Details
    ISSN: 0887-624X
    Keywords: ambifunctional monomers ; 1-propenyl ethers ; 1-butenyl ethers ; vinyl ethers ; cationic polymerization ; photopolymerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of a novel series of ambifunctional monomers containing cationically polymerizable vinyl and 1-propenyl ether or 1-butenyl ether groups in the same molecule has been carried out. Studies of the onium salt-induced photopolymerizations of these monomers indicate that both functional groups are highly reactive and that they undergo extensive copolymerization. © 1996 John Wiley & Sons, Inc.
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    The effect of solvents and polyethylene glycol on the synthesis of linear and cyclic poly(methylene sulfide) (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1083-1085 
    Details
    ISSN: 0887-624X
    Keywords: poly(metyhylene sulfide) ; condensation polymerization ; catalysis ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The condensation polymerization of sodium sulfide with methylene chloride in various solvents was studied in order to assess the influence of polarity on the yield and composition of condensation products. The effect of addition of polyethylene glycol was also studied. It has been found that the overall yield of polythiomethylenes rises from 13.9% in methanol to 85.2% (methanol, PEG15000). The use of solvents of higher polarity promotes the linear oligomers, whereas in methanol the cyclic products predominate. In presence of PEG the this equilibrium is shifted towards tetrathiane. The observed phenomena are discussed in terms of solvents polarity and reaction media viscosity. © 1996 John Wiley & Sons, Inc.
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    Commentry: Reflections on “recent developments in polymerization by an alternating intra-intermolecular mechanism,” by George B. Butler, j. polym. sci., XLVIII, 279 (1960) (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 909-910 
    Details
    ISSN: 0887-624X
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/pola.1996.822
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    Triallylstannyllithium-allyllithium as an initiator for the anionic reversible chain transfer polymerization of 1,3-butadiene (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1183-1188 
    Details
    ISSN: 0887-624X
    Keywords: anionic polymerization ; polybutadiene ; triallylstannyllithium ; star polymer ; reversible chain transfer ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The anionic polymerization of 1,3-butadiene using a novel metalloidal anion initiator, triallylstannyllithium (TALi)-allyllithium (ALi), was studied. The TALi-ALi initiated anionic polymerization of 1,3-butadiene gave the star polymer along with the linear polybutadiene (PBD). The star polymer consisted of three PBD branches and a central tin atom. What is striking is a fact that the number-average molecular weights (Mn) and molecular weight distribution of three PBD branches and linear PBD were almost identical. A reversible chain transfer polymerization mechanism, which includes the equilibrium between tri(macroallyl)-stannyllithium and macroallylic anion, is proposed. © 1996 John Wiley & Sons, Inc.
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    Evidence and mechanisms of filling polymerization by plasma-induced graft polymerization (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1203-1208 
    Details
    ISSN: 0887-624X
    Keywords: plasma polymerization ; graft polymerization ; polyethylene ; poly(methylacrylate) ; membrane ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using a plasma-induced graft polymerization technique, which is well known as a surface modification method, the grafted polymer was formed in pores of the porous material. This study examined the filling mechanism. Five thin porous films were sandwiched together, and employed as the substrate. The substrate was treated by plasma, and the change in surface tension and radical formation was measured for each sheet after the sheet was separated. The only surface on which surface-tension change was detected, was that of the sheet directly exposed to the plasma. Although plasma treatment made polymer radicals primarily on the outer surface of the sheet, the treatment also formed a few radicals inside the sheets. The radicals inside the sheets reacted with methylacrylate and grafted polymer formed in the pores. The location of grafted polymer depended on the balance between monomer diffusivity and reactivity. The grafting rate depended on which monomer solvent was used for the polymerization. Thus, the grafted membrane morphology could be controlled by varying the grating solvent composition. © 1996 John Wiley & Sons, Inc.
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    Synthesis and properties of aromatic polyamides based on non-, methyl-, and phenyl-substituted 4,4′-bis(1,4-phenylenedioxy)dibenzoic acids (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1433-1441 
    Details
    ISSN: 0887-624X
    Keywords: aromatic polyamides ; ether-dicarboxylic acids ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 4,4′-(1,4-Phenylenedioxy)dibenzoic acid (3), 4,4′-(2,5-tolylenedioxy)dibenzoic acid (Me-3), and 4,4′-(2,5-biphenylenedioxy)dibenzoic acid (Ph-3) were prepared by the nucleophilic substitution reaction of p-fluorobenzonitrile with hydroquinone, methylhydroquinone, and phenylhydroquinone, respectively, followed by alkaline hydrolysis. Several aromatic polyamides having inherent viscosities of 0.66-1.34 dL/g were directly prepared by a Yamazaki phosphorylation polyamidation technique from dicarboxylic acids 3, Me-3, and Ph-3, respectively, with aromatic diamines using triphenyl phosphite and pyridine as condensing agents. The solubility of methyl- or phenyl-substituted polyamides was remarkably enhanced when compared to that of nonsubstituted analogues. Most of the substituted polyamides revealed an amorphous nature and were readily soluble in a variety of organic solvents including N,N-dimethylacetamide (DMAc), N-methyl-2-pyrrolidone (NMP), N,N-dimethylformamide, dimethyl sulfoxide, and m-cresol. Transparent, flexible, and tough films of these polymers could be cast from the DMAc or NMP solutions. These films had tensile strength of 60-100 MPa, elongation to break of 6-11%, and tensile modulus of 1.68-2.25 GPa. The glass transition temperatures (Tg) of most polyamides could be determined by differential scanning calorimetry (DSC) and were in the range of 200-232°C. Thermogravimetric analyses established that these polymers were fairly stable up to 450°C, and the 10% weight loss temperatures were recorded in the range of 458-535°C in nitrogen and 468-528°C in air atmosphere. In general, the phenyl-substituted polyamides exhibited relatively higher Tg, thermal stability, and solubility. © 1996 John Wiley & Sons, Inc.
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    Permselectivity between two anions in anion exchange membranes crosslinked with various diamines in electrodialysis (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1475-1482 
    Details
    ISSN: 0887-624X
    Keywords: anion exchange membranes ; electrodialysis ; relative transport number between two anions ; effect of hydrophobicity on anion transport ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A membranous copolymer crosslinked with divinylbenzene reacted with N,N,N′,N′-tetra-methylethylenediamine, N,N,N′,N′-tetramethyl-1,3-propanediamine, and N,N,N′,N′-tetramethyl-1,6-hexanediamine to prepare highly crosslinked anion exchange membranes. More than 80% of both tertiary amino groups of the diamines reacted with chloromethyl groups of the membrane to form crosslinkage. After formation of the high crosslinkage of the membrane was confirmed with dialysis of a neutral molecule, electrochemical properties of the obtained membranes (mainly, relative transport number between two anions in electrodialysis) were evaluated: nitrate ions to chloride ions, sulfate ions to chloride ions, fluoride ions to chloride ions, and bromide ions to chloride ions. Though larger anions, in general, were difficult to permeate through the membranes due to high crosslinkage, the number of methylene groups of the diamines (which means the increase in hydrophobicity of anion exchange groups) also affected the relative transport number between two anions. The lower the hydration of anions, the higher the relative transport number of the anions through the membranes with the hydrophobic anion exchange groups. © 1996 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    Investigation of bismaleimide containing naphthalene unit. II. Thermal behavior and properties of polymer (1996)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 34 (1996), S. 1493-1500 
    Details
    ISSN: 0887-624X
    Keywords: 2,7-bis(4-maleimidophenoxy)naphthalene ; bismaleimide ; Michael addition ; naphthalene ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Crosslinking of 2,7-bis(4-maleimidophenoxy)naphthalene (BMPN) and 4,4-bismaleimi-dophenylmethane (BMPM) was investigated in the presence of 4,4-diaminodiphenylmethane (DDM) at the 2/1 molar ratio of bismaleimide/DDM. Their curing behaviors were characterized by infrared spectroscopy and differential scanning calorimetry. The presence of a naphthalene group in the backbone of the bismaleimide increased the curing temperature and reduced the polymerization reactivity. The exotherm was shifted to a lower temperature as the amine addition lead to chain extension. Thermal behavior and properties of cured products were investigated by thermogravimetric analyses and dynamic mechanical analyses. Also, at this molar ratio, the properties of the BMPN/DDM showed better Tg, thermal decomposition temperature, and moisture resistance than the epoxy derived from 2,7-dihydroxynapthalene cured with DDM system (DGEDN/DDM). © 1996 John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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