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  • 1995-1999  (4,594)
  • 1997  (4,594)
  • Polymer and Materials Science  (3,277)
  • Biochemistry and Biotechnology  (1,317)
  • Engineering General
  • Nuclear reactions
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  • 1995-1999  (4,594)
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  • 1
    Electronic Resource
    Electronic Resource
    Acetyl-CoA enolization in citrate synthase: A quantum mechanical/molecular mechanical (QM/MM) study (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 9-25 
    Details
    ISSN: 0887-3585
    Keywords: CHARMM ; enzyme reaction intermediate ; strong hydrogen bonds ; Marcus formalism analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Citrate synthase forms citrate by deprotonation of acetyl-CoA followed by nucleophilic attack of this substrate on oxaloacetate, and subsequent hydrolysis. The rapid reaction rate is puzzling because of the instability of the postulated nucleophilic intermediate, the enolate of acetyl-CoA. As alternatives, the enol of acetyl-CoA, or an enolic intermediate sharing a proton with His-274 in a “low-barrier” hydrogen bond have been suggested. Similar problems of intermediate instability have been noted in other enzymic carbon acid deprotonation reactions. Quantum mechanical/molecular mechanical calculations of the pathway of acetyl-CoA enolization within citrate synthase support the identification of Asp-375 as the catalytic base. His-274, the proposed general acid, is found to be neutral. The acetyl-CoA enolate is more stable at the active site than the enol, and is stabilized by hydrogen bonds from His-274 and a water molecule. The conditions for formation of a low-barrier hydrogen bond do not appear to be met, and the calculated hydrogen bond stabilization in the reaction is less than the gas-phase energy, due to interactions with Asp-375 at the active site. The enolate character of the intermediate is apparently necessary for the condensation reaction to proceed efficiently. Proteins 27:9-25 © 1997 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    Crystal structure of a recombinant form of the maltodextrin-binding protein carrying an inserted sequence of a B-cell epitope from the preS2 region of hepatitis B virus (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 1-8 
    Details
    ISSN: 0887-3585
    Keywords: viral antigen ; epitope insertion ; recombinant protein ; x-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We report the crystal structure of MalE-B133, a recombinant form of the maltodextrin-binding protein (MBP) of Escherichia coli carrying an inserted amino-acid sequence of a B-cell epitope from the preS2 region of the hepatitis B virus (HBV). The structure was determined by molecular replacement methods and refined to 2.7 Å resolution. MalE-B133 is an insertion/deletion mutant of MBP in which residues from positions 134 to 142, an external α helix in the wild-type structure, are replaced by a foreign peptide segment of 19 amino acids. The inserted residues correspond to the preS2 sequence from positions 132 to 145 and five flanking residues that arise from the creation of restriction sites. The conformation of the recombinant protein, excluding the inserted segment, closely resembles that of wild-type MBP in the closed maltose-bound form. MalE-B133 was shown by previous studies to display certain immunogenic and antigenic properties of the hepatitis B surface antigen (HBsAg), which contains the preS2 region. The crystal structure reveals the conformation of the first nine epitope residues (preS2 positions 132 to 140) exposed on the surface of the molecule. The remaining five epitope residues (preS2 positions 141 to 145) are not visible in electron density maps. The path of the polypeptide chain in the visible portion of the insert differs from that of the deleted segment in the structure of wild-type MBP, displaying a helical conformation at positions 134 to 140 (preS2 sequence numbering). A tripeptide (Asp-Pro-Arg) at the N terminus of the helix forms a stable structural motif that may be implicated in the cross-reactivity of anti-HBsAg antibodies with the hybrid protein. Proteins 27:1-8 © 1997 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Improvement of protein secondary structure prediction using binary word encoding (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 36-46 
    Details
    ISSN: 0887-3585
    Keywords: GOR ; neural networks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We propose a binary word encoding to improve the protein secondary structure prediction. A binary word encoding encodes a local amino acid sequence to a binary word, which consists of 0 or 1. We use an encoding function to map an amino acid to 0 or 1. Using the binary word encoding, we can statistically extract the multiresidue information, which depends on more than one residue. We combine the binary word encoding with the GOR method, its modified version, which shows better accuracy, and the neural network method. The binary word encoding improves the accuracy of GOR by 2.8%. We obtain similar improvement when we combine this with the modified GOR method and the neural network method. When we use multiple sequence alignment data, the binary word encoding similarly improves the accuracy. The accuracy of our best combined method is 68.2%. In this paper, we only show improvement of the GOR and neural network method, we cannot say that the encoding improves the other methods. But the improvement by the encoding suggests that the multiresidue interaction affects the formation of secondary structure. In addition, we find that the optimal encoding function obtained by the simulated annealing method relates to non-polarity. This means that nonpolarity is important to the multiresidue interaction. Proteins 27:36-46 © 1997 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    Construction and analysis of a detailed three-dimensional model of the ligand binding domain of the human B cell receptor CD40 (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 59-70 
    Details
    ISSN: 0887-3585
    Keywords: comparative protein modeling ; sequence similarity ; sequence-structure compatibility ; model quality ; CD40 receptor-ligand interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The interaction between the human B cell receptor CD40 and its ligand on T cells is critical for B cell proliferation and the regulation of humoral immune responses. CD40 is a member of the tumor necrosis factor receptor (TNFR) family. We report here the construction and analysis of a detailed three-dimensional model of the TNFR-homologous extracellular region of CD40. This study provides an example for structure-based model building in the presence of low sequence similarity. The assessment of model quality and sequence-structure compatibility is emphasized, and limitations of the model are discussed. The current CD40 model predicts structural details beyond the backbone level. Features of the CD40 ligand binding site are discussed in conjunction with the results of a previous mutagenesis study. Proteins 27:59-70 © 1997 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    Perturbation of conformational dynamics, enzymatic activity, and thermostability of β-glycosidase from archaeon Sulfolobus solfataricus by pH and sodium dodecyl sulfate detergent (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 71-79 
    Details
    ISSN: 0887-3585
    Keywords: thermophilic β-glycosidase ; protein conformational dynamics ; frequency domain fluorometry ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The conformational dynamics of β-glycosidase from Sulfolobus solfataricus was investigated by following the emission decay arising from the large number of tryptophanyl residues that are homogeneously dispersed in the primary structure. The fluorescence emission is characterized by a bimodal lifetime distribution, suggesting that the enzyme structure contains rigid and flexible regions, properly located in the macromolecule. The enzyme activity and thermostability appear to be related to the dynamic properties of these regions as evidenced by perturbation studies of the enzyme structure at alkaline pH and by addition of detergents such as SDS. The pH increase affects the protein dynamics with a remarkable loss of thermal stability and activity; these changes occur without any significant variation in the secondary structure as revealed by far-UV dichroic measurements. In the presence of 0.02% (w/v) SDS at alkaline pH, the enzymatic activity and thermostability are recovered. Under these conditions, the conformational dynamics appear to be similar to that evidenced at neutral pH. Further increases in SDS concentration, at alkaline pH, render the activity and thermostability of β-glycosidase similar to those observed in the absence of detergent. Proteins 27:71-79 © 1997 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Homology model for the human GSTT2 theta class glutathione transferase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 118-130 
    Details
    ISSN: 0887-3585
    Keywords: homology modeling ; glutathione transferases ; theta class GSTs ; glutathione ; menaphthyl sulfate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A tertiary model of the human GSTT2 Theta class glutathione transferase is presented based on the recently solved crystal structure of a related thetalike isoenzyme from Lucilia cuprina. Although the N-terminal domains are quite homologous, the C-terminal domains share less than about 20% identity. The model is used to consolidate the role of Ser 11 in the active site of the enzyme as well as to identify other residues and mechanisms of likely catalytic importance. The T2 subfamily of theta class enzymes have been shown to inactivate reactive sulfate esters arising from arylmethanols. A possible reaction pathway involving the conjugation of glutathione with one such sulfate ester, 1-menaphthyl-sulfate, is described. It is also proposed that the C-terminal region of the enzyme plays an important role in allowing substrate access to the active site. Proteins 27:118-130 © 1997 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    The family of the IL-6-Type cytokines: Specificity and promiscuity of the receptor complexes (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 96-109 
    Details
    ISSN: 0887-3585
    Keywords: IL-6/IL-6R complex ; gp130 ; cytokines ; model building ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The cytokines IL-6, LIF, CNTF, OSM, IL-11, and CT-1 have been grouped into the family of IL-6-type cytokines, since they all require gp130 for signal transduction. Interestingly, gp130 binds directly to OSM, whereas complex formation with the other cytokines depends on additional receptor subunits. Only limited structural information on these cytokines and their receptors is available. X-ray structures have been solved for the cytokines LIF and CNTF, whose up-up-down-down four-helix bundle is common to all of these cytokines, and for the receptors of hGH and prolactin, which contain two domains with a fibronectin III-like fold. Since cocrystallization and x-ray analysis of the up to four different proteins forming the receptor complexes of the IL-6-type cytokines is unlikely to be achieved in the near future, model building based on the existing structural information is the only approach for the time being. Here we present model structures of the complexes of human and murine IL-6 with their receptors. Their validity can be deduced from the fact that published mutagenesis data and the different receptor specificity of human and murine IL-6 can be understood. It is now possible to predict the relative positions and contacts for all molecules in their respective complexes. Such information can be used for the rational design of cytokine and receptor antagonists, which may have a valuable therapeutic perspective. Proteins 27:96-109 © 1997 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    Structural homology of spinach acyl carrier protein and Escherichia coli acyl carrier protein based on NMR data (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 131-143 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; protein dynamics ; molecular mechanics ; NOE ; NMR ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Acyl carrier proteins (ACPs) from spinach and from Escherichia coli have been used to demonstrate the utility of proton NMR for comparison of homologous structures. The structure of E. coli ACP had been previously determined and modeled as a rapid equilibrium among multiple conformational forms (Kim and Prestegard, Biochemistry 28:8792-8797, 1989). Spinach ACP showed two slowly exchanging forms and could be manipulated into one form for structural study. Here we compare this single form to postulated multiple forms of E. coli ACP using the limited amount of NOE data available for the spinach protein. A number of long-range NOE contacts were present between homologous residues in both spinach and E. coli ACP, suggesting tertiary structural homology. To allow a more definitive structural comparison, a method was developed to use spinach ACP NOE constraints to search for regions of structural divergence from two postulated forms of E. coli ACP. The homologous regions of the two protein sequences were aligned, additional distance constraints were extracted from the E. coli structure, and these were mapped onto the spinach sequence. These distance constraints were combined with experimental NOE constraints and a distance geometry simulated annealing protocol was used to test for compatibility of the constraints. All of the experimental spinach NOE constraints could be successfully combined with the E. coli data, confirming the general hypothesis of structural homology. A better fit was obtained with one form, suggesting a preferential stabilization of that form in the spinach case. Proteins 27:131-143 © 1997 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Comparative modeling of the three-dimensional structure of the calmodulin-related TCH2 protein from arabidopsis (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 144-153 
    Details
    ISSN: 0887-3585
    Keywords: calcium ; plant ; environmental stress ; TCH genes ; signal transduction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Plants adapt to various stresses by developmental alterations that render them less easily damaged. Expression of the TCH2 gene of Arabidopsis is strongly induced by stimuli such as touch and wind. The gene product, TCH2, belongs to the calmodulin (CaM) family of proteins and contains four highly conserved Ca2+-binding EF-hands. We describe here the structure of TCH2 in the fully Ca2+-saturated form, constructed using comparative molecular modeling, based on the x-ray structure of paramecium CaM. Like known CaMs, the overall structure consists of two globular domains separated by a linker helix. However, the linker region has added flexibility due to the presence of 5 glycines within a span of 6 residues. In addition, TCH2 is enriched in Lys and Arg residues relative to other CaMs, suggesting a preference for targets which are more negatively charged. Finally, a pair of Cys residues in the C-terminal domain, Cys126 and Cys131, are sufficiently close in space to form a disulfide bridge. These predictions serve to direct future biochemical and structural studies with the overall aim of understanding the role of TCH2 in the cellular response of Arabidopsis to environmental stimuli. Proteins 27:144-153 © 1997 Wiley-Liss, Inc.
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  • 10
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary crystallographic data of a neutrophil migration-inducing lectin (KM+) extracted from the seed of Artocarpus integrifolia (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 157-159 
    Details
    ISSN: 0887-3585
    Keywords: crystallization ; lectin ; plant lectin ; neutrophil migration ; erythrocyte agglutination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The tetrameric KM+ lectin from the seeds of Artocarpus integrifolia has, when compared to other plant lectins, the singular property of directly inducing neutrophil migration into the peritoneal cavity or into the air pouch of rats. This protein crystals have been grown and they belong to the orthorhombic system with space group C2221. The unit cell parameters are a = 54.4 Å, b = 127.9 Å and c = 99.8 Å. A native diffraction dataset to 2.8 Å was collected and an analysis of the self-rotation function has shown the presence of only one independent non-crystallographic 2-fold axis orthogonal to the crystal b-axis, compatible with a dimer in the asymmetric unit. Proteins 27:157-159 © 1997 Wiley-Liss, Inc.
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  • 11
    Electronic Resource
    Electronic Resource
    Insight via simulations: Publishing results and methods (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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  • 12
    Electronic Resource
    Electronic Resource
    Stability of secondary structural elements in a solvent-free environment: the α helix (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 165-170 
    Details
    ISSN: 0887-3585
    Keywords: α helix ; secondary structure ; gas phase ; molecular mechanics ; mass spectrometry ; kinetic energy release ; melittin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The stability of the α helix as an element of secondary structure is examined in the absence of solvation, in the gas phase. Mass-analyzed ion kinetic energy (MIKE) spectrometry was applied to measure intercharge repulsion and intercharge distance in multiply protonated melittin, a polypeptide known to possess a stable helical structure in a number of different environments. The experimental results, interpreted in combination with molecular mechanics calculations, suggest that triply charged melittin retains its secondary structure in the gas phase. The stability if the α-helical conformation of the polypeptide in the absence of solvent molecules reflects the fact that a network of intrinsic helical hydrogen bonds is energetically more favorable than unfolded conformations. © 1997 Wiley-Liss, Inc.
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  • 13
    Electronic Resource
    Electronic Resource
    Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: Crystallographic refinement of 2 Å data (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 184-195 
    Details
    ISSN: 0887-3585
    Keywords: aspartic protease ; HIV-1 ; complex with inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a complex between a hexapeptide-based inhibitor, MVT-101, and the chemically synthesized (Aba 67,95,167,195; Aba: l-α-amino-n-butyric acid) protease from the human immunodeficiency virus (HIV-1), reported previously at 2.3 Å has now been refined to a crystallographic R factor of 15.4% at 2.0 Å resolution. Root mean square deviations from ideality are 0.18 Å for bond lengths and 2.4° for the angles. The inhibitor can be fitted to the difference electron density map in two alternative orientations. Drastic differences are observed for positions and interactions at P3/S3 and P3′/S3′ subsites of the two orientations due to different crystallographic environments. © 1997 Wiley-Liss, Inc.
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  • 14
    Electronic Resource
    Electronic Resource
    Analysis of the structure of HIV-1 protease complexed with a hexapeptide inhibitor. Part II: Molecular dynamic studies of the active site region (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 195-203 
    Details
    ISSN: 0887-3585
    Keywords: aspartic protease ; HIV-1 ; molecular dynamics ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Six models of the catalytic site of HIV-1 protease complexed with a reduced peptide inhibitor, MVT-101, were investigated. These studies focused on the details of protonation of the active site, its total net charge and hydrogen bonding pattern, which was consistent with both the observed coplanar configuration of the acidic groups of the catalytic aspartates (Asp-25 and Asp-125) and the observed binding mode of the inhibitor. Molecular dynamic simulations using AMBER 4.0 indicated that the active site should be neutral. The planarity of the aspartate dyad may be due to the formation of two hydrogen bonds: one between the inner Oδ1oxygen atoms of the two catalytic aspartates and another between the Oδ2atom of Asp-125 and the nitrogen atom of the reduced peptide bond of the bound inhibitor. This would require two additional protonations, either of both aspartates, or of one Asp and the amido nitrogen atom of Nle-204. Our results favor the Asp-inhibitor protonation but the other one is not excluded. Implications of these findings for the mechanism of enzymatic catalysis are discussed. Dynamic properties of the hydrogen bond network in the active site and an analysis of the interaction energy between the inhibitor and the protease are presented. © 1997 Wiley-Liss, Inc.
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  • 15
    Electronic Resource
    Electronic Resource
    Conformation and stability of streptokinases from nephritogenic and nonnephritogenic strains of streptococci (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 26-35 
    Details
    ISSN: 0887-3585
    Keywords: streptokinase variants ; Streptococcus equisimilis ; Streptococcus pyogenes ; circular dichroism ; fluorescence spectroscopy ; differential scanning calorimetry ; limited proteolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Conformation and stability of three Sks from Streptococcus equisimilis strain H46A, Streptococcus pyogenes strain A374, and Streptococcus pyogenes strain AT27 were compared by limited proteolysis, CD, and fluorescence measurements and by DSC. The general similarity of the peptide CD spectra in the spectral region 185 to 260 nm indicates the same type of folding for the three proteins. Fluorescence and aromatic CD spectra are consistent with a predominant surface localization of the aromatic amino acids and a low rigidity of their surroundings. A major difference among the three Sks is shown by deconvolution of their excessive heat capacity functions. Deconvolution reveals two energetic folding units in Sk H46A but three energetic folding units in Sk A374 and Sk AT27. Digestion of the Sks with trypsin indicates a reduced sensitivity of the C-terminal region of Sk A374 and Sk AT27 in comparison to Sk H46A. This suggests that amino acids of the C-terminal region participate in the formation of the third folding unit of Sk A374 and Sk AT27. Proteins 27:26-35 © 1997 Wiley-Liss, Inc.
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  • 16
    Electronic Resource
    Electronic Resource
    A disulfide bridge near the active site of carbapenem-hydrolyzing class A β-lactamases might explain their unusual substrate profile (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 47-58 
    Details
    ISSN: 0887-3585
    Keywords: β-lactamase ; homology-modeling ; carbapenems ; disulfide bridge ; kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacterial resistance to β-lactam antibiotics, a clinically worrying and recurrent problem, is often due to the production of β-lactamases, enzymes that efficiently hydrolyze the amide bond of the β-lactam nucleus. Imipenem and other carbapenems escape the activity of most active site serine β-lactamases and have therefore become very popular drugs for antibacterial chemotherapy in the hospital environment. Their usefulness is, however, threatened by the appearance of new β-lactamases that efficiently hydrolyze them. This study is focused on the structure and properties of two recently described class A carbapenemases, produced by Serratia marcescens and Enterobacter cloacae strains and leads to a better understanding of the specificity of β-lactamases. In turn, this will contribute to the design of better antibacterial drugs. Three-dimensional models of the two class A carbapenemases were constructed by homology modeling. They suggested the presence, near the active site of the enzymes, of a disulfide bridge (C69-C238) whose existence was experimentally confirmed. Kinetic parameters were measured with the purified Sme-1 carbapenemase, and an attempt was made to explain its specific substrate profile by analyzing the structures of minimized Henri-Michaelis complexes and comparing them to those obtained for the “classical” TEM-1 β-lactamase. The peculiar substrate profile of the carbapenemases appears to be strongly correlated with the presence of the disulfide bridge between C69 and C238. Proteins 27:47-58 © 1997 Wiley-Liss, Inc.
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  • 17
    Electronic Resource
    Electronic Resource
    Ricin A-chain structural determinant for binding substrate analogues: A molecular dynamics simulation analysis (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 80-95 
    Details
    ISSN: 0887-3585
    Keywords: ribosome-inactivating proteins ; N-glycosidase ; protein-RNA interactions ; molecular recognition ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ricin A-chain is a cytotoxic protein that attacks ribosomes by hydrolyzing a specific adenine base from a highly conserved, single-stranded rRNA hairpin containing the tetraloop sequence GAGA. Molecular-dynamics simulation methods are used to analyze the structural determinant for three substrate analogues bound to the ricin A-chain molecule. Simulations were applied to the binding of the dinucleotide adenyl-3′,5′-guanosine employing the x-ray crystal structure of the ricin complex and a modeled CGAGAG hexanucleotide loop taken from the NMR solution structure of a 29-mer oligonucleotide hairpin. A third simulation model is also presented describing a conformational search of the docked 29-mer structure by using a simulated-annealing method. Analysis of the structural interaction energies for each model shows the overall binding dominated by nonspecific interactions, which are mediated by specific arginine contacts from the highly basic region on the protein surface. The tetraloop conformation of the 29-mer was found to make specific interactions with conserved protein residues, in a manner that favored the GAGA sequence. A comparison of the two docked loop conformations with the NMR structure revealed significant positional deviations, suggesting that ricin may use an induced fit mechanism to recognize and bind the rRNA substrate. The conserved Tyr-80 may play an important confirmational entropic role in the binding and release of the target adenine in the active site. Proteins 27:80-95 © 1997 Wiley-Liss, Inc.
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  • 18
    Electronic Resource
    Electronic Resource
    Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 110-117 
    Details
    ISSN: 0887-3585
    Keywords: small-angle scattering ; x-rays ; allosteric enzymes ; crystal structure ; rigid body modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Solution scattering curves evaluated from the crystal structures of the T and R states of the allosteric enzyme aspartate transcarbamylase from Escherichia coli were compared with the experimental x-ray scattering patterns. Whereas the scattering from the crystal structure of the T state agrees with the experiment, large deviations reflecting a significant difference between the quaternary structures in the crystal and in solution are observed for the R state. The experimental curve of the R state was fitted by rigid body movements of the subunits in the crystal R structure which displace the latter further away from the T structure along the reaction coordinates of the T→R transition observed in the crystals. Taking the crystal R structure as a reference, it was found that in solution the distance between the catalytic trimers along the threefold axis is 0.34 nm larger and the trimers are rotated by 11° in opposite directions around the same axis; each of the three regulatory dimers is rotated by 9° around the corresponding twofold axis and displaced by 0.14 nm away from the molecular center along this axis. Proteins 27:110-117 © 1997 Wiley-Liss, Inc.
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  • 19
    Electronic Resource
    Electronic Resource
    Expression, purification, crystallization, and preliminary X-Ray diffraction analysis of the homodimeric bacterial hemoglobin from Vitreoscilla stercoraria (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 154-156 
    Details
    ISSN: 0887-3585
    Keywords: dimeric bacterial hemoglobin ; Vitreoscilla stercoraria ; crystal growth ; x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The recombinant homodimeric hemoglobin from the strictly aerobe gram-negative bacterium Vitreoscilla stercoraria has been expressed in Escherichia coli, purified to homogeneity, and crystallized by vapor diffusion techniques, using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group P21 and diffract to HIGH resolution. The unit cell parameters are a = 62.9, b = 42.5, c = 63.2 Å, β = 106.6°; the asymmetric unit contains the homodimeric hemoglobin, with a volume solvent content of 42%. Proteins 27:154-156 © 1997 Wiley-Liss, Inc.
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    Crystallization and preliminary X-Ray analysis of recombinant staphylokinase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 160-161 
    Details
    ISSN: 0887-3585
    Keywords: protein crystallization ; x-ray crystallography ; thrombolytic agents ; staphylokinase ; STAR ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Diffraction quality crystals of recombinant staphylokinase (STAR) have been grown by the hanging drop vapor diffusion technique from a solution containing MgCl2, Tris buffer (pH 8.5), and polyethylene glycol 4000. The crystals belong to the monoclinic space group C2 with unit cell dimensions a = 60.6 Å, b = 43.7 Å, c = 54.3 Å, and β = 115.6°. Å complete native data set to 1.8 Å resolution has been collected using synchrotron radiation. Proteins 27:160-161 © 1997 Wiley-Liss, Inc.
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    Adams, Paul D., Engelman, Donald M., Brünger, Axel T. Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching. Proteins 26:257-261, 1996. (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 162-162 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Predicting the equilibrium protein folding pathway: Structure-based analysis of staphylococcal nuclease (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 171-183 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The equilibrium folding pathway of staphylococcal nucleas (SNase) has been approximated using a statistical thermodynamic formalism that utilizes the high-resolution structure of the native state as a template to generate a large ensemble of partially folded states. Close to 400,000 different states ranging from the native to the completely unfolded states were included in the analysis. The probability of each state was estimated using an empirical structural parametrization of the folding energetics. It is shown that this formalism predicts accurately the stability of the protein, the cooperativity of the folding/unfolding transition observed by differential scanning calorimetry (DSC) or urea denaturation and the thermodynamic parameters for unfolding. More importantly, this formalism provides a quantitative account of the experimental hydrogen exchange protection factors measured under native conditions for SNase. These results suggest that the computer-generated distribution of states approximates well the ensemble of conformations existing in solution. Furthermore, this formalism represents the first model capable of quantitatively predicting within a unified framework the probability distribution of states seen under native conditions and its change upon unfolding. © 1997 Wiley-Liss, Inc.
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    Rab7: NMR and kinetics analysis of intact and C-terminal truncated constructs (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 204-209 
    Details
    ISSN: 0887-3585
    Keywords: rab7 ; GTPase ; vesicle ; targeting ; crystal ; kinetics ; NMR ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Rab proteins are a family of ˜25kD ras-related GTPases which are associated with distinct intracellular membranes where they control vesicle traffic between intracellular compartments. The late-endosomal rab protein rab71-207, (lacking only the C-terminal lipids of the native molecule) and three C-terminal truncated constructs rab71-202, rab71-197and rab71-182were purified using an E. coli expression system. The C-terminal tail region of rab proteins is of special interest because it is thought to target rab proteins to particular intracellular membranes. A comparison of TOCSY-NMR spectra from intact rab71-207and the tail-less construct rab71-182suggested that much of the C-terminal tail is flexible in solution. The GTP hydrolysis, and GDP association and dissociation rates for all the truncated and intact constructs were similar, showing that the tail region of rab71-207has little influence on the hydrolysis and exchange rates of the nucleotide. © 1997 Wiley-Liss, Inc.
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    Geometric versus topological clustering: An insight into conformation mapping (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 213-226 
    Details
    ISSN: 0887-3585
    Keywords: conformation space ; potential energy surface ; connectivity ; topological mapping ; family clustering ; principal coordinate projections ; visualization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Clustering molecular conformations into “families” is a common procedure in conformational analysis of molecular systems. An implicit assumption which often underlies this clustering approach is that the resulting geometric families reflect the energetic structure of the system's potential energy surface. In a broader context we address the question whether structural similarity is correlated with energy basins, i.e., whether conformations that belong to the same energy basin are also geometrically similar. “Topological mapping” and principal coordinate projections are used here to address this question and to assess the quality of the “family clustering” procedure. Applying the analysis to a small tetrapeptide it was found that the general correlation that exists between energy basins and structural similarity is not absolute. Clusters generated by the geometric “family clustering” procedure do not always reflect the underlying energy basins. In particular it was found that the “family tree” that is generated by the “family clustering” procedure is completely inconsistent with its real topological counterpart, the “disconnectivity” graph of this system. It is also demonstrated that principal coordinate analysis is a powerful visualization technique which, at least for this system, works better when distances are measured in dihedral angle space rather than in cartesian space. © 1997 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    Is cyanate a carbonic anhydrase substracte? (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 272-278 
    Details
    ISSN: 0887-3585
    Keywords: anion hydrolysis ; CA inhibitors ; substrates/inhibitors adducts ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A study was undertaken to investigate whether diverse carbonic anhydrase (CA) isozymes (both native Zn as well as cobalt-substituted) are able to catalyze the hydrolysis of anions such as cyanide, cyanate, and thiocyanate. A controversy exists between the crystallographic and spectroscopic data of CA II-anion adducts. In the former case it has been shown that “metal poisons” such as CN-and CNO-are not directly coordinated to the active site Zn(II) ion whereas spectroscopic studies indicate otherwise. A theoretical study in the above systems did not resolve this controversy, since it was calculated that all three anions can act as CA substrates. In this paper we prove experimentally that none of them may act as substrates of CA and propose an explanation to the above controversy, discussing the mode of binding of small molecules within the enzyme active site. © 1997 Wiley-Liss, Inc.
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    Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 249-271 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; secondary structure ; protein conformation ; protein backbone structure ; protein structure classification ; helix capping ; strand capping ; neural networks ; structural building blocks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To study local structures in proteins, we previously developed an autoassociative artificial neural network (autoANN) and clustering tool to discover intrinsic features of macromolecular structures. The hidden unit activations computed by the trained autoANN are a convenient low-dimensional encoding of the local protein backbone structure. Clustering these activation vectors results in a unique classification of protein local structural features called Structural Building Blocks (SBBs). Here we describe application of this method to a larger database of proteins, verification of the applicability of this method to structure classification, and subsequent analysis of amino acid frequencies and several commonly occurring patterns of SBBs. The SBB classification method has several interesting properties: 1) it identifies the regular secondary structures, α helix and β strand; 2) it consistently identifies other local structure features (e.g., helix caps and strand caps); 3) strong amino acid preferences are revealed at some positions in some SBBs; and 4) distinct patterns of SBBs occur in the “random coil” regions of proteins. Analysis of these patterns identifies interesting structural motifs in the protein backbone structure, indicating that SBBs can be used as “building blocks” in the analysis of protein structure. This type of pattern analysis should increase our understanding of the relationship between protein sequence and local structure, especially in the prediction of protein structures. © 1997 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    Crystallization and preliminary crystallographic analysis of ribosomal protein S8 from Thermus thermophilus (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 309-310 
    Details
    ISSN: 0887-3585
    Keywords: crystals ; ribosomes ; extreme thermophile ; translation repressor ; x-ray analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals have been obtained for recombinant ribosomal protein S8 from Thermus thermophilus produced by Escherichia coli. The protein crystals have been grown in 40 mM potassium phosphate buffer (pH 6.0) in hanging drops equilibrated against saturated ammonium sulfate (unbuffered) with 2-methyl-2,4-pentandiol (v/v). The crystals belong to the space group P41(3)212 with cell parameters a= b= 67.65 Å, c= 171.12 Å. They diffract x-rays to 2.9 Å resolution. © 1997 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    Crystallization and preliminary X-ray crystallographic study of the Ras-GTPase-activating domain of human p120GAP (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 315-318 
    Details
    ISSN: 0887-3585
    Keywords: catalytic domain ; cross-linking ; hanging drop ; p21 ; seeding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ras-GTPase-activating proteins (Ras-GAPs) are important regulators of the biological activity of Ras within the framework of intracellular communication where GTP-bound Ras (Ras: GTP) is a key signal transducing molecule (Trahey and McCormick, Science 238:542-545, 1987; Boguski and McCormick, Nature 366:643-654, 1993). By accelerating Ras-mediated GTP hydrolysis, Ras-GAPs provide an efficient means to reset the Ras-GTPase cycle to the GDP-bound “OFF”-state and terminate the Ras-mediated signal. Here we report the crystallization of the GTPase-activating domain of the human p120GAP. The crystals belong to the orthorhombic space group symmetry P212121with unit cell dimensions of a = 42.2 Å, b = 55.6 Å, c = 142.2 Å, α = β = γ = 90°. Assuming a Matthews parameter of 2.2 Å3/Da, there is one molecule per asymmetric unit. Applying micro-seeding techniques, we grew large single crystals that could not be obtained by other routine methods for crystal improvement. They diffracted to a resolution of approximately 3 Å using X-rays from a rotating anode generator and to better than 1.8 Å in a synchrotron beam. Chemical cross-linking led to reduction of the maximum resolution but to significantly increased stability against mechanical and heavy atom stress. © 1997 Wiley-Liss, Inc.
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    Expression, purification, and crystallization of the DNA-binding domain from the Saccharomyces cerevisae cell-cycle transcription factor MBP-1 (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 325-327 
    Details
    ISSN: 0887-3585
    Keywords: transcriptional control ; cell-cycle ; DNA-binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A 124-residue N-terminal fragment corresponding to the DNA-binding domain of the Saccharomyces cerevisae cell-cycle transcription factor MBP-1 has been expressed with a hexahistidine affinity tag in E. coli and purified to apparent homogeneity. Crystals have been grown using PEG 3350 as precipitant which diffract x-rays to greater than 2.6 Å resolution. The space group is tetragonal, P43212 or P41212 with unit cell dimensions a= b= 42.2 Å, c= 123.2 Å and a monomer in the asymmetric unit. © 1997 Wiley-Liss, Inc.
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    Seventy-five percent accuracy in protein secondary structure prediction (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 329-335 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; protein sequence analysis ; hydrogen bonds ; sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this study we present an accurate secondary structure prediction procedure by using a query and related sequences. The most novel aspect of our approach is its reliance on local pairwise alignment of the sequence to be predicted with each related sequence rather than utilization of a multiple alignment. The residue-by-residue accuracy of the method is 75% in three structural states after jack-knife tests. The gain in prediction accuracy compared with the existing techniques, which are at best 72%, is achieved by secondary structure propensities based on both local and long-range effects, utilization of similar sequence information in the form of carefully selected pairwise alignment fragments, and reliance on a large collection of known protein primary structures. The method is especially appropriate for large-scale sequence analysis efforts such as genome characterization, where precise and significant multiple sequence alignments are not available or achievable. Proteins 27:329-335, 1997. © 1997 Wiley-Liss, Inc.
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    Structure of Semliki Forest virus core protein (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 345-359 
    Details
    ISSN: 0887-3585
    Keywords: alphavirus structure ; Semliki Forest virus capsid protein ; autocatalysis ; capsid assembly ; conformational changes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Alphaviruses are enveloped, insect-borne viruses, which contain a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 Å and 3.3 Å resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize the same monomer surface regions as found in the crystalline dimer interfaces. Proteins 27:345-359, 1997. © 1997 Wiley-Liss, Inc.
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    The metal site of Pseudomonas aeruginosa azurin, revealed by a crystal structure determination of the co(II) derivative and co-EPR spectroscopy (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 385-394 
    Details
    ISSN: 0887-3585
    Keywords: azurin ; cobalt ; x-ray crystallography ; EPR ; Pseudomonas aeruginosa ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of cobalt-substituted azurin from Pseudomonas aeruginosa has been determined to final crystallographic R value of 0.175 at 1.9 Å resolution. There are four molecules in the asymmetric unit in the structure, and these four molecules are packed as a dimer of dimers. The dimer packing is very similar to that of the wild-type Pseudomonas aeruginosa azurin dimer. Replacement of the native copper by the cobalt ion has only small effects on the metal binding site presumably because of the existence of an extensive network of hydrogen bonds in its immediate neighborhood. Some differences are obvious, however. In wild-type azurin the copper atom occupies a distorted trigonal bipyramidal site, while cobalt similar to zinc and nickel occupy a distorted tetrahedral site, in which the distance to the Met121,Sδ atom is increased to 3.3-3.5 Å and the distance to the carbonyl oxygen of Gly45 has decreased to 2.1-2.4 Å. The X-band EPR spectrum of the high-spin Co(II) in azurin is well resolved (apparent g values gx′ = 5.23; gy′ = 3.83; gz′ = 1.995, and hyperfine splittings Ax′ = 31; Ay′ = 20-30; Az′ = 53 G) and indicates that the ligand field is close to axial. Proteins 27:385-394, 1997. © 1997 Wiley-Liss, Inc.
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    Shuffling of structural elements in filamentous bacteriophages (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 405-409 
    Details
    ISSN: 0887-3585
    Keywords: class II filamentous bacteriophages ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: All class II filamentous bacteriophage coat proteins contain a conserved, 12-amino acid sequence highly homologous to the loop portion of the EF-hand Ca2+-binding motif. The Pf3 coat protein contains two regions of homology to this sequence. The 12-amino acid sequence corresponds to a region of the Pf1 coat protein whose structure is controversial. In some models of the virus structure, this region is α-helical. In others, it forms a loop that folds back on itself. The similarity of this region to the loop in the helix-loop-helix Ca2+-binding motif suggests that it takes on a loop structure in the virion. Each filamentous phage lacks at least one residue normally involved in Ca2+-coordination, consistent with the relatively weak Ca2+ binding properties of the filamentous phages. Consideration of the structure of the coat protein in the membrane and in the virus particle indicates that the protein may be more effective in binding cations in its membrane-bound form than in the virus particle. This suggests that release of cations from this loop may be an obligate step during assembly of the proteins into the virus particle. Proteins 27:405-409, 1997. © 1997 Wiley-Liss, Inc.
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    A predicted consensus structure for the N-Terminal fragment of the heat shock protein HSP90 family (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 450-458 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; prediction contest ; protein sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A secondary structure has been predicted for the heat shock protein HSP90 family from an aligned set of homologous protein sequences by using a transparent method in both manual and automated implementation that extracts conformational information from patterns of variation and conservation within the family. No statistically significant sequence similarity relates this family to any protein with known crystal structure. However, the secondary structure prediction, together with the assignment of active site positions and possible biochemical properties, suggest that the fold is similar to that seen in N-terminal domain of DNA gyrase B (the ATPase fragment). Proteins 27:450-458, 1997. © 1997 Wiley-Liss, Inc.
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    Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 425-437 
    Details
    ISSN: 0887-3585
    Keywords: hinge bending ; hinge axis ; principal component analysis ; essential dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations. For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by modes of motion external to the domains. To analyze the molecular dynamics trajectory, a principal component analysis tailored specifically to analyze interdomain motions is applied. A method based on the curl of the atomic displacements is described, which yields a sharp discrimination of domains, and which defines a unique interdomain screw-axis. Hinge axes are defined and classified as twist or closure axes depending on their direction. The methods have been tested on lysozyme. A remarkable correspondence was found between the first normal mode axis and the first principal mode axis, with both axes passing within 3 Å of the alpha-carbon atoms of residues 2, 39, and 56 of human lysozyme, and near the interdomain helix. The axes of the first modes are overwhelmingly closure axes. A lesser degree of correspondence is found for the second modes, but in both cases they are more twist axes than closure axes. Both analyses reveal that the interdomain connections allow only these two degrees of freedom, one more than provided by a pure mechanical hinge. Proteins 27:425-437, 1997. © 1997 Wiley-Liss, Inc.
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    Homology modeling of rabbit prolactin hormone complexed with its receptor (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 459-468 
    Details
    ISSN: 0887-3585
    Keywords: binding site ; comparative study ; cytokines ; dimerization ; growth hormone ; prolactin hormone ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The pituitary hormone prolactin (prl) is implicated in a number of biological functions, especially lactation, which is mediated through specific lactogenic receptors (PrlR). Human growth hormone (hGH) is also a pituitary hormone responsible for linear growth. While the growth hormone receptor (hGHR) binds only hGH, hPrlR can interact with both hGH and hPrl. Using structural information from the human growth hormone (hGH)/receptor (hGHR) complex, we modeled by homology a complex between rabbit prolactin hormone (rbPrl) and its receptor (rbPrlR). While the somatogenic hormone/somatogenic receptor (hGH/hGHR) and somatogenic hormone/lactogenic receptor (hGH/hPrlR) interactions are now known and well studied, here we propose a model for the interaction of the lactogenic hormone with its receptor (rbPrl/rbPrlR), and compare these three kinds of ligand/receptor interaction. We identified residues contributing to the active site and tested the potential dimerization of the receptor. Biochemical studies and information deduced from the modeled complex do not exclude a homodimeric form but point to a functional heterodimeric complex. Proteins 27: 459-468, 1997. © 1997 Wiley-Liss, Inc.
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    Structure and dynamics of the M13 coat signal sequence in membranes by multidimensional high-resolution and solid-state NMR spectroscopy (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 481-492 
    Details
    ISSN: 0887-3585
    Keywords: leader peptide ; micelle ; bilayer ; 1H-2H-exchange ; α-helix ; topology ; circular dichroism (CD) ; solid-phase peptide synthesis ; membrane insertion, and translocation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The polypeptide corresponding to the signal sequence of the M13 coat protein and the five N-terminal residues of the mature protein was prepared by solid-phase peptide synthesis with a 15N isotopic label at the alanine-12 position. Multidimensional solution NMR spectroscopy and molecular modeling calculations indicate that this polypeptide assumes helical conformations between residues 5 and 20, in the presence of sodium dodecylsulfate micelles. This is in good agreement with circular dichroism spectroscopic measurement, which shows an α-helix content of approximately 42%. The α-helix comprises an uninterrupted hydrophobic stretch of ≤12 amino acids, which is generally believed to be too short for a stable transmembrane alignment in a biological bilayer. The monoexponential proton-deuterium exchange kinetics of this hydrophobic helical region is characterized by half-lives of 15-75 minutes (pH 4.2, 323 K). When the polypeptide is reconstituted into phospholipid bilayers, the broad anisotropy of the proton-decoupled 15N solid-state NMR spectroscopy indicates that the hydrophobic helix is immobilized close to the lipid bilayer surface at the time scale of 15N solid-state NMR spectroscopy (10-4 seconds). By contrast, short correlation times, immediate hydrogen-deuterium exchange as well as nuclear Overhauser effect crosspeak analysis suggest that the N and C termini of this polypeptide exhibit a mobile random coil structure. The implications of these structural findings for possible mechanisms of membrane insertion and translocation as well as for membrane protein structure prediction algorithms are discussed. © 1997 Wiley-Liss Inc.
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    High resolution fast quantitative docking using fourier domain correlation techniques (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 493-506 
    Details
    ISSN: 0887-3585
    Keywords: docking ; correlation ; DFT ; grid-method ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A ‘docking’ method based on finite grid forcefield sampling is proposed for fast evaluation of interaction energies between macromolecules and ligands. Forcefield used to calculate interaction energies utilizes a potential energy function composed of a 1/r-dependent electrostatic term and a (6-12) Lennard-Jones term for van der Waals interactions. Fast evaluation makes use of the convolution theorem allowing a point-by-point N-dimensional correlation in direct space to be replaced by a simple multiplication in spatial frequency space. Predictive accuracy was assessed by using seven protein-ligand complexes available from the Brookhaven Data Bank and determined crystallographically to high resolution. Successful prediction of ligand position and determination of ligand-protein interaction enthalpy was dependent on forcefield sampling grid size. Minimum interaction enthalpy calculated for four protein-ligand complexes coincided with crystallographic structures that used sampling grid sizes of 0.25 Å resolution and was independent of ligand starting position and orientation. Successful docking was obtained for the remaining complexes at same grid resolution provided ligand starting positions were not randomized. Sensitivity of the docking algorithm to starting orientation was a consequence of tight fit of respective ligand structures with their protein target sites for these three cases and can be circumvented by using finer rotational sampling grids for the ligand. Boltzmann statistics derived from calculated interaction energies successfully extracted the observed ribonuclease A cytidylic acid complex from a manifold of similar interaction energies. The proposed method was able to reproduce the observed crystallographic complex by using a dynamical description of ligand. © 1997 Wiley-Liss Inc.
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    Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 523-544 
    Details
    ISSN: 0887-3585
    Keywords: protonation equilibrium ; protein conformation ; continuum electrostatics ; potential of mean force ; force fields ; mean field theory ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Solution pH is a determinant parameter on protein function and stability, and its inclusion in molecular dynamics simulations is attractive for studies at the molecular level. Current molecular dynamics simulations can consider pH only in a very limited way, through a somewhat arbitrary choice of a set of fixed charges on the titrable sites. Conversely, continuum electrostatic methods that explicitly treat pH effects assume a single protein conformation whose choice is not clearly defined. In this paper we describe a general method that combines both titration and conformational freedom. The method is based on a potential of mean force for implicit titration and combines both usual molecular dynamics and pH-dependent calculations based on continuum methods. A simple implementation of the method, using a mean field approximation, is presented and applied to the bovine pancreatic trypsin inhibitor. We believe that this constant-pH molecular dynamics method, by correctly sampling both charges and conformation, can become a valuable help in the understanding of the dependence of protein function and stability on pH. © 1997 Wiley-Liss Inc.
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    The reaction pathway of the isomerization of d-xylose catalyzed by the enzyme d-xylose isomerase: A theoretical study (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 545-555 
    Details
    ISSN: 0887-3585
    Keywords: semi-empirical ; PM3 method ; quantum mechanics ; molecular mechanics ; reaction pathway ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Different pathways of the metal-induced isomerization of D-xylose to D-xylulose are investigated and compared in detail using energy minimization and molecular dynamics simulation. Two theoretical models are constructed for the reaction: in vacuum and in the enzyme D-xylose isomerase. The vacuum model is constructed based on the X-ray structure of the active site of D-xylose isomerase. It contains the atoms directly involved in the reaction and is studied using a semi-empirical molecular orbital method (PM3). The model in the enzyme includes the effects of the enzyme environment on the reaction using a combined quantum mechanical and molecular mechanical potential. For both models, the structures of the reactants, products, and intermediate complexes along the isomerization pathway are optimized. The effects of the position of the “catalytic Mg2+ ion” on the energies of the reactions are studied. The results indicate: 1) in vacuum, the isomerization reaction is favored when the catalytic metal cation is at site A, which is remote from the substrate; 2) in the enzyme, the catalytic metal cation, starting from site A, moves and stays at site B, which is close to the substrate; analysis of the charge redistribution of the active site during the catalytic process shows that the metal ion acts as a Lewis acid to polarize the substrate and catalyze the hydride shift; these results are consistent with previous experimental observations; and 3) Lys183 plays an important role in the isomerization reaction. The ε-NH3+ group of its side chain can provide a proton to the carboxide ion of the substrate to form a hydroxyl group after the hydride shift step. This role of Lys183 has not been suggested before. Based on our calculations, we believe that this is a reasonable mechanism and consistent with site-directed mutation experiments. © 1997 Wiley-Liss Inc.
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    Purification and preliminary crystallographic studies on the sporulation response regulatory phosphotransferase protein, spo0B, from Bacillus subtilis (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 597-600 
    Details
    ISSN: 0887-3585
    Keywords: signal transduction ; phosphotransferase ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The phosphotransferase protein Spo0B, a component of the sporulation signal transduction system in Bacillus subtilis was expressed from the Escherichia coli strain BL21DE3. It was purified, crystallized, and 2.25 Å data measured using the synchrotron source at the Stanford Linear Accelerator Center. The search for heavy atom derivatives is in progress. © 1997 Wiley-Liss Inc.
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    Crystallization and preliminary x-ray analysis of the flavoenzyme vanillyl-alcohol oxidase from Penicillium Simplicissimum (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 601-603 
    Details
    ISSN: 0887-3585
    Keywords: FAD ; catalysis ; X-ray crystallography ; molecular symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vanillyl-alcohol oxidase catalyses the oxidation of several 4-hydroxybenzyl alcohols by using 8-α-(N3-histidyl)-FAD as a covalently bound prosthetic group. Crystals of vanillyl-alcohol oxidase from Penicillium simplicissimum have been grown by using the vapor diffusion technique. The space group was found to be I4, with cell dimensions a = b = 140.5 Å, c = 132.9 Å. Diffraction data have been recorded to 3.2 Å resolution by using a laboratory source and to 2.5 Å resolution on flash freezing the crystal at the ELETTRA Synchrotron X-ray diffraction beam line. Proteins 27:601-603, 1997. © 1997 Wiley-Liss Inc.
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    NADP-Dependent enzymes. I: Conserved stereochemistry of cofactor binding (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 10-28 
    Details
    ISSN: 0887-3585
    Keywords: nicotinamide adenine dinucleotide ; nicotinamide adenine dinucleotide phosphate ; dinucleotide binding pockets ; molecular recognition ; protein structures ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The ubiquitous redox cofactors nicotinamide adenine dinucleotides [NAD and NADP] are very similar molecules, despite their participation in substantially different biochemical processes. NADP differs from NAD in only the presence of an additional phosphate group esterified to the 2′-hydroxyl group of the ribose at the adenine end and yet NADP is confined with few exceptions to the reactions of reductive biosynthesis, whereas NAD is used almost exclusively in oxidative degradations. The discrimination between NAD and NADP is therefore an impressive example of the power of molecular recognition by proteins. The many known tertiary structures of NADP complexes affords the possibility for an analysis of their discrimination. A systematic analysis of several crystal structures of NAD(P)-protein complexes show that: 1) the NADP coenzymes are more flexible in conformation than those of NAD; 2) although the protein-cofactor interactions are largely conserved in the NAD complexes, they are quite variable in those of NADP; and 3) in both cases the pocket around the nicotinamide moiety is substrate dependent. The conserved and variable interactions between protein and cofactors in the respective binding pockets are reported in detail. Discrimination between NAD and NADP is essentially a consequence of the overall pocket and not of a few residues. A clear fingerprint in NAD complexes is a carboxylate side chain that chelates the diol group at the ribose near the adenine, whereas in NADP complexes an arginine side chain faces the adenine plane and interacts with the phosphomonoester. The latter type of interaction might be a general feature of recognition of nucleotides by proteins. Other features such as strand-like hydrogen bonding between the NADP diphosphate moeties and the protein are also significant. The NADP binding pocket properties should prove useful in protein engineering and design. © 1997 Wiley-Liss Inc.
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    NADP-Dependent enzymes. II: Evolution of the mono- and dinucleotide binding domains (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 29-40 
    Details
    ISSN: 0887-3585
    Keywords: molecular evolution ; nicotinamide adenine dinucleotide ; nicotinamide adenine dinucleotide phosphate ; dinucleotide bonding domains ; mononucleotide binding domains ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Nicotinamide adenine dinucleotides [NAD and NADP with both referred to as NAD(P)] are among the more diffuse redox cofactors. Despite their stereochemical similarity where the only difference is a phosphomonoester on the ribose near the adenine of NADP, they show different biochemical reactivities with NAD behaving as an oxidant and NADP as a reductant. NAD(P)-dependent enzymes generally share a common open α/β fold with few exceptions only recently structurally characterized. This study of the molecular evolution of the NAD(P) binding domains, possible given the large number of known molecular structures, addresses two main questions: 1) can a common fold exist in different biological systems (divergent evolution) and 2) does a relationship exist among similar biological systems that display different folds (convergent evolution)? Both the structures of mono- and dinucleotide binding domains have been classified by cluster analysis based on the similarity evaluated by their main chain Cα superposition. Moreover, the cofactor conformations and the stereochemical characteristics of their pockets have also been classified by analogous methods on the basis of the published tertiary structures. Two primary results appear: 1) the classification of the mononucleotide binding domains is different from that of the dinucleotide binding folds and 2) both divergent and convergent evolutionary pathways can be hypothesized, the latter less frequently observed and less pronounced but nevertheless evident. The generally accepted hypothesis that dinucleotide binding domains have evolved by gene duplication of primordial genes coding for the smaller mononucleotide binding domains is acceptable but the two halves of the resulting dinucleotide binding domains are evolutionarly uncorrelated. The NH2-terminal mononucleotide binding domain is less variable than the COOH-terminal half, probably because it involves the binding of the ADP moiety of NAD(P) invariant in all examined systems. There is evidence to postulate that evolutionary pathways for NAD(P)-dependent enzymes are both divergent and convergent. In fact, nearly all combinations of similarity/dissimilarity in overall fold, cofactor conformation, and cofactor binding pocket structural characteristics for each enzyme pair examined are possible. The NAD(P)-dependent enzymes apparently provide a canonical example of an evolutionary principle that “anything goes.” © 1997 Wiley-Liss Inc.
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    Helical preferences of alanine, glycine, and aminoisobutyric homopeptides (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 83-93 
    Details
    ISSN: 0887-3585
    Keywords: helical conformations ; polypeptides ; homopeptides ; apolar solvents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The stability between helical conformations of homopeptides of alanine, glycine, and aminoisobutyric acid has been studied by means of quantum-mechanical methods. The influence of peptide length on the relative stability between helical conformations has also been analyzed by means of systematic studies for peptides of size up to 11 residues. Finally, the influence of the solvent has been examined by using self-consistent reaction field methods. The results provide a detailed picture of the modulation exerted by these factors on the helical preferences of these peptides. © 1997 Wiley-Liss Inc.
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    An evolutionary treasure: unification of a broad set of amidohydrolases related to urease (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 72-82 
    Details
    ISSN: 0887-3585
    Keywords: protein family analysis ; genome analysis ; homology modeling ; molecular evolution ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The recent determination of the three-dimensional structure of urease revealed striking similarities of enzyme architecture to adenosine deaminase and phosphotriesterase, evidence of a distant evolutionary relationship that had gone undetected by one-dimensional sequence comparisons. Here, based on an analysis of conservation patterns in three dimensions, we report the discovery of the same active-site architecture in an even larger set of enzymes involved primarily in nucleotide metabolism. As a consequence, we predict the three-dimensional fold and details of the active site architecture for dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases, and proteins involved in animal neuronal development. Two member families are common to archaea, eubacteria, and eukaryota. Thirteen other functions supported by the same structural motif and conserved chemical mechanism apparently represent later adaptations for different substrate specificities in different cellular contexts. © 1997 Wiley-Liss Inc.
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    Mechanical property of a TIM-barrel protein (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 109-116 
    Details
    ISSN: 0887-3585
    Keywords: normal mode analysis ; Delauney tessellation ; bond distance ; compressibility ; volume fluctuation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The mechanical response of a TIM-barrel protein to an applied pressure has been studied. We generated structures under an applied pressure by assuming the volume change to be a linear function of normal mode variables. By Delaunay tessellation, the space occupied by protein atoms is divided uniquely into tetrahedra, whose four vertices correspond to atomic positions. Based on the atoms that define them, the resulting Delaunay tetrahedra are classified as belonging to various secondary structures in the protein. The compressibility of various regions identified with respect to secondary structural elements in this protein is obtained from volume changes of respective regions in two structures with and without an applied pressure. We found that the β barrel region located at the core of the protein is quite soft. The interior of the β barrel, occupied by side chains of β strands, is the softest. The helix, strand, and loop segments themselves are extremely rigid, while the regions existing between these secondary structural elements are soft. These results suggest that the regions between secondary structural elements play an important role in protein dynamics. Another aspect of tetrahedra, referred to as bond distance, is introduced to account for rigidities of the tetrahedra. Bond distance is a measure of separation of the atoms of a tetrahedron in terms of number of bonds along the polypeptide chain or side chains. Tetrahedra with longer bond distances are found to be softer on average. From this behavior, we derive a simple empirical equation, which well describes the compressibilities of various regions. © 1997 Wiley-Liss Inc.
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    Protein Methods, 2nd edit., by Daniel M. Bollag, Michael D. Rozycki, and Stuart J. Edelstein. New York: Wiley-Liss, Inc. (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 140-140 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    NMR as a Structural Tool for Macromolecules: Current Status and Future Directions, edited by B.D. Nageswara Rao and M.D. Kemple (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 141-141 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Comment to Daura, X., et al., Proteins 25:89-103, 1996. (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 143-143 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    NMR studies on the flexibility of nucleoside diphosphate kinase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 150-152 
    Details
    ISSN: 0887-3585
    Keywords: Dictyostelium NDP kinase ; human NDP kinase ; nm23 ; NMR dynamic filtering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human NDP kinase B, product of the nm23-H2 gene, binds DNA. It has been suggested that a helix hairpin on the protein surface, part of the nucleotide substrate binding site, could accommodate DNA binding by swinging away. The presence of flexible regions was therefore investigated by 1H NMR dynamic filtering. Although TOCSY peaks could be assigned to five residues at the N terminus of Dictyostelium NDP kinase, no flexible region was detected in the human enzyme. These data favor the idea that the protein offers different binding sites to mono- and polynucleotides. Proteins 28:150-152, 1997. © 1997 Wiley-Liss Inc.
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    The kinetics of protein-protein recognition (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 153-161 
    Details
    ISSN: 0887-3585
    Keywords: collision theory ; protein-protein association ; electrostatic interactions ; dipole steering ; barnase-barstar complex ; rotational-translational entropy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We examine a simple kinetic model for association that incorporates the basic features of protein-protein recognition within the rigid body approximation, that is, when no large conformation change occurs. Association starts with random collision at the rate kcoll predicted by the Einstein-Smoluchowski equation. This creates an encounter pair that can evolve into a stable complex if and only if the two molecules are correctly oriented and positioned, which has a probability pr. In the absence of long-range interactions, the bimolecular rate of association is pr kcoll. Long-range electrostatic interactions affect both kcoll and pr. The collision rate is multiplied by qt, a factor larger than 1 when the molecules carry net charges of opposite sign as coulombic attraction makes collisions more frequent, and less than 1 in the opposite case. The probability pr is multiplied by a factor qr that represents the steering effect of electric dipoles, which preorient the molecules before they collide. The model is applied to experimental data obtained by Schreiber and Fersht (Nat. Struct. Biol. 3:427-431, 1996) on the kinetics of barnase-barstar association. When long-range electrostatic interactions are fully screened or mutated away, qtqr ≈1, and the observed rate of productive collision is pr kcoll ≈105 M-1 · s-1. Under these conditions, pr ≈1.5 · 10-5 is determined by geometric constraints corresponding to a loss of rotational freedom. Its value is compatible with computer docking simulations and implies a rotational entropy loss ΔSrot ≈ 22 e.u. in the transition state. At low ionic strength, long-range electrostatic interactions accelerate barnase-barstar association by a factor qtqrof up to 105 as favorable charge-charge and charge-dipole interactions work together to make it much faster than free diffusion would allow. Proteins 28:153-161, 1997. © 1997 Wiley-Liss Inc.
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    Role of electrostatics at the catalytic metal binding site in xylose isomerase action: Ca2+-inhibition and metal competence in the double mutant D254E/D256E (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 183-193 
    Details
    ISSN: 0887-3585
    Keywords: D-xylose isomerase ; protein crystallography ; enzyme kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The catalytic metal binding site of xylose isomerase from Arthrobacter B3728 was modified by protein engineering to diminish the inhibitory effect of Ca2+ and to study the competence of metals on catalysis. To exclude Ca2+ from Site 2 a double mutant D254E/D256E was designed with reduced space available for binding. In order to elucidate structural consequences of the mutation the binary complex of the mutant with Mg2+ as well as ternary complexes with bivalent metal ions and the open-chain inhibitor xylitol were crystallized for x-ray studies. We determined the crystal structures of the ternary complexes containing Mg2+, Mn2+, and Ca2+ at 2.2 to 2.5 Å resolutions, and refined them to R factors of 16.3, 16.6, and 19.1, respectively. We found that all metals are liganded by both engineered glutamates as well as by atoms O1 and O2 of the inhibitor. The similarity of the coordination of Ca2+ to that of the cofactors as well as results with Be2+ weaken the assumption that geometry differences should account for the catalytic noncompetence of this ion. Kinetic results of the D254E/D256E mutant enzyme showed that the significant decrease in Ca2+ inhibition was accompanied by a similar reduction in the enzymatic activity. Qualitative argumentation, based on the protein electrostatic potential, indicates that the proximity of the negative side chains to the substrate significantly reduces the electrostatic stabilization of the transition state. Furthermore, due to the smaller size of the catalytic metal site, no water molecule, coordinating the metal, could be observed in ternary complexes of the double mutant. Consequently, the proton shuttle step in the overall mechanism should differ from that in the wild type. These effects can account for the observed decrease in catalytic efficiency of the D254E/D256E mutant enzyme. Proteins 28:183-193, 1997. © 1997 Wiley-Liss Inc.
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    Expression, crystallization and preliminary X-ray diffraction study of FtsY, the docking protein of the signal recognition particle of E. coli (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 285-288 
    Details
    ISSN: 0887-3585
    Keywords: SRP ; SRP receptor ; GTPase ; expression ; crystallization ; x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: FtsY is the docking protein or SRα homologue in E. coli. It is involved in targeting secretory proteins to the cytoplasmic membrane by interacting with the signal recognition particle, controlled by guanosine 5′-triphosphate. Two different constructs have been used in crystallization studies: the full-length protein and a truncated fragment with a his-tag at the C terminus. Only the second construct resulted in crystals suitable for x-ray diffraction. The crystals belong to the monoclinic space group P21 with cell dimensions a = 32.20 Å, b = 79.57 Å, c = 59.21 Å, and β = 94.45, and contain one molecule per asymmetric unit. At cryogenic temperatures the crystals diffract to a resolution limit of 2.5 Å by using a rotating anode, and beyond 1.8 Å by using synchrotron radiation. Proteins 28:285-288, 1997. © 1997 Wiley-Liss Inc.
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    Purification and crystallization of Pseudomonas aeruginosa chloramphenicol acetyltransferase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 298-300 
    Details
    ISSN: 0887-3585
    Keywords: chloramphenicol acetyltransferase ; protein structure ; x-ray crystallography ; antibiotic resistance ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A chloramphenicol acetyltransferase from Pseudomonas aeruginosa genomic DNA has been overexpressed, refolded, purified, and crystallized. Crystals suitable for a three-dimensional x-ray structure determination were obtained from solutions of polyethyleneglycol methyl ether 2000 containing NiCl2 at pH 8.5. These crystals belong to the cubic space group P41/332 (a = 154.8 Å) and diffract x-rays to ≈3.2 Å resolution. Proteins 28:298-300, 1997. © 1997 Wiley-Liss Inc.
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    Generation of pseudonative protein structures for threading (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 522-529 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein fold recognition ; empirical energy function ; protein folding force field ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The threading approach to protein structure prediction suffers from the limited number of substantially different folds available as templates. A method is presented for the generation of artificial protein structures, amenable to threading, by modification of native ones. The artificial structures so generated are compared to the native ones and it is shown that, within the accuracy of the pseudoenergy function or force field used, these two types of structures appear equally useful for threading. Since a multitude of pseudonative artificial structures can be generated per native structure, the pool of pseudonative template structures for threading can be enormously enlarged by the inclusion of the pseudonative artificial structures. Proteins 28:522-529, 1997. © 1997 Wiley-Liss, Inc.
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    Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 481-493 
    Details
    ISSN: 0887-3585
    Keywords: model-free approach ; generalized order parameters ; protein dynamics ; NMR relaxation ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation experiments and molecular dynamics (MD) simulations commonly are used to describe the intramolecular dynamical properties of proteins. To assess the relative accuracy and precision of experimental and simulated model-free parameters, three independent data sets derived from backbone 15N NMR relaxation experiments and two independent data sets derived from MD simulations of Escherichia coli ribonuclease HI are compared. The widths of the distributions of the differences between the order parameters for pairs of NMR data sets are congruent with the uncertainties derived from statistical analyses of individual data sets; thus, current protocols for analyzing NMR data encapsulate random uncertainties appropriately. Large differences in order parameters for certain residues are attributed to systematic differences between samples for intralaboratory comparisons and unknown, possibly magnetic field-dependent, experimental effects for interlaboratory comparisons. The widths of distributions of the differences between the order parameters for two NMR sets are similar to widths of distributions for an NMR and an MD set or for two MD sets. The linear correlations between the order parameters for an MD set and an NMR set are within the range of correlations observed between pairs of NMR sets. These comparisons suggest that the NMR and MD generalized order parameters for the backbone amide N - H bond vectors are of comparable accuracy for residues exhibiting motions on a fast time scale (〈100 ps). Large discrepancies between NMR and MD order parameters for certain residues are attributed to the occurrence of “rare” motional events over the simulation trajectories, the disruption of an element of secondary structure in one of the simulations, and lack of consensus among the experimental data sets. Consequently, (easily detectable) severe distortions of local protein structure and infrequent motional events in MD simulations appear to be the most serious artifacts affecting the accuracy and precision, respectively, of MD order parameters relative to NMR values. In addition, MD order parameters for motions on a fast (〈100 ps) timescale are more precisely determined than their NMR counterparts, thereby permitting more detailed dynamic characterization of biologically important residues by MD simulation than is sometimes possible by experimental methods. Proteins 28:481-493, 1997. © 1997 Wiley-Liss, Inc.
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    On the reaction mechanism of class Pi glutathione S-transferase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 530-542 
    Details
    ISSN: 0887-3585
    Keywords: glutathione S-transferase ; GST class Pi ; enzyme mechanism ; X-ray diffraction ; molecular dynamics ; free energy perturbation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Theoretical calculations were performed to examine the ionization of the phenolic group of Tyr7 and the thiol group of glutathione in aqueous solution and in the protein class-pi glutathione S-transferase (GST-Pi). Three model systems were considered for simulations in the protein environment: the free enzyme, the complex between glutathione and the enzyme, and the complex between 1-chloro-2.4-dinitrobenzene, glutathione, and the enzyme. The structures derived from Molecular Dynamics simulations were compared with the crystallographic data available for the complex between the inhibitor S-(p-nitrobenzyl)glutathione and GST-Pi, the glutathione-bound form of GST-Pi, and the free enzyme carboxymethylated in Cys47. Free-energy perturbation techniques were used to determine the thermodynamics quantities for ionization of the phenol and thiol groups. The functional implications of Tyr7 in the activation of the glutathione thiol group are discussed in the light of present results, which in agreement with previous studies suggest that Tyr7 in un-ionized form contributes to the catalytic process of glutathione S-transferase, the thiolate anion being stabilized by hydrogen bond with Tyr7 and by interactions with hydrating water molecules. Proteins 28:530-542, 1997 © 1997 Wiley-Liss, Inc.
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    Molecular mechanic study of nerve agent O-ethyl S-[2-(diisopropylamino)ethyl]methylphosphonothioate (VX) bound to the active site of Torpedo californica acetylcholinesterase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 543-555 
    Details
    ISSN: 0887-3585
    Keywords: serine esterase ; enantiomeric inhibition ; stochastic dynamics ; ab initio calculations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Herein a molecular mechanic study of the interaction of a lethal chemical warfare agent, O-ethyl S-[2-(diisopropylamino)ethyl]methylphosphonothioate (also called VX), with Torpedo californica acetylcholinesterase (TcAChE) is discussed. This compound inhibits the enzyme by phosphonylating the active site serine. The chirality of the phosphorus atom induces an enantiomeric inhibitory effect resulting in an enhanced anticholinesterasic activity of the SP isomer (VXS) versus its RP counterpart (VXR). As formation of the enzyme-inhibitor Michaelis complex is known to be a crucial step in the inhibitory pathway, this complex was addressed by stochastic boundary molecular dynamics and quantum mechanical calculations. For this purpose two models of interaction were analyzed: in the first, the leaving group of VX was oriented toward the anionic subsite of TcAChE, in a similar way as it has been suggested for the natural substrate acetylcholine; in the second, it was oriented toward the gorge entrance, placing the active site serine in a suitable position for a backside attack on the phosphorus atom. This last model was consistent with experimental data related to the high inhibitory effect of this compound and the difference in activity observed for the two enantiomers. Proteins 28:543-555, 1997. © 1997 Wiley-Liss, Inc.
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    Escher: A new docking procedure applied to the reconstruction of protein tertiary structure (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 556-567 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; automated docking ; protein domains ; secondary structure elements ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Evaluation of Surface Complementarity, Hydrogen bonding, and Electrostatic interaction in molecular Recognition (ESCHER) is a new docking procedure consisting of three modules that work in series. The first module evaluates the geometric complementarity and produces a set of rough solutions for the docking problem. The second module identifies molecular collisions within those solutions, and the third evaluates their electrostatic complementarity. We describe the algorithm and its application to the docking of cocrystallized protein domains and unbound components of protein-protein complexes. Furthermore, ESCHER has been applied to the reassociation of secondary and supersecondary structure elements. The possibility of applying a docking method to the problem of protein structure prediction is discussed. Proteins 28:556-567, 1997. © 1997 Wiley-Liss, Inc.
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    Flexible glycine rich motif of Escherichia coli deoxyuridine triphosphate nucleotidohydrolase is important for functional but not for structural integrity of the enzyme (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 568-579 
    Details
    ISSN: 0887-3585
    Keywords: Gly-rich motif ; phosphate binding P-loop ; Motif 5 of dUTPases ; MgdUDP binding ; limited trypsinolysis ; circular dichroism spectroscopy ; secondary structure determination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Deoxyuridine triphosphate nucleotidohydrolase (dUTPase), a ubiquitous enzyme of DNA metabolism, has been implicated as a novel target of anticancer and antiviral drug design. This task is most efficiently accomplished by X-ray crystallography of the relevant protein-inhibitor complexes. However, the topic of the present investigation, a glycine-rich strictly conserved structural motif of dUTPases, could not be located in the crystal structure of the Escherichia coli enzyme, probably due to its increased flexibility. The present work shows that removal of a C-terminal 11-residue fragment, including this motif, by limited trypsinolysis strongly impairs catalytic activity. Kinetic analysis of the intact and digested variants showed that kcat decreases 40-fold, while KM increases less than twofold upon digestion. The tryptic site was identified by mass spectrometry, amino acid analysis and N-terminal sequencing. The shortened enzyme variant retains the secondary, tertiary, and quaternary (trimeric) structure of the intact species as suggested by UV absorption, fluorescence and circular dichroism spectroscopy, and analytical gel filtration. Moreover, binding affinity of the shortened variant toward the substrate analogue MgdUDP is identical to the one displayed by the intact enzyme. I conclude that the glycine-rich motif is functionally relevant for E. coli dUTPase. It may play a role in enzymatic catalysis by contributing to the formation of the catalytically potent enzyme-substrate complex. Proteins 28:568-579, 1997. © 1997 Wiley-Liss, Inc.
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    Hydrophobic patches on protein subunit interfaces: Characteristics and prediction (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 333-343 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; oligomeric structure ; subunit interface ; molecular recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic patches, defined as clusters of neighboring apolar atoms deemed accessible on a given protein surface, have been investigated on protein subunit interfaces. The data were taken from known tertiary structures of multimeric protein complexes. Amino acid composition and preference, patch size distribution, and patch contact complementarity across associating subunits were examined and compared with hydrophobic patches found on the solvent-accessible surface of the multimeric complexes. The largest or second largest patch on the accessible surface of the entire subunit was involved in multimeric interfaces in 90% of the cases. These results should prove useful for subunit design and engineering as well as for prediction of subunit interface regions. Proteins 28:333-343, 1997. © 1997 Wiley-Liss, Inc.
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    Refined solution structure of the anti-mammal and anti-insect LqqIII scorpion toxin: Comparison with other scorpion toxins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 360-374 
    Details
    ISSN: 0887-3585
    Keywords: scorpion ; toxin ; NMR ; structure ; hydrophobic potentials ; electrostatic potentials ; CSαβ motif ; sodium channel ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution structure of the anti-mammal and anti-insect LqqIII toxin from the scorpion Leiurus quinquestriatus quinquestriatuswas refined and compared with other long-chain scorpion toxins. This structure, determined by 1H-NMR and molecular modeling, involves an α-helix (18-29) linked to a three-stranded β-sheet (2-6, 33-39, and 43-51) by two disulfide bridges. The average RMSD between the 15 best structures and the mean structure is 0.71 Å for Cα atoms. Comparison between LqqIII, the potent anti-mammal AaHII, and the weakly active variant-3 toxins revealed that the LqqIII three-dimensional structure is closer to that of AaHII than to the variant-3 structure. Moreover, striking analogies were observed between the electrostatic and hydrophobic potentials of LqqIII and AaHII. Several residues are well conserved in long-chain scorpion toxin sequences and seem to be important in protein structure stability and function. Some of them are involved in the CSαβ (Cysteine Stabilized α-helix β-sheet) motif. A comparison between the sequences of the RII rat brain and the Drosophila extracellular loops forming scorpion toxin binding-sites of Na+ channels displays differences in the subsites interacting with anti-mammal or anti-insect toxins. This suggests that hydrophobic as well as electrostatic interactions are essential for the binding and specificity of long-chain scorpion toxins. Proteins 28:360-374, 1997 © 1997 Wiley-Liss, Inc.
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    A potential processing enzyme in prokaryotes: Oligopeptidase B, a new type of serine peptidase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 375-379 
    Details
    ISSN: 0887-3585
    Keywords: protease II ; prohormone convertase ; paired basic amino acid cleaving enzyme ; ionic strength ; substrate inhibition ; rate-limiting step ; kinetic deuterium isotope effect ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Basic amino acid pairs in polypeptides represent important markers for processing enzymes to produce biologically active products. Such enzymes related to the serine peptidase subtilisin have recently been identified in eukaryotes. Herein is described and kinetically characterized a new type of processing enzyme, oligopeptidase B, which is encountered in the prokaryote Escherichia coli, and belongs to the prolyl oligopeptidase family of serine peptidases. The enzyme hydrolyzes the peptides at the carboxy end of dibasic sites by two orders of magnitude faster with respect to monobasic substrates. The kcat/Km is extremely high, 63 μM-1 s-1, for the substrate benzyloxycarbonyl-L-arginyl-L-arginyl-7-(4- methylcoumaryl)amide. The bell-shaped pH dependence of the rate constant is perturbed by some ionizing group(s). This effect is abolished at 1 M NaCl. In addition, high ionic strength inhibits the reaction considerably by increasing Km, which is indicative of an electrostatic interaction between the arginyl residues and the enzymatic carboxy groups. In distinction from that found with most serine endopeptidases, kinetic deuterium isotope measurements with oligopeptidase B indicate that the rate-limiting step of the reaction is a physical step rather than a chemical one characterized by general acid/base catalysis. The present result will contribute to our understanding of the processing phenomena in prokaryotes, as well as in higher organisms. Proteins 28:375-379, 1997. © 1997 Wiley-Liss, Inc.
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    Picosecond dynamical changes on denaturation of yeast phosphoglycerate kinase revealed by quasielastic neutron scattering (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 380-387 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; denatured states ; fast diffusive motions ; internal dynamics ; phosphoglycerate kinase ; incoherent quasielastic neutron scattering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Quasielastic neutron scattering experiments performed on yeast phosphoglycerate kinase in the native form and denatured in 1.5 M guanidinium chloride reveal a change in the fast (picosecond time scale) diffusive internal dynamics of the protein. The momentum and energy transfer dependences of the scattering for both states are fitted by an analytical model in which, on the experimentally accessible picosecond time scale and angstrom length scale, the dynamics of a fraction of the nonexchangeable hydrogens in the protein is described as a superposition of vibrations with uniform diffusion in a sphere, the rest of the hydrogens undergoing only vibrational motion. The fraction diffusing changes, from ≈60% in the native protein to ≈82% in the denatured protein. The radius of the sphere also changes slightly, from ≈1.8 Å in the native protein to ≈2.2 Å in the denatured protein. Possible implications of these results for the general protein folding problem are discussed. Proteins 28:380-387, 1997 © 1997 Wiley-Liss, Inc.
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    Predicting helical segments in proteins by a helix-coil transition theory with parameters derived from a structural database of proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 344-359 
    Details
    ISSN: 0887-3585
    Keywords: helix stabilizing/destabilizing interactions ; helix-capping motifs ; helical boundaries ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A novel helix-coil transition theory has been developed. This new theory contains more types of interactions than similar theories developed earlier. The parameters of the models were obtained from a database of 351 nonhomologous proteins. No manual adjustment of the parameters was performed. The interaction parameters obtained in this manner were found to be physically meaningful, consistent with current understanding of helix stabilizing/destabilizing interactions. Novel insights into helix stabilizing/destabilizing interactions have also emerged from this analysis. The theory developed here worked well in sorting out helical residues from amino acid sequences. If the theory was forced to make prediction on every residue of a given amino acid sequence, its performance was the best among ten other secondary structural prediction algorithms in distinguishing helical residues from nonhelical ones. The theory worked even better if one only required it to make prediction on residues that were “predictable” (identifiable by the theory); 〉90% predictive reliability could be achieved. The helical residues or segments identified by the helix-coil transition theory can be used as secondary structural contraints to speed up the prediction of the three-dimensional structure of a protein by reducing the dimension of a computational protein folding problem. Possible further improvements of this helix-coil transition theory are also discussed. Proteins 28:344-359, 1997. © 1997 Wiley-Liss, Inc.
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    Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 292-308 
    Details
    ISSN: 0887-3585
    Keywords: knowledge-based potentials ; virtual bonds ; coupling between bond torsions and bond angles ; secondary structure propensities ; inverse folding experiments ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A statistical analysis of known structures is made for an assessment of the utility of short-range energy considerations. For each type of amino acid, the potentials governing (1) the torsions and bond angle changes of virtual Cα-Cα bonds and (2) the coupling between torsion and bond angle changes are derived. These contribute approximately -2 RT per residue to the stability of native proteins, approximately half of which is due to coupling effects. The torsional potentials for the α-helical states of different residues are verified to be strongly correlated with the free-energy change measurements made upon single-site mutations at solvent-exposed regions. Likewise, a satisfactory correlation is shown between the β-sheet potentials of different amino acids and the scales from free-energy measurements, despite the role of tertiary context in stabilizing β-sheets. Furthermore, there is excellent agreement between our residue-specific potentials for α-helical state and other thermodynamic based scales. Threading experiments performed by using an inverse folding protocol show that 50 of 62 test structures correctly recognize their native sequence on the basis of short-range potentials. The performance is improved to 55, upon simultaneous consideration of short-range potentials and the nonbonded interaction potentials between sequentially distant residues. Interactions between near residues along the primary structure, i.e., the local or short-range interactions, are known to be insufficient, alone, for understanding the tertiary structural preferences of proteins alone. Yet, knowledge of short-range conformational potentials permits rationalizing the secondary structure propensities and aids in the discrimination between correct and incorrect tertiary folds. Proteins 29:292-308, 1997. © 1997 Wiley-Liss, Inc.
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    Solution structure of maurotoxin, a scorpion toxin from Scorpio maurus, with high affinity for voltage-gated potassium channels (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 321-333 
    Details
    ISSN: 0887-3585
    Keywords: scorpion neurotoxin ; NMR ; structure ; potassium channel ; maurotoxin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Maurotoxin (MTX), purified from the scorpionid Scorpio maurus is a potent ligand for potassium channels. It shows a broad specificity as being active on Kv1.1 (Kd = 37 nM), Kv1.2 (Kd = 0.8 nM), Kv1.3 (Kd = 150 nM) voltage-gated potassium channels, as well as on small-conductance calcium-activated potassium channels. It has a unique disulfide pairing among the scorpion toxins family. The solution structure of MTX has been determined by 2D-NMR techniques, which led to the full description of its 3D conformation: a bended helix from residues 6 to 16 connected by a loop to a two-stranded antiparallel β sheet (residues 23 to 26 and 28 to 31). The interaction of MTX with the pore region of the Kv1.2 potassium channel has been modeled according to their charge anisotropy. The structure of MTX is similar to other short scorpion toxins despite its peculiar disulfide pairing. Its interaction with the Kv1.2 channel involves a dipole moment, which guides and orients the toxin onto the pore, toward the binding site, and which thus is responsible for the specificity. Proteins 29:321-333, 1997. © 1997 Wiley-Liss, Inc.
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    Glucoamylase structural, functional, and evolutionary relationships (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 334-347 
    Details
    ISSN: 0887-3585
    Keywords: evolution ; glucoamylase ; hydrophobic folding ; protein parsimony analysis ; structure/function ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To correlate structural features with glucoamylase properties, a structure-based multisequence alignment was constructed using information from catalytic and starch-binding domain models. The catalytic domain is composed of three hydrophobic folding units, the most labile and least hydrophobic of them being missing in the most stable glucoamylase. The role of O-glycosylation in stabilizing the most hydrophobic folding unit, the only one where thermostabilizing mutations with unchanged activity have been made, is described. Differences in both length and composition of interhelical loops are correlated with stability and selectivity characteristics. Two new glucoamylase subfamilies are defined by using homology criteria. Protein parsimony analysis suggests an ancient bacterial origin for the glucoamylase gene. Increases in length of the belt surrounding the active site, degree of O-glycosylation, and length of the linker probably correspond to evolutionary steps that increase stability and secretion levels of Aspergillus-related glucoamylases. Proteins 29:334-347, 1997. © 1997 Wiley-Liss, Inc.
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    Insights into thermal resistance of proteins from the intrinsic stability of their α-helices (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 309-320 
    Details
    ISSN: 0887-3585
    Keywords: protein thermostability ; α-helix stability ; RecA protein family ; L-lactate dehydrogenases ; seryl-tRNA synthetases ; aspartate aminotransferases ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To investigate the role of α helices in protein thermostability, we compared energy characteristics of α helices from thermophilic and mesophilic proteins belonging to four protein families of known three-dimensional structure, for at least one member of each family. The changes in intrinsic free energy of α-helix formation were estimated using the statistical mechanical theory for describing helix/coil transitions in peptide helices [Munoz, V., Serrano, L. Nature Struc. Biol. 1:399-409, 1994; Munoz, V., Serrano, L. J. Mol. Biol. 245:275-296, 1995; Munoz, V., Serrano, L. J. Mol. Biol. 245:297-308, 1995]. Based on known sequences of mesophilic and thermophilic RecA proteins we found that (1) a high stability of α helices is necessary but is not a sufficient condition for thermostability of RecA proteins, (2) the total helix stability, rather than that of individual helices, is the factor determining protein thermostability, and (3) two facets of intrahelical interactions, the intrinsic helical propensities of amino acids and the side chain-side chain interactions, are the main contributors to protein thermostability. Similar analysis applied to families of L-lactate dehydrogenases, seryl-tRNA synthetases, and aspartate amino transferases led us to conclude that an enhanced total stability of α helices is a general feature of many thermophilic proteins. The magnitude of the observed decrease in intrinsic free energy on α-helix formation of several thermoresistant proteins was found to be sufficient to explain the experimentally determined increase of their thermostability. Free energies of intrahelical interactions of different RecA proteins calculated at three temperatures that are thought to be close to its normal environmental conditions were found to be approximately equal. This indicates that certain flexibility of RecA protein structure is an essential factor for protein function. All RecA proteins analyzed fell into three temperature-dependent classes of similar α-helix stability (ΔGint = 45.0 ± 2.0 kcal/mol). These classes were consistent with the natural origin of the proteins. Based on the sequences of protein α helices with optimized arrangement of stabilizing interactions, a natural reserve of RecA protein thermoresistance was estimated to be sufficient for conformational stability of the protein at nearly 200°C. Proteins 29:309-320, 1997. © 1997 Wiley-Liss, Inc.
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    Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasteurianum ferredoxin as an example (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 348-358 
    Details
    ISSN: 0887-3585
    Keywords: ferredoxin ; NMR ; paramagnetic ; relaxation ; solution structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The possibility of using the relaxation properties of nuclei for solution structure determination of paramagnetic metalloproteins is critically evaluated. First of all, it is theoretically and experimentally demonstrated that magnetization recovery in non-selective inversion recovery experiments can be approximated to an exponential in both diamagnetic and paramagnetic systems. This permits the estimate of the contribution of paramagnetic relaxation when dominant or sizable. Then, it is shown that the averaging of paramagnetic relaxation rates due to cross relaxation is often tolerably small with respect to the use of paramagnetic relaxation rates as constraints for structural determination. Finally, a protocol is proposed to use such paramagnetic relaxation rates, which depend on the sixth power of the metal to resonating nucleus distance, as constraints for solution structure determination of proteins. As an example, the available solution structure of the oxidized ferredoxin from Clostridium pasteurianum has been significantly improved in resolution especially in the proximity of the metal ions by using 69 new constraints based on paramagnetic relaxation. Proteins 29:348-358, 1997. © 1997 Wiley-Liss, Inc.
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    SHBG region of the anticoagulant cofactor protein S: Secondary structure prediction, circular dichroism spectroscopy, and analysis of naturally occurring mutations (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 478-491 
    Details
    ISSN: 0887-3585
    Keywords: secondary structure prediction ; vitamin k-dependent ; blood coagulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein S (PS) and growth arrest specific factor 6 (GAS6) are vitamin K-dependent proteins with similar structures. They are mosaic proteins possessing a carboxyl-terminal region presenting sequence similarity with plasma sex hormone binding globulin (plasma SHBG), although apparently not involved in steroid binding. The SHBG-like modules have sequence similarity with the G repeats of the chain A of laminin. Laminin G repeats have been reported to contain mainly β-strands (about 40-50%) but no or little α structure by circular dichroism (CD) spectroscopy. Secondary structure predictions carried out in the present work unexpectedly showed a 20 to 27% helices content in the SHBG region of PS/GAS6 (about 100 residues), while plasma SHBG and laminin G repeats had around 10% helices. CD measurements for human PS indicated also that its SHBG region had about 100 residues in α-helical structure. These data suggest that the SHBG region of PS/GAS6 on the one hand, and the laminin G repeats and possibly plasma SHBG on the other hand, could present important structural differences. Previously reported polymorphisms and point mutations leading to PS deficiency and thrombophilia have been analyzed with our structural predictions. We found a good agreement between these structural predictions, CD measurements, experimental and clinical data. This information allows us to gain insights into the three-dimensional structure of PS that will be helpful for the design of new experiments and future clinical investigations. Proteins 29:478-491, 1997. © 1997 Wiley-Liss, Inc.
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    New insights into the molecular basis of lectin-carbohydrate interactions: A calorimetric and structural study of the association of hevein to oligomers of N-acetylglucosamine (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 467-477 
    Details
    ISSN: 0887-3585
    Keywords: protein-saccharide interactions ; isothermal titration calorimetry ; binding and dehydration energetics ; molecular interactions in vacuum ; hydrogen bonds ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Isothermal titration calorimetry was used to characterize thermodynamically the association of hevein, a lectin from the rubber tree latex, with the dimer and trimer of N-acetylglucosamine (GlcNAc). Considering the changes in polar and apolar accessible surface areas due to complex formation, we found that the experimental binding heat capacities can be reproduced adequately by means of parameters used in protein-unfolding studies. The same conclusion applies to the association of the lectin concanavalin A with methyl-α-mannopyranoside. When reduced by the polar area change, binding enthalpy values show a minimal dispersion around 100°C. These findings resemble the convergence observed in protein-folding events; however, the average of reduced enthalpies for lectin-carbohydrate associations is largely higher than that for the folding of proteins. Analysis of hydrogen bonds present at lectin-carbohydrate interfaces revealed geometries closer to ideal values than those observed in protein structures. Thus, the formation of more energetic hydrogen bonds might well explain the high association enthalpies of lectin-carbohydrate systems. We also have calculated the energy associated with the desolvation of the contact zones in the binding molecules and from it the binding enthalpy in vacuum. This latter resulted 20% larger than the interaction energy derived from the use of potential energy functions. Proteins 29:467-477, 1997. © 1997 Wiley-Liss, Inc.
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    Flexible protein-ligand docking by global energy optimization in internal coordinates (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 215-220 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; ligand binding ; flexible docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eight protein-ligand complexes were simulated by using global optimization of a complex energy function, including solvation, surface tension, and side-chain entropy in the internal coordinate space of the flexible ligand and the receptor side chains [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:983-1002, 1994]. The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. J. Comp. Chem. 15:488-506, 1994] and a Biased-Probability multitorsion move [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235:983-1002, 1994], each accompanied by full local energy minimization. The best docking solutions were further ranked according to the interaction energy, which included intramolecular deformation energies of both receptor and ligand, the interaction energy, surface tension, side-chain entropic contribution, and an electrostatic term evaluated as a boundary element solution of the Poisson equation with the molecular surface as a dielectric boundary. The geometrical accuracy of the docking solutions ranged from 30% to 70% according to the relative displacement error measure at a 1.5 Å scale. Similar results were obtained when the explicit receptor atoms were replaced with a grid potential. Proteins, Suppl. 1:215-220, 1997. © 1998 Wiley-Liss, Inc.
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    Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 185-191 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; potentials of mean force ; ab initio folding ; structural motifs ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple approach to protein tertiary structure prediction is described, based on the assembly of recognized supersecondary structural fragments taken from highly resolved protein structures by using a simulated annealing algorithm. The results of blind-testing this method on CASP2 target T0042 (pig NK-lysin) are presented. The predicted structure had a Cα root-mean-square deviation of only 6.2 Å from the experimental structure (and less than 5.0 Å over the first 66 residues), and clearly had the correct fold when judged by using a number of objective measures. Despite the significant degree of success in this case, there is clearly much more development required before predictions with the accuracy of a good homology model can be made with this kind of approach. Proteins, Suppl. 1:185-191, 1997. © 1998 Wiley-Liss, Inc.
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    Critical evaluation of the research docking program for the CASP2 challenge (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 205-209 
    Details
    ISSN: 0887-3585
    Keywords: molecular docking ; CASP2 ; molecular simulation ; Monte Carlo ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The binding positions of six small-molecule ligands in their complexes with target proteins were predicted using our Research docking program for the CASP2 challenge. Research uses a Monte Carlo procedure with pairwise energies and allows for the conformational searching of ligand torsional space. We were able to predict 2 of the 5 noncovalent complexes within 2 Å root-mean-square (RMS) of the experimental structures as ranked by interaction energy or by a score calculated using our interaction evaluation program, Outrank. In addition, for 4 of the 5 noncovalent structures we found a docking within 2 Å RMS of the experimental structure within the top 20 dockings as ranked by energy. The main limitation in our approach is in the ability of the energy function and Outrank to discriminate among the lowest energy dockings. On the other hand, our success in exploring the multidimensional docking space of position, orientation and conformation is encouraging. Proteins, Suppl. 1:205-209, 1997. © 1998 Wiley-Liss, Inc.
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    Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 226-230 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; protein structure modeling ; antigen prediction ; conformational changes ; CASP2 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A single protein-protein pair, the complex of the influenza virus hemagglutinin with an antibody (Fab BH151), was suggested for prediction at the second experiment on the Critical Assessment of Techniques for Protein Structure Prediction. To predict the structure of the complex, we applied our docking program GRAMM at a decreased resolution (to accommodate the conformational inaccuracies). The lowest-energy match showed a remarkable “low-resolution” surface complementarity between the molecular structures. After receiving the experimental structure of the complex we had a chance to verify our assumptions and results. The analysis of the hemagglutinin-antibody interface revealed several significant conformational changes in the side chains, which resulted in deep interpenetrations of the hemagglutinin and the antibody structures. This confirmed our initial assumption that the structural changes will be beyond the tolerance of high-resolution rigid-body docking. The comparison of the predicted low-resolution match, submitted as the solution, and the experimentally determined complex showed significant structural discrepancies in the orientation of the antibody, due to the low-resolution character of the docking. Because of the severe structural errors, no residue-residue contacts were predicted correctly. However, a significant part of the antigenic site was determined. This illustrates the practical value of the present methodology for the initial prediction of the binding site, as well as points out the problem of transition from the low-resolution predictions of protein-protein complexes to the accurate structure. Proteins, Suppl. 1:226-230, 1997. © 1998 Wiley-Liss, Inc.
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    Synthesis and characterization of biodegradable homopolymers and block copolymers based on adipic anhydride (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 183-192 
    Details
    ISSN: 0887-624X
    Keywords: polyanhydride ; adipic anhydride ; ring-opening polymerization ; block copolymers ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Homopolymers of adipic anhydride (AA) and block copolymers of ∊-caprolactone (∊-CL) and AA have been synthesized with aluminum triisopropoxide as an initiator. Homopolymerization was studied at 20°C in toluene and methylene chloride (CH2Cl2). The end-group analysis agrees with a coordination insertion mechanism based on the acyl-oxygen cleavage of the AA ring. Living poly(∊-caprolactone) (PCL) chains are very efficient macro-initiators for the polymerization of AA, with formation of diblock copolymers of a narrow molecular weight distribution. At our best knowledge, low molecular weight ω-aluminum alkoxide PCL macroinitiators (Mn 〈 1000) allow the first valuable synthesis of PAA with a molecular weight as high as 58,000 and a quite narrow polydispersity (Mw/Mn = 1.2). Size-exclusion chromatography (SEC) and 13C NMR confirm the blocky structure of the copolymers, in agreement with DSC that shows two melting endotherms and two glass transitions characteristic of the crystalline and amorphous phases of PCL and PAA, respectively. Block copolymers of ∊-CL and AA are also sensitive to hydrolysis, which makes them possible candidates for biomedical applications. Initiation of the AA polymerization in bulk with aluminum triisopropoxide in the presence of various ligands is also discussed. © 1997 John Wiley & Sons, Inc.
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    Binary frontal polymerization: A new method to produce simultaneous interpenetrating polymer networks (SINs) (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 227-230 
    Details
    ISSN: 0887-624X
    Keywords: IPN ; frontal polymerization ; propagating front ; SIN ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report a new method for the preparation of a simultaneous interpenetrating polymer network (SIN) using a thermal propagating front of two independent and noninterfering polymerization mechanisms. The system consists of the free radical crosslinking of triethylene glycol dimethacrylate (TGDMA) and the amine/BCl3 · amine curing of diglycidyl ether of bisphenol A (DGEBA). The front velocity dependence on the percentage of each monomer shows a minimum at 45% TGDMA. Temperature profile measurements indicate that a single reaction front propagates. A colored opaque material is produced, but SEM and TEM analysis were inconclusive whether phase separation occurred. Samples as large as 5 cm in diameter were prepared with this method. We conclude that this method should be especially suited for preparing large samples of IPNs in which significant phase separation occurs. © 1997 John Wiley & Sons, Inc.
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    Controlled synthesis of amphiphilic block copolymers with pendant glucose residues by living cationic polymerization (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 255-261 
    Details
    ISSN: 0887-624X
    Keywords: controlled synthesis ; amphiphilic block copolymer ; pendant glucose residues ; vinyl ether ; living cationic polymerization ; microphase-separated structure ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amphiphilic block copolymers of vinyl ethers (VEs) of the type  - [CH2CH(OCH2CH2OR)]m - [CH2CH(OiBu)]n - were synthesized by living cationic polymerization, where R is a D-glucose residue, and m and n are the degrees of polymerization (m = 20-50; n = 11-89). To obtain them, sequential living block copolymerization of isobutyl vinyl ether (IBVE) and the vinyl ether carrying 1,2:5,6-diisopropylidene-D-glucose residue was conducted by using the HCl adduct of IBVE, CH3CH(OiBu)Cl, as initiator in conjunction with zinc iodide. These precursor block copolymers had a narrow molecular weight distribution (M̄w/M̄n ∼ 1.1) and a controlled composition. Treatment of them with a trifluoroacetic acid/water mixture led to the target amphiphiles. The solubility of the amphiphilic block copolymers in various solvents depended strongly on composition or the m/n ratio. Their solvent-cast thin films were observed, under a transmission electron microscope, to exhibit various microphase-separated surface morphologies such as spheres, cylinders, and lamellae, depending on composition. © 1997 John Wiley & Sons, Inc.
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    Transient species in pulse-irradiated poly(methyl methacrylate) pure and doped with pyrene (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 299-305 
    Details
    ISSN: 0887-624X
    Keywords: poly(methylmethacrylate) ; pulse radiolysis ; charge scavenging ; doped polymers ; excited states ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectra of transients produced in pulse-irradiated pure poly(methyl methacrylate), PMMA, at room and ∼ 130 K temperatures were measured. The intermediates were identified as PMMA radicals and radical anions. In the pulse-irradiated PMMA-pyrene (Py) system the solute excited states and radical ions were produced. Scavenging of negative charges by Py was directly observed at 130 K in a µs time scale. Py fluorescence was found to be produced mainly as a result of Čerenkov photoexcitation. At room temperature, some contribution of ionic mechanism to Py fluorescence formation was found. © 1997 John Wiley & Sons, Inc.
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    Noncoordinating anions in carbocationic polymerization (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 329-344 
    Details
    ISSN: 0887-624X
    Keywords: carbocationic polymerization ; isobutylene ; metallocenes ; noncoordinating anions ; styrenics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The initiation and catalysis of isobutylene polymerization from several new metallocene and nonmetallocene initiator-catalysts that contain the noncoordinating anions (NCA), B(C6F5)4- and RB(C6F6)3-, is reported. Application of these initiator-catalysts is extended to styrenics and vinyl ethers. The NCA does not contribute to termination and can be used in low concentrations compared with conventional Lewis acids. These qualities provide for isobutylene polymerizations that yield low Mn oligomers or high Mn polymer, dependent upon the initiator and polymerization conditions. Mechanistic aspects of initiation, transfer and termination as well as the participation of adventitious water are considered for each class of initiator-catalyst. The influence of the NCA on the stereoregularity of cationic styrene polymerization is also considered. NCAs do not cause the stereospecific carbocationic polymerization of styrene. We suggest that under conditions not conducive to carbocationic polymerization, NCA/metallocenes mediate the coordination polymerization of styrene. © 1997 John Wiley & Sons, Inc.
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    Synthesis and enzymatic hydrolysis of lactic acid-depsipeptide copolymers with functionalized pendant groups (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 377-383 
    Details
    ISSN: 0887-624X
    Keywords: biodegradability ; poly(lactic acid) ; lactic acid-depsipeptide copolymer ; ring-opening copolymerization ; functionalized side-group ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Since poly(lactic acid) is the biodegradable polyester having low immunogenicity and good biocompatibility, it is utilized as a medical material. However, poly(lactic acid) is a water-insoluble crystalline polymer having no reactive side-chain group. Thus, the use of poly(lactic acid) is limited. To modify the properties of poly(lactic acid) and to introduce the functionalized pendant groups to poly(lactic acid), we synthesized two kinds of lactic acid-depsipeptide copolymers with reactive pendant groups, namely poly[LA-(Glc-Lys)] and poly[LA-(Glc-Asp)]. This was done through ring-opening copolymerizations of L-lactide with the corresponding protected cyclodepsipeptides, cyclo[Glc-Lys(Z)] and cyclo[Glc-Asp(OBzl)], and subsequent deprotection of benzyloxycarbonyl and benzyl groups, respectively. By changing the mole fraction of the corresponding depsipeptide units, the solubility, thermal transition and degradation behavior of the modified poly(lactic acid) could be varied. © 1997 John Wiley & Sons, Inc.
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    Fluorescence lifetime of terbium(III) as a probe for the ion-binding properties of tactic poly(methacrylic acids) (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 393-398 
    Details
    ISSN: 0887-624X
    Keywords: terbium ; poly(methacrylic acid) ; tacticity ; fluorescence ; lifetime ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding properties of trivalent metal ions to polyelectrolytes were investigated through the use of terbium [Tb(III)] in fluorescence studies. The fluorescence intensity and lifetimes of the lanthanide ions are directly dependent upon the number of water molecules bound to their inner coordination sphere. The more efficiently a ligand coordinates to a lanthanide ion, the more water molecules are expelled and consequently, the greater the fluorescence intensity and lifetime. This effect was used to probe for differences in the complexation behavior of tactic polymers. Aqueous solutions of isotactic and syndiotactic poly(methacrylic acid) (PMA) were neutralized and complexed with Tb(III) ions. The fluorescence intensity of the 286 nm hypersensitive excitation band was monitored and the lifetimes were measured using several excitation wavelengths. It was found that the isotactic PMA/Tb(III) complex exhibited a six times greater fluorescence intensity than the syndiotactic PMA complex. Lifetime measurements gave the number of water molecules coordinated by Tb(III) in the isotactic complex to be 2.4 while 3.4 waters remained bound to the Tb(III) ion in the syndiotactic PMA complex. These results indicate that isotactic PMA has the greater binding affinity towards Tb(III) ions. © 1997 John Wiley & Sons, Inc.
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    Ring opening during the cationic polymerization of 2-methylene-1,3-dioxepane: Cyclic ketene acetal initiation with sulfuric acid supported on carbonSee Reference 1. (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 485-491 
    Details
    ISSN: 0887-624X
    Keywords: 2-methylene-1,3-dioxepane ; cyclic ketene acetal ; cationic polymerization ; activated carbon black ; 1,2-polymerization ; ring-opening polymerization ; ring-retained polymerization ; initiator ; catalyst ; heterogeneous catalysis ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---The stable cyclic ketene acetal, 2-methylene-1,3-dioxepane, 7, has been polymerized cationically in pentane, CH2Cl2 and THF at 25°C to form a polymer which is composed of both ring-opened (40-50%) and ring-retained (50-60%) structures. Initiation was catalyzed by using H2SO4-supported on activated carbon black. This unique outcome differs significantly from the cationic polymerization of several other five- and six-membered ring cyclic ketene acetals which gave 100% 1,2-vinylpolymerization under these conditions. As the polymerization temperature increased in cationic polymerization of 7 the ring-opened content increased and the molecular weight of the polymers decreased in such solvents as cyclohexane, 1,2-dichloroethane, dimethoxyethane, and bis-(2-methoxyethyl) ether. The mechanism of this polymerization is discussed. This research also illustrated the ability to initiate the cationic polymerization of cyclic ketene acetals by acidified carbon black while avoiding subsequent polymer decomposition. © 1997 John Wiley & Sons, Inc.
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    An application of arene-iron chemistry in the synthesis of a novel liquid crystalline polymer (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 447-453 
    Details
    ISSN: 0887-624X
    Keywords: polyether ; polyester ; aryl ether ; nucleophilic substitution ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Arene-iron chemistry was applied in the synthesis of a novel liquid crystalline polymer. The chemistry, which is based on iron cyclopentadienyl (FeCp) arene complexes, allows sequential nucleophilic substitution of the chlorides from 1,3-dichlorobenzene-FeCp complex and photolytic decomplexation of the products to afford asymmetrical aryl ethers. This methodology provides easy access to novel polyether-esters, and is potentially useful in the synthesis of various functional polyarylates. © 1997 John Wiley & Sons, Inc.
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    Aggregation kinetics and precipitation phenomena in poly(phenylisocyanide) (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 439-446 
    Details
    ISSN: 0887-624X
    Keywords: poly(phenylisocyanide) ; NMR ; GPC ; light-scattering techniques ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The preparation of N-phenyl-substituted poly(isocyanide) (N-φ-PIM) utilizing a Ni(II) catalyst in methanol yields a brown material having a number average molecular weight of about 2000. Analysis of this “as prepared” polymer indicates that a rigid rod structure is present in the derived solid. Dissolution of this “as prepared” N-φ-PIM in halocarbon solvents or THF apparently leads to unraveling of the helical polymer with subsequent aggregation and precipitation of materials that have different properties from the original. These processes have been investigated by NMR, GPC, and light-scattering techniques in THF and other solvents. UV spectroscopy has been utilized to follow the kinetics of the aggregation process in solution. X-ray diffraction (XRD) measurements have been employed to investigate the changes attendant with precipitation. An explanation of these observations is offered that implicates the uncoiling of the rigid rod helix as the most important step in defining subsequent physical and chemical properties of the ultimate amorphous polymer. © 1997 John Wiley & Sons, Inc.
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    π-Conjugated soluble and fluorescent poly(thiophene-2,5-diyl)s with phenolic, hindered phenolic and p-C6H4OCH3 substituents. Preparation, optical properties, and redox reaction (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 463-474 
    Details
    ISSN: 0887-624X
    Keywords: π-conjugated polymer ; polythiophene ; phenolic substituent ; hindered phenolic substituent ; nickel-promoted ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dehalogenation polycondensation of 3-(4-methoxyphenyl)-2,5-dibromothiophene with Mg and a zerovalent nickel complex as well as chemical oxidative polymerization of 3-(4-methoxyphenyl)thiophene with FeCl3 gives poly[3-(4-methoxyphenyl)thiophene-2,5-diyl] P3(4-MeOPh)Th. Treatment of soluble P3(4-MeOPh)Th with BBr3 converts the OCH3 group to an OH group and gives poly[3-(4-hydroxyphenyl)thiophene-2,5-diyl] P3(4-OHPh)Th. Oxidative polymerization of 3-[3,5-di-t-butyl-4-{(trimethylsilyl)oxy}phenyl]thiophene with FeCl3 in an aqueous medium directly affords another kind of polythiophene with a sterically hindered phenolic group, poly[3-(3,5-di-t-butyl-4-hydroxyphenyl)thiophene-2,5-diyl] P3(4-OH-3,5-tBu2Ph)Th. An organometallic dehalogenation polymerization using a nickel complex also affords P3(4-OH-3,5-tBu2Ph)Th. All the polymers described above show strong photoluminescence in a region of 500-600 nm. Oxidation of P3(4-OH-3,5-tBu2Ph)Th with PbO2 gives stable radical species as confirmed by IR and ESR spectroscopy. Electrochemical redox behavior of the polymers is compared with that of other polythiophenes. © 1997 John Wiley & Sons, Inc.
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    Synthesis of polyamides and polyureas containing leucine-tyrosine linkages (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 499-507 
    Details
    ISSN: 0887-624X
    Keywords: amino acids ; leucine-tyrosine ; polyureas ; polyamides ; polyesteramide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monomers with leucine-tyrosine linkages were synthesized using diphenyl phosphoryl azide as a coupling reagent. Leucyltyrosylpoly(propylene glycol) bis(2-aminopropyl ether) tyrosylleucine (monomer 1) has a longer spacer: poly(propylene glycol) bis(2-aminopropyl ether) (Jeffamine® D-400), and leucyltyrosyliminohexamethyleneiminotyrosylleucine (monomer 2) has a shorter spacer: hexamethylenediamine. Polyureas from monomers 1 and 2 with hexamethylene diisocyanate and methylenedi-p-phenyl diisocyanate were synthesized. Polyamide, polyesteramide from monomer 2 were synthesized. The characterization of these polymers using 1H-NMR, 13C-NMR, solid-state 13C-NMR, IR, GPC, and also thermal analysis are presented. © 1997 John Wiley & Sons, Inc.
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    Synthesis and characterization of biodegradable block copolymers of ∊-caprolactone and D,L-lactide initiated by potassium poly(ethylene glycol)ate (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 703-708 
    Details
    ISSN: 0887-624X
    Keywords: anionic ring-opening polymerization ; poly(ethylene glycol) ; poly(∊-caprolactone) ; poly(D,L-lactide) ; block copolymer ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly(D,L-lactide)-poly(∊-caprolactone)-poly(ethylene glycol)-poly(∊-caprolactone)-poly(D,L-lactide) block copolymer (PLA-PCL-PEG-PCL-PLA) was prepared by copolymerization of ∊-caprolactone (∊-CL) and D,L-lactide (D,L-LA) initiated by potassium poly(ethylene glycol)ate in THF at 25°C. The copolymers with different composition were synthesized by adjusting the mole ratio of reaction mixture. The resulted copolymers were characterized by 1H-NMR, 13C-NMR, IR, DSC, and GPC. Efforts to prepare copolymers with the corresponding structure of PCL-PLA-PEG-PLA-PCL and D,L-lactide/∊-caprolactone random copolymers were not successful. © 1997 John Wiley & Sons, Inc.
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    Polymer-supported reagents. II. Kinetics of esterification of acrylic acid with n-butanol using polymer supported titanium tetrachloride as catalyst (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 727-733 
    Details
    ISSN: 0887-624X
    Keywords: titanium tetrachloride ; esterification ; polymer-supported catalyst ; kinetic study ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Crosslinked poly(4-vinylpyridine-co-styrene) was prepared and functionalized with titanium tetrachloride to afford the corresponding poly(4-vinylpyridine-co-styrene)-titanium tetrachloride complex. This insoluble functionalized polymer-supported catalyst shows good catalytic activity for esterification reactions. In this article, the kinetics of esterification of acrylic acid with n-butanol is reported. The rate of formation of product depends on many experimental parameters, viz., stirring speed, concentration of acrylic acid, catalyst amount, temperature, percent active site, percent crosslinking, and mesh size of the polymer catalyst. The reaction rates were found to increase with increase in the stirring speed, concentration of acrylic acid, catalyst amount, and temperature, and decreases with increasing percentage crosslinking and mesh size of the polymer beads. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 727-733, 1997
    Additional Material: 3 Ill.
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    Macrocyclic oligoimides. I. Preparation of macrocyclic oligoetherimides via Kricheldorf substitution polymerization (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 759-767 
    Details
    ISSN: 0887-624X
    Keywords: oligoetherimide ; cyclic oligomer ; macrocyclic imide ; bisphenol silylether ; fluorophthalimide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Macrocyclic oligoetherimides were synthesized by means of Kricheldorf's nucleophilic aromatic substitution polycondensation. A solution containing equimolar quantities of bis(trimethylsilyl ether) of bisphenol and arylenebis(fluorophthalimide) was continuously added into a high boiling solvent containing CsF catalyst under a pseudo-high dilution condition. The resulting reaction mixture contained a high yield of cyclic oligomers which could be isolated by solvent extraction. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 759-767, 1997
    Additional Material: 4 Ill.
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    Optically active dimethylsiloxane copolymers with nucleophilic chiral sulfur groups pendant to the polysiloxane chain (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 879-888 
    Details
    ISSN: 0887-624X
    Keywords: polysiloxanes ; cyclosiloxanes ; dimethylsiloxane copolymers ; optically active polymers ; addition to vinylsiloxanes ; ring-opening polymerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polydimethylsiloxanes with part of the siloxane units bearing an optically active sulfoxide group were synthesized. These copolymers had chiral sulfur centres connected to the siloxane chain by a dimethylene bridge. They were obtained mostly by the kinetically controlled anionic ring-opening polymerization of 1-(2-organothioethyl)1,3,3,5,5-pentamethylcyclotrisiloxanes, followed by stereoselective oxidation of prochiral groups to yield partially enantiomeric sulfoxide groups. Sulfoxides bearing cyclic monomers were also used. Polymers were characterized by spectroscopy and polarimetry. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 879-888, 1997
    Additional Material: 4 Ill.
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  • 94
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    Solid-state 13C-NMR analysis of hypercrosslinked polystyrene (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 695-701 
    Details
    ISSN: 0887-624X
    Keywords: hypercrosslinked polystyrene ; solids NMR ; structure ; relaxation measurements ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Hypercrosslinked polystyrenes, synthesized by reaction of linear or lightly crosslinked polystyrene with chloromethyl methyl ether (CME) and a Lewis acid in a good solvent, swell even in nonsolvents for polystyrene. Structures and dynamics of hypercrosslinked polystyrenes in both dry solid and solvent-swollen gel states have been determined by 13C-NMR spectroscopy. Deconvolution of 13C solid-state CP/MAS spectra gave the relative numbers of quaternary carbon atoms in monosubstituted and disubstituted benzenes. A typical sample, crosslinked by reaction of a mixture containing 0.5 mol of CME per mol of repeat units, contains 35% of unreacted and 65% of crosslinked aromatic rings, and no residual chloromethyl groups. Gels swollen in CDCl3 and in CH3OH have residual static dipolar interactions enabling crosspolarization and require magic angle spinning (MAS) and high power 1H decoupling to reduce chemical shift anisotropy from ∼ 104 Hz to ∼ 103 Hz. A single proton spin-lattice relaxation time in the rotating frame measured from all peaks in the 13C spectra of dry samples indicates homogeneity on a nanometer scale. Proton NMR line widths indicate no substantial molecular motions in a dry hypercrosslinked polystyrene up to at least 200°C. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 695-701, 1997
    Additional Material: 5 Ill.
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    Stereospecific polymerization of benzyl α-(alkoxymethyl) acrylates (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 721-726 
    Details
    ISSN: 0887-624X
    Keywords: benzyl α-(alkoxymethyl)acrylate ; stereospecific polymerization ; anionic polymerization ; isotactic polymer ; tacticity ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: α-(Alkoxymethyl) acrylates, such as methyl α-(phenoxymethyl) acrylate, benzyl α-(methoxymethyl)acrylate (BMMA), benzyl α-(benzyloxymethyl)acrylate, and benzyl α-(tert-butoxymethyl)acrylate, were synthesized, and their polymerizability and the stereoregularity of the polymers obtained by radical and anionic methods were investigated. The radically obtained polymers were found to be atactic by 13C- and 1H-NMR analyses, but the polymers obtained with lithium reagents in toluene at -78°C were highly isotactic. Further, it is noteworthy that isotactic polymers were also produced with lithium reagents even in tetrahydrofuran. Effects of polymerization temperature and counter cation on stereoregularity were clearly observed in the polymerization of BMMA, and a potassium reagent afforded an almost atactic polymer. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35:721-726, 1997
    Additional Material: 6 Ill.
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  • 96
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    Preparation of porous hydrophilic monoliths: Effect of the polymerization conditions on the porous properties of poly (acrylamide-co-N,N′-methylenebisacrylamide) monolithic rods (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 1013-1021 
    Details
    ISSN: 0887-624X
    Keywords: macroporous monoliths ; acrylamide copolymers ; polymerization in mold ; porogens ; polymerization kinetics ; porous properties ; morphology ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molded macroporous monoliths with pores sizes up to 1000 nm have been prepared by copolymerization of the hydrophilic monomers, acrylamide, and N,N′-methylenebisacrylamide, in the presence of a porogenic diluent. A combination of dimethylsulfoxide and 2-heptanol was selected from a broad spectrum of solvents and water soluble polymers to achieve the optimum composition of the porogenic mixture. In addition to the composition of the porogen the porous properties of the monolithic rods can also be optimized through changes in the percentage of both N,N′-methylene-bisacrylamide (crosslinking monomer) and azobisisobutyronitrile (free radical initiator) used for the polymerization. The hydrophilic monoliths may be used in the separation of biological polymers, solid-phase extraction, or for immobilization of proteins. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 1013-1021, 1997
    Additional Material: 5 Ill.
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  • 97
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    Propagation velocity of the reaction front in addition polymerization systems (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 1047-1059 
    Details
    ISSN: 0887-624X
    Keywords: propagating polymerization fronts ; frontal polymerization ; ceiling temperature ; traveling waves ; constant pattern ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Traveling polymerization fronts in unstirred solutions of methylmethacrylate, methacrylic acid, or acrylamide with some free radicals initiators (through thermal decomposition) have been observed experimentally. A local heating of the initial reactant mixture, under suitable conditions, leads to a reaction front that propagates along the space coordinate with a constant velocity. In this article, a physical interpretation of this phenomenon is provided through a mathematical model that accounts for the depolimerization reaction and is based on the constant pattern approach. Moreover, an approximate explicit analytic expression for the velocity of propagation of the polymerization front is proposed. The theoretical values are compared with those measured experimentally as a function of the initiator concentration for different addition polymerization systems. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35:1047-1059, 1997
    Additional Material: 9 Ill.
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    Synthesis and characterization of aromatic polyamides containing S-triazine rings in the main chain (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 1077-1085 
    Details
    ISSN: 0887-624X
    Keywords: s-triazine ring ; thermal stability ; polyamide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ten new aromatic polyamides containing s-triazine rings in the main chain were synthesized by the low temperature interfacial polycondensation technique involving the reactions of each of the two s-triazine containing diacylchlorides, viz., 2,4-bis (4-chlorocarbonylphenoxy)-6-methoxy-s-triazine and 2,4-bis(3-chlorocarbonylphenoxy)-6-methoxy-s-triazine, with five aromatic diamines namely, 4,4′-bis(4-aminophenoxy)diphenyl sulfone, 4,4′-bis(3-aminophenoxy)diphenyl sulfone, 2,2-bis[4(4-aminophenoxy) phenyl] propane, 1,4 bis (4-amino-phenoxy) benzene, and 1,3-bis (4-aminophenoxy)benzene. The resulting polyamides were characterized by viscosity measurements, IR and 1H-NMR spectroscopy, solubility tests, x-ray diffraction, and thermogravimetry. The polyamides had inherent viscosities in the range of 0.16-1.06 dL/g in N,N-dimethylacetamide at 30°C. Most of the s-triazine containing polyamides dissolved readily at room temperature in polar solvents. Except for the polyamide PA-2, the polyamides did not lose weight below 350°C under a nitrogen atmosphere. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 1077-1085, 1997
    Additional Material: 4 Ill.
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    Synthesis of polycarbonates by a silicon-assisted alkoxy/carbonylimidazolide coupling reaction (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 1133-1137 
    Details
    ISSN: 0887-624X
    Keywords: aliphatic linear polycarbonate ; AB polymerization ; cyclohexanediol ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The investigation of a silicon-mediated coupling reaction between hydroxyl and carbonylimidazolide functional groups in the preparation of carbonate linkages is described. Application of this reaction to the formation of aliphatic polycarbonates was accomplished by the polymerization of an AB monomer unit, which was composed of 1,4-cyclohexanediol, where one of the hydroxyl groups was protected as a dimethylphenylsilyl ether and the other carried the carbonylimidazolide functionality. Reaction of this monomer with cesium fluoride removed the silicon protecting group and the resulting alkoxy anion promoted polymerization. Poly(1,4-cyclohexanecarbonate)s with typical molecular weights of Mw = 20,000 and Mn = 7300 a.m.u. (from GPC based upon polystyrene standards) were prepared in ca. 65% yield. The polymer showed a glass transition temperature at 138°C by DSC. TGA gave 85% mass loss between 275 and 350°C. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 1133-1137, 1997.
    Additional Material: 1 Tab.
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  • 100
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    PAmXD,6/PP-g-MA blend. II. Rheology and phase inversion location (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part A: Polymer Chemistry 35 (1997), S. 917-925 
    Details
    ISSN: 0887-624X
    Keywords: polymer blend ; phase inversion ; compatibilization ; PP-g-MA ; PAmXD,6 ; Brabender torque ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This work deals with the study of the phase inversion phenomenon in blends of poly(m-xylylene adipamide) and maleic anhydride functionalized polypropylene (PAmXD,6/PP-g-MA blends) processed in a Brabender plastograph at 265 ± 5°C and 45 rpm. The viscosity of the components has been modelized by the Brabender torque and the phase inversion composition was determined by means of a solvent dispersion technique (SDT). The compatibilization, i.e., the amount of copolymer in the blend, does not modify the phase inversion location. The phase inversion composition is determined early during the process and is weakly or even not at all affected by further modification of viscosity ratio of the components versus mixing time. This work demonstrates that the only key parameter of the phase inversion composition is the viscosity ratio of the components at the first stage of the mixing process. An empirical equation linking volume fraction ratio for the phase inversion composition and the square root of the viscosity ratio of the components is proposed. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 917-925, 1997
    Additional Material: 9 Ill.
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