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  • 1995-1999  (1.363)
  • 1985-1989
  • 1980-1984  (508)
  • 1975-1979
  • 1965-1969
  • 1997  (1.363)
  • 1983  (508)
  • Biochemistry and Biotechnology  (1.721)
  • Ultrastructure
Datenquelle
Materialart
Erscheinungszeitraum
  • 1995-1999  (1.363)
  • 1985-1989
  • 1980-1984  (508)
  • 1975-1979
  • 1965-1969
Jahr
Schlagwörter
  • 101
    Digitale Medien
    Digitale Medien
    Rab7: Crystallization of intact and C-terminal truncated constructs complexed with GDP and GppNHp (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 210-212 
    Details
    ISSN: 0887-3585
    Schlagwort(e): rab7 ; crystal ; GDP ; GTP ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The GTP/GDP conformational switch of members of the rab family of ras-related GTP-ases control specific intracellular vesicle transport pathways. We report the crystallization of the late-endosomal rab protein rab7, in both GTP and GDP conformations. X-ray data from crystals of rab71-207GppNHp (i.e., intact rab7, without C-terminal bound lipid, complexed with a non-hydrolysable GTP analog), rab71-197GppNHp and rab71-197GDP were collected to 1.9Å (0°C), 1.76Å (100°K) and 1.75Å (100°K) respectively. Rab7-GDP crystals diffract to at least 1.35Å. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Tab.
    Materialart: Digitale Medien
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  • 102
    Digitale Medien
    Digitale Medien
    A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 227-233 
    Details
    ISSN: 0887-3585
    Schlagwort(e): peptide conformation ; ramachandran plot ; PDB search ; peptide dynamics ; BPTI ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four Cαatoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudo-dihedral involving four sequential Cαatoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple φ,ψ pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 103
    Digitale Medien
    Digitale Medien
    Automated docking of monosaccharide substrates and analogues and methyl α-Acarviosinide in the glucoamylase active site (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 235-248 
    Details
    ISSN: 0887-3585
    Schlagwort(e): acarviosinide ; active site ; docking ; glucoamylase ; molecular mechanics ; monosaccharides ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Glucoamylase is an important industrial glucohydrolase with a large specificity range. To investigate its interaction with the monosaccharides D-glucose, D-mannose, and D-galactose and with the substrate analogues 1-deoxynojirimycin, D-glucono-1,5-lactone, and methyl αacarviosinide, MM3(92)-optimized structures were docked into its active site using AutoDock 2.1. The results were compared to structures of glucoamylase complexes obtained by protein crystallography. Charged forms of some substrate analogues were also docked to assess the degree of protonation possessed by glucoamylase inhibitors. Many forms of methyl αa-carviosinide were conformationally mapped by using MM3(92), characterizing the conformational pH dependence found for the acarbose family of glucosidase inhibitors. Their significant conformers, representing the most common states of the inhibitor, were used as initial structures for docking. This constitutes a new approach for the exploration of binding modes of carbohydrate chains. Docking results differ slightly from x-ray crystallographic data, the difference being of the order of the crystallographic error. The estimated energetic interactions, even though agreeing in some cases with experimental binding kinetics, are only qualitative due to the large approximations made by AudoDock force field. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 104
    Digitale Medien
    Digitale Medien
    A predicted consensus structure for the C terminus of the beta and gamma chains of fibrinogen (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 279-289 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein structure prediction ; prediction contest ; protein sequence alignment ; compensatory covariation ; CASP2 ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A secondary structure has been predicted for the C termini of the fibrinogen β and γ chains from an aligned set of homologous protein sequences using a transparent method that extracts conformational information from patters of variation and conservation, parsing strings, and patterns of amphiphilicity. The structure is modeled to form two domains, the first having a core parallel sheet flanked on one side by at least two helices and on the other by an antiparallel amphiphilic sheet, with an additional helix connecting the two sheets. The second domain is built entirely from β strands. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 105
    Digitale Medien
    Digitale Medien
    A method for the prediction of surface “U”-turns and transglobular connections in small proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 290-308 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; protein structure ; supersecondary structure ; structure prediction ; turn prediction ; statistical potentials ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, “U” turns, and assigning the dominant secondary structure of the intervening transglobular blocks in small, single-domain globular proteins has been developed. Since the emphasis of the method is on the prediction of the major topological elements that comprise the global structure of the protein rather than on a detailed local secondary structure description, this approach is complementary to standard secondary structure prediction schemes. Consequently, it may be useful in the early stages of tertiary structure prediction when establishment of the structural class and possible folding topologies is of interest. Application to a set of small proteins of known structure indicates a high level of accuracy. The prediction of the approximate location of the surface turns/loops that are responsible for the change in overall chain direction is correct in more than 95% of the cases. The accuracy for the dominant secondary structure assignment for the linear blocks between such surface turns/loops is in the range of 82%. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 106
    Digitale Medien
    Digitale Medien
    Crystallization and preliminary studies of lima bean trypsin inhibitor (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 311-314 
    Details
    ISSN: 0887-3585
    Schlagwort(e): thermostability ; cubic ; trypsin-agarose/sepharose chromatography vapor diffusion method ; self-rotation function ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Crystals of lima bean trypsin inhibitor (LBTI) were obtained by using the vapor phase equilibration technique with sodium/potassium tartrate as the precipitating agent. The space group was determined to be cubic, I213 with a= 110.2 Å. These crystals diffract to about 1.9 Å resolution. Preliminary analysis of self-rotation maps (calculated from native x-ray intensity data) suggests the presence of two monomers in the asymmetric unit. LBTI is very thermostable and retains activity even after boiling for 10 minutes. This property is exploited as part of its purification procedure. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 107
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): catalytic domain ; cross-linking ; hanging drop ; p21 ; seeding ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 108
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): transcriptional control ; cell-cycle ; DNA-binding ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Materialart: Digitale Medien
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  • 109
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): protein structure ; protein sequence analysis ; hydrogen bonds ; sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 110
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): molecular evolution ; nicotinamide adenine dinucleotide ; nicotinamide adenine dinucleotide phosphate ; dinucleotide bonding domains ; mononucleotide binding domains ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 111
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): helical conformations ; polypeptides ; homopeptides ; apolar solvents ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 112
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): protein family analysis ; genome analysis ; homology modeling ; molecular evolution ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 113
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): normal mode analysis ; Delauney tessellation ; bond distance ; compressibility ; volume fluctuation ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 114
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 115
    Digitale Medien
    Digitale Medien
    Subtilisin enzymes: Practical protein engineering, edited by Richard Bott and Christian Betzel. New York: Plenum Press, 1996, $79.50 (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 461-462 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 116
    Digitale Medien
    Digitale Medien
    Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 32-58 
    Details
    ISSN: 0887-3585
    Schlagwort(e): computer-aided ligand design ; multiple copy simultaneous search ; poliovirus ; rhinovirus ; structure-based drug design ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A combinatorial ligand design approach based on the multiple copy simultaneous search (MCSS) method and a simple scheme for joining MCSS functional group sites was applied to the binding pocket of P3/Sabin poliovirus and rhinovirus 14. The MCSS method determines where specific functional (chemical) groups have local potential energy minima in the binding site. Before the virus application, test calculations were run to determine the optimal set of input parameters to be used in evaluating the MCSS results. The MCSS minima are analyzed and selected minima are connected with (CH2)n linkers to form candidate ligands, whose structures are optimized in the binding site. Estimates of the binding strength were made for the ligands and compared with those for known drugs. The results indicate that the proposed ligands should bind to P3/Sabin poliovirus at least as well as the best of the existing drugs, and that they should also bind to P1/Mahoney poliovirus and rhinovirus 14. A detailed comparison of the poliovirus and rhinovirus binding pockets and an analysis of drug binding specificity is presented. Proteins 29:32-58, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 15 Ill.
    Materialart: Digitale Medien
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  • 117
    Digitale Medien
    Digitale Medien
    Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 15-31 
    Details
    ISSN: 0887-3585
    Schlagwort(e): metalloprotein ; lipoxygenase ; X-ray structure ; fatty acid ; electron transfer ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Soybean lipoxygenase isoenzyme L3 represents a second example (after L1) of the X-ray structure (R = 17% at 2.6 Å resolution) for a member of the large family of lipoxygenases. L1 and L3 have different characteristics in catalysis, although they share 72% sequence identity (the changes impact 255 amino acids) and similar folding (average Cα rms deviation of 1 Å). The critical nonheme iron site has the same features as for L1: 3O and 3N in pseudo C3v orientation, with two oxygen atoms (from Asn713 and water) at a nonbinding distance. Asn713 and His518 are strategically located at the junction of three cavities connecting the iron site with the molecule surface. The most visible differences between L1 and L3 isoenzymes occur in and near these cavities, affecting their accessibility and volume. Among the L1/L3 substitutions Glu256/Thr274, Tyr409/His429, and Ser747/Asp766 affect the salt bridges (L1: Glu256…His248 and Asp490…Arg707) that in L1 restrict the access to the iron site from two opposite directions. The L3 molecule has a passage going through the whole length of the helical domain, starting at the interface with the Nt-domain (near 25-27 and 254-278) and going to the opposite end of the Ct-domain (near 367, 749). The substrate binding and the role of His513, His266, His776 (and other residues nearby) are illustrated and discussed by using models of linoleic acid binding. These hypotheses provide a possible explanation for a stringent stereospecificity of catalytic products in L1 (that produces predominantly 13-hydroperoxide) versus the lack of such specificity in L3 (that turns out a mixture of 9- and 13-hydroperoxides and their diastereoisomers). Proteins 29:15-31, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 118
    Digitale Medien
    Digitale Medien
    Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductaseThis work appears in preliminary form in Gschwend et al., J. Mol. Recognit. 9:175-186, 1996 (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 59-67 
    Details
    ISSN: 0887-3585
    Schlagwort(e): species-specificity ; DOCK ; molecular docking ; lead discovery ; antifungal ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Specificity is an important aspect of structure-based drug design. Distinguishing between related targets in different organisms is often the key to therapeutic success. Pneumocystis carinii is a fungal opportunist which causes a crippling pneumonia in immunocompromised individuals. We report the identification of novel inhibitors of P. cariniidihydrofolate reductase (DHFR) that are selective versus inhibition of human DHFR using computational molecular docking techniques. The Fine Chemicals Directory, a database of commercially available compounds, was screened with the DOCK program suite to produce a list of potential P. carinii DHFR inhibitors. We then used a postdocking refinement directed at discerning subtle structural and chemical features that might reflect species specificity. Of 40 compounds predicted to exhibit anti-PneumocystisDHFR activity, each of novel chemical framework, 13 (33%) show IC50 values better than 150 μM in an enzyme assay. These inhibitors were further assayed against human DHFR: 10 of the 13 (77%) bind preferentially to the fungal enzyme. The most potent compound identified is a 7 μM inhibitor of P. carinii DHFR with 25-fold selectivity. The ability of molecular docking methods to locate selective inhibitors reinforces our view of structure-based drug discovery as a valuable strategy, not only for identifying lead compounds, but also for addressing receptor specificity. Proteins 29:59-67, 1997. © 1997 Wiley-Liss, Inc.
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  • 119
    Digitale Medien
    Digitale Medien
    Extreme heat- and pressure-resistant 7-kDa protein P2 from the archaeon Sulfolobus solfataricus is dramatically destabilized by a single-point amino acid substitution (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 381-390 
    Details
    ISSN: 0887-3585
    Schlagwort(e): piezostability ; thermostability ; hydrostatic pressure ; circular dichroism ; Fourier transform infrared spectroscopy ; nuclear magnetic resonance ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: This study reports the characterization of the recombinant 7-kDa protein P2 from Sulfolobus solfataricus and the mutants F31A and F31Y with respect to temperature and pressure stability. As observed in the NMR, FTIR, and CD spectra, wild-type protein and mutants showed substantially similar structures under ambient conditions. However, midpoint transition temperatures of the denaturation process were 361, 334, and 347 K for wild type, F31A, and F31Y mutants, respectively: thus, alanine substitution of phenylalanine destabilized the protein by as much as 27 K. Midpoint transition pressures for wild type and F31Y mutant could not be accurately determined because they lay either beyond (wild type) or close to (F31Y) 14 kbar, a pressure at which water undergoes a phase transition. However, a midpoint transition pressure of 4 kbar could be determined for the F31A mutant, implying a shift in transition of at least 10 kbar. The pressure-induced denaturation was fully reversible; in contrast, thermal denaturation of wild type and mutants was only partially reversible. To our knowledge, both the pressure resistance of protein P2 and the dramatic pressure and temperature destabilization of the F31A mutant are unprecedented. These properties may be largely accounted for by the role of an aromatic cluster where Phe31 is found at the core, because interactions among aromatics are believed to be almost pressure insensitive; furthermore, the alanine substitution of phenylalanine should create a cavity with increased compressibility and flexibility, which also involves an impaired pressure and temperature resistance. Proteins 29:381-390, 1997. © 1997 Wiley-Liss, Inc.
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  • 120
    Digitale Medien
    Digitale Medien
    Highly constrained multiple-copy refinement of protein crystal structures (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 426-432 
    Details
    ISSN: 0887-3585
    Schlagwort(e): overdamped langevin dynamics ; thermal motion ; neurotrophin ; glutamine synthetase ; atomic displacement parameter ; x-ray diffraction data ; loop mobility ; disorder ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In the course of refining atomic protein structures, one often encounters difficulty with molecules that are unusually flexible or otherwise disordered. We approach the problem by combining two relatively recent developments: simultaneous refinement of multiple protein conformations and highly constrained refinement. A constrained Langevin dynamics refinement is tested on two proteins: neurotrophin-3 and glutamine synthetase. The method produces closer agreement between the calculated and observed scattering amplitudes than standard, single-copy, Gaussian atomic displacement parameter refinement. This is accomplished without significantly increasing the number of fitting parameters in the model. These results suggest that loop motion in proteins within a crystal lattice can be extensive and that it is poorly modeled by isotropic Gaussian distributions for each atom. Proteins 29:426-432, 1997. © 1997 Wiley-Liss, Inc.
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  • 121
    Digitale Medien
    Digitale Medien
    Chaos in protein dynamics (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 417-425 
    Details
    ISSN: 0887-3585
    Schlagwort(e): nonlinear dynamics ; chaotic motion in complex systems ; protein folding pathways ; molecular dynamics ; Lyapunov exponent ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: MD simulations, currently the most detailed description of the dynamic evolution of proteins, are based on the repeated solution of a set of differential equations implementing Newton's second law. Many such systems are known to exhibit chaotic behavior, i.e., very small changes in initial conditions are amplified exponentially and lead to vastly different, inherently unpredictable behavior. We have investigated the response of a protein fragment in an explicit solvent environment to very small perturbations of the atomic positions (10-3-10-9 Å). Independent of the starting conformation (native-like, compact, extended), perturbed dynamics trajectories deviated rapidly, leading to conformations that differ by approximately 1 Å RMSD within 1-2 ps. Furthermore, introducing the perturbation more than 1-2 ps before a significant conformational transition leads to a loss of the transition in the perturbed trajectories. We present evidence that the observed chaotic behavior reflects physical properties of the system rather than numerical instabilities of the calculation and discuss the implications for models of protein folding and the use of MD as a tool to analyze protein folding pathways. Proteins 29:417-425, 1997. © 1997 Wiley-Liss, Inc.
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  • 122
    Digitale Medien
    Digitale Medien
    Mechanisms of signaling and related enzymes (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 401-416 
    Details
    ISSN: 0887-3585
    Schlagwort(e): nucleophilic substitution at phosphorus ; associative mechanisms ; dissociative mechanisms ; transition-state structures ; Staphylococcal nuclease ; protein kinases ; tyrosine kinases ; G proteins ; F1 ATPase ; myosin ATPase ; phosphoserine-phosphothreonine protein phosphatases ; phosphotyrosine protein phosphatases ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Most enzymes involved in cell signaling, such as protein kinases, protein phosphatases, GTPases, and nucleotide cyclases catalyze nucleophilic substitutions at phosphorus. When possible, the mechanisms of such enzymes are most clearly described quantitatively in terms of how associative or dissociative they are. The mechanisms of cell signaling enzymes range from ≤8% associative (cAMP-dependent protein kinase) to ≈50% associative (G protein Giα1). Their catalytic powers range from 105.7 (p21ras) to 1011.7 (λ Ser-Thr protein phosphatase), usually comparable in magnitude with those of nonsignaling enzymes of the same mechanistic class. Exceptions are G proteins, which are 103- to 105-fold poorer catalysts than F1 and myosin ATPases. The lower catalytic powers of G proteins may be ascribed to the absence of general base catalysis, and additionally in the case of p21ras, to the absence of a catalytic Arg residue, which interacts with the transition state. From kinetic studies of mutant and metal ion substituted enzymes, the catalytic powers of cell signaling and related enzymes can be rationalized quantitatively by factors contributed by metal ion catalysis (≥105), general acid catalysis (≈103±1), general base catalysis (≈103±1), and transition-state stabilization by cationic and hydrogen bond donating residues (≈103±1). Proteins 29:401-416, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
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  • 123
    Digitale Medien
    Digitale Medien
    Prediction of the secondary structure of the nicotinic acetylcholine receptor nontransmembrane regions (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 391-398 
    Details
    ISSN: 0887-3585
    Schlagwort(e): neural networks ; automatic predictions ; RAMAN spectroscopy ; IR spectroscopy ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A consensus prediction for the secondary structure of the muscle nicotinic acetylcholine receptor (α, β, γ, and δ subunits) extracellular regions is presented. This protein is a member of the ligand-gated ion channel superfamily, which also encompasses the 5HT3, GABAA, and glycine receptors. The strategy used here is based on the application of six different prediction methods to an alignment of 118 sequences of this superfamily. A consensus prediction was finally produced for each of the four different subunits of the muscle nicotinic receptor nonmembrane regions. The predicted percentages, with respect to the total receptor length, and averaged for the four subunits are as follows: α-helix 29.7%, β-sheet 24.9%, and turn+coil 21.7%. When adding to these values the estimations of the secondary structure reported for the transmembrane region only, the results are in agreement with those obtained experimentally by Yager et al.1 and Méthot et al.2 The deviations with respect to these experimental estimations are α-helix +2.8%, β-sheet -4/-5% and turn+coil +3/+2%, respectively. Considering the predictions made for individual subunits, the best approximation was obtained for the α subunit, with deviations of -0.2% for α-helix, -2.5/-1.5% for β-sheet, and +0.9/+1.9% for turn+coil. The prediction was used to infer the residues involved in forming three helices that presumably flank the ligand-binding pocket and to propose mechanism for transferring the information of the ligand binding to the ion channel. Proteins 29:391-398, 1997. © 1997 Wiley-Liss, Inc.
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  • 124
    Digitale Medien
    Digitale Medien
    Protein modeling by multiple sequence threading and distance geometry (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 38-42 
    Details
    ISSN: 0887-3585
    Schlagwort(e): distance geometry ; homology modeling ; fold recognition ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The application of homology modeling is often limited by the lack of known structures with sufficiently high sequence similarity to the target protein. The recent development of threading methods now enable the identification of likely folding patterns in a number of cases where the structural relatedness between target and template(s) is not detectable at the sequence level. We devised a hybrid method in which fold recognition was performed using the Multiple Sequence Threading (MST) method. The structural equivalences deduced from the threading output were used to guide the distance geometry program DRAGON in the construction of low-resolution Cα/Cβ models. The initial structures were converted to full-atom representation and refined using the general-purpose molecular modeling package QUANTA. The performance of the approach is illustrated on the CASP2 target T0004 (polyribonucleotide nucleotidyltransferase S1 motif (PNS1) from Escherichia coli, PDB code: 1SRO) for which no obvious homologues with known structure were available. The correct fold of PNS1 was successfully identified, and the model was found to be more similar to the experimental PNS1 structure than the scaffold (Cα RMSD of 6.2 Å compared with 6.4 Å). Our results indicate that a sensitive fold recognition algorithm coupled with a distance geometry program capable of rapidly generating initial structures can successfully complement high-resolution homology modeling methods in cases where sequential similarity is low. Proteins, Suppl. 1:38-42, 1997. © 1998 Wiley-Liss, Inc.
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  • 125
    Digitale Medien
    Digitale Medien
    Evolution of model proteins on a foldability landscape (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 461-466 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; molecular evolution ; lattice models ; fitness landscapes ; neutral networks ; spin-glass theory ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non self-averaging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process. Proteins 29:461-466, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 126
    Digitale Medien
    Digitale Medien
    A retrospective analysis of CASP2 threading predictions (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 83-91 
    Details
    ISSN: 0887-3585
    Schlagwort(e): fold recognition ; protein threading ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Analysis of CASP2 protein threading results shows that the success rate of structure predictions varies widely among prediction targets. We set “critical” thresholds in fold recognition specificity and threading model accuracy at the points where “incorrect” CASP2 predictions just outnumber “correct” predictions. Using these thresholds we find that correct predictions were made for all of those targets and for only those targets where more than 50% of target residues may be superimposed on previously known structures. Three-fourths of these correct predictions were furthermore made for targets with greater than 12% residue identity in structural alignment, where characteristic sequence motifs are also present. Based on these observations we suggest that the sustained performance of threading methods is best characterized by counting the numbers of correct predictions for targets of increasing “difficulty.” We suggest that target difficulty may be assigned, once the true structure of the target is known, according to the fraction of residues superimposable onto previously known structures and the fraction of identical residues in those structural alignments. Proteins, Suppl. 1:83-91, 1997. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 127
    Digitale Medien
    Digitale Medien
    Distant homology recognition using structural classification of proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 105-112 
    Details
    ISSN: 0887-3585
    Schlagwort(e): CASP ; fold recognition ; SCOP ; superfamily ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Protein structure prediction is arguably the biggest unsolved problem of structural biology. The notion of the number of naturally occurring different protein folds being limited allows partial solution of this problem by the use of fold recognition methods, which “thread” the sequence in question through a library of known protein folds. The fold recognition methods were thought to be superior to the distant homology recognition methods when there is no significant sequence similarity to known structures. We show here that the Structural Classification of Proteins (SCOP) database, organizing all known protein folds according their structural and evolutionary relationships, can be effectively used to enhance the sensitivity of the distant homology recognition methods to rival the “threading” methods. In the CASP2 experiment, our approach correctly assigned into existing SCOP superfamilies all of the six “fold recognition” targets we attempted. For each of the six targets, we correctly predicted the homologous protein with a very similar structure; often, it was the most similar structure. We correctly predicted local alignments of the sequence features that we found to be characteristic for the protein superfamily containing a given target. Our global alignments, extended manually from these local alignments, also appeared to be rather accurate. Proteins, Suppl. 1:105-112, 1997. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
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  • 128
    Digitale Medien
    Digitale Medien
    Protein folds from pair interactions: A blind test in fold recognition (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 129-133 
    Details
    ISSN: 0887-3585
    Schlagwort(e): knowledge-based potentials ; energy functions ; molecular modeling ; prediction of protein structure ; prediction evaluation ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We submitted nine predictions to CASP2 using our fold recognition program ProFIT. Two of these structures were still unsolved by the end of the experiment, six had a recognizable fold, and one fold was new. Four predictions of the six recognizable folds were correct. Two models were excellent in terms of alignment quality (T0031, T0004): in one the alignment was partially correct (T0014), and one fold was correctly identified (T0038). We discuss improvements of the program and analyze the prediction results. Proteins, Suppl. 1:129-133, 1997. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 129
    Digitale Medien
    Digitale Medien
    CASP2: Report on ab initio predictions (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 151-166 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein structure prediction ; assessment of models ; CASP ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Submissions in the ab initio category included predictions of secondary structure, three-dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 ≥ 68 (Q3 = % of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three-dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK-lysin (target 42), a 78-residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue-residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Benner for segment contacts. Proteins, Suppl. 1:151-166, 1997. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 10 Ill.
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  • 130
    Digitale Medien
    Digitale Medien
    Ab initio protein folding simulations with genetic algorithms: Simulations on the complete sequence of small proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 179-184 
    Details
    ISSN: 0887-3585
    Schlagwort(e): genetic algorithms ; torsion space Monte Carlo ; potential of mean force ; arginine repressor ; protein g3p ; NK-lysin ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Ab-initio folding simulations have been performed on three small proteins using a genetic algorithm- (GA-) based search method which operates on an all atom representation. Simulations were also performed on a number of small peptides expected to be inde pendent folding units. The present genetic algorithm incorporates the results of developments made to the method first tested in CASP1. Additional operators have been introduced into the search in order to allow the simulation of longer sequences and to avoid premature free energy convergence. Secondary structure information derived from a consensus of eight methods and Monte Carlo simulations on sets of homologous sequences has been used to bias the starting populations used in the GA simulations. For the fragment simulations, the results generally have approximately correct local structure, but tend to be too compact, leading to poor RMS error values. One of the three small protein structures has the topology and most of the general organization correct, although many of the details are incorrect. Proteins, Suppl. 1:179-184, 1997. © 1998 Wiley-Liss, Inc.
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  • 131
    Digitale Medien
    Digitale Medien
    More news from proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. i 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 132
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): streptokinase variants ; Streptococcus equisimilis ; Streptococcus pyogenes ; circular dichroism ; fluorescence spectroscopy ; differential scanning calorimetry ; limited proteolysis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 133
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): β-lactamase ; homology-modeling ; carbapenems ; disulfide bridge ; kinetics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 134
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): ribosome-inactivating proteins ; N-glycosidase ; protein-RNA interactions ; molecular recognition ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 10 Ill.
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  • 135
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): small-angle scattering ; x-rays ; allosteric enzymes ; crystal structure ; rigid body modeling ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 136
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): dimeric bacterial hemoglobin ; Vitreoscilla stercoraria ; crystal growth ; x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 1 Tab.
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  • 137
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): protein crystallization ; x-ray crystallography ; thrombolytic agents ; staphylokinase ; STAR ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 138
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 139
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 9 Ill.
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  • 140
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): rab7 ; GTPase ; vesicle ; targeting ; crystal ; kinetics ; NMR ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 141
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): conformation space ; potential energy surface ; connectivity ; topological mapping ; family clustering ; principal coordinate projections ; visualization ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
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  • 142
    Digitale Medien
    Digitale Medien
    Purification, crystallization, and preliminary X-ray studies of 10-formyltetrahydrofolate synthetase from Clostridia acidici-urici (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 319-321 
    Details
    ISSN: 0887-3585
    Schlagwort(e): tetrahydrofolate ; protein crystallization ; folate coenzymes ; purine synthesis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The monofunctional enzyme 10-formyltetrahydrofolate synthetase (THFS), which is responsible for the recruitment of single carbon units from the formate pool into a variety of folate-dependent biosynthetic pathways, has been subcloned, purified, and crystallized. The crystals belong to space group P21, with unit cell dimensions a= 102.4 Å b= 116.5 Å c= 115.8 Å and β = 103.5 Å. The crystal unit cell and diffraction is consistent with an asymmetric unit consisting of the enzyme tetramer, and a specific volume of the unit cell of 2.7 Å3/Da. The crystals diffract to at least 2.3 Å resolution after flash-cooling, when using a rotating anode x-ray source and an RAXIS image plate detector. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Ill.
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  • 143
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): 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
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 8 Ill.
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  • 144
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): crystals ; ribosomes ; extreme thermophile ; translation repressor ; x-ray analysis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 1 Ill.
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  • 145
    Digitale Medien
    Digitale Medien
    Protein structure prediction force fields: Parametrization with quasi-newtonian dynamics (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 367-384 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; force field ; structure prediction ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were-determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field was generated after optimizing less than 70 adjustable parameters, but shows a strong ability to discriminate between native structures and compact misfolded-alternatives. The functional form of the force field was chosen as in molecular mechanics and is not table-driven. It is continuous with continuous derivatives and is thus suitable for use with algorithms such as energy minimization or newtonian dynamics. Proteins 27:367-384, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 146
    Digitale Medien
    Digitale Medien
    Solvent structure at a hydrophobic protein surface (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 395-404 
    Details
    ISSN: 0887-3585
    Schlagwort(e): hydration ; solvation ; protein-solvent interactions ; molecular dynamics ; computer simulation ; GROMOS ; SPC water ; radial distribution function ; solvent residence times ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The impact of an extensive, uniform and hydrophobic protein surface on the behavior of the surrounding solvent is investigated. In particular, focus is placed on the possible enhancement of the structure of water at the interface, one model for the hydrophobic effect. Solvent residence times and radial distribution functions are analyzed around three types of atomic sites (methyl, polar, and positively charged sites) in 1 ns molecular dynamics simulations of the α-helical polypeptide SP-C in water, in methanol and in chloroform. For comparison, water residence times at positively and negatively charged sites are obtained from a simulation of a highly charged α-helical polypeptide from the protein titin in water. In the simulations the structure of water is not enhanced at the hydrophobic protein surface, but instead is disrupted and devoid of positional correlation beyond the first solvation sphere. Comparing solvents of different polarity, no clear trend toward the most polar solvent being more ordered is found. In addition, comparison of the water residence times at nonpolar, polar, positively charged, or negatively charged sites on the surface of SP-C or titin does not reveal pronounced or definite differences. It is shown, however, that the local environment may considerably affect solvent residence times. The implications of this work for the interpretation of the hydrophobic effect are discussed. Proteins 27:395-404, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 147
    Digitale Medien
    Digitale Medien
    A new method for modeling large-scale rearrangements of protein domains (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 410-424 
    Details
    ISSN: 0887-3585
    Schlagwort(e): domain movements ; inter-domain linkers ; conformational calculations ; Monte Carlo-minimization method ; Bence-Jones protein ; lysine/arginine/ornithine-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A method for modeling large-scale rearrangements of protein domains connected by a single- or a double-stranded linker is proposed. Multidomain proteins may undergo substantial domain displacements, while their intradomain structure remains essentially unchanged. The method allows automatic identification of an interdomain linker and builds an all-atom model of a protein structure in internal coordinates. Torsion angles belonging to the interdomain linkers and side chains potentially able to form domain interfaces are set free while all remaining torsions, bond lengths, and bond angles are fixed. Large-scale sampling of the reduced torsion conformational subspace is effected with the “biased probability Monte Carlo-minimization” method [Abagyan, R.A., Totrov, M.M. (1994): J. Mol. Biol. 235, 983-1002]. Solvation and side-chain entropic contributions are added to the energy function. A special procedure has been developed to generate concerted deformations of a double-stranded interdomain linker in such a way that the polypeptide chain continuity is preserved. The method was tested on Bence-Jones protein with a single-stranded linker and lysine/arginine/ornithine-binding (LAO) protein with a double-stranded linker. For each protein, structurally diverse low-energy conformations with ideal covalent geometry were generated, and an overlap between two sets of conformations generated starting from the crystallographically determined “closed” and “open” forms was found. One of the low-energy conformations generated in a run starting from the LAO “closed” form was only 2.2 Å away from the structure of the “open” form. The method can be useful in predicting the scope of possible domain rearrangements of a multidomain protein. Proteins 27:410-424, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 148
    Digitale Medien
    Digitale Medien
    Hydroxynitrile lyase from Hevea brasiliensis: Molecular characterization and mechanism of enzyme catalysis (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 438-449 
    Details
    ISSN: 0887-3585
    Schlagwort(e): α/β hydrolase fold ; catalytic triad ; cyanolysis ; heterologous expression ; Saccharomyces cerevisiae ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: (S)-Hydroxynitrile lyase (Hnl) from the tropical rubber tree Hevea brasiliensis is a 29 kDa single chain protein that catalyses the breakdown or formation of a C(SINGLE BOND)C bond by reversible addition of hydrocyanic acid to aldehydes or ketones. The primary sequence of Hnl has no significant homology to known proteins. Detailed homology investigations employing PROFILESEARCH and secondary structure prediction algorithms suggest that Hnl is a member of the α/β hydrolase fold protein family and contains a catalytic triad as functional residues for catalysis. The significance of the predicted catalytic residues was tested and confirmed by site-directed mutagenesis and expression of mutant and wild-type proteins in the yeast, Saccharomyces cerevisiae. Based on these data we suggest a mechanistic model for the (S)-cyanohydrin synthesis catalyzed by hydroxynitrile lyase from Hevea brasiliensis. Proteins 27:438-449, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 149
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): azurin ; cobalt ; x-ray crystallography ; EPR ; Pseudomonas aeruginosa ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 150
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): class II filamentous bacteriophages ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 151
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): protein structure prediction ; prediction contest ; protein sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 152
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): hinge bending ; hinge axis ; principal component analysis ; essential dynamics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
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  • 153
    Digitale Medien
    Digitale Medien
    Molten globule state of equine β-Lactoglobulin (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 567-575 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; lipocalin ; calycin ; α helix ; β sheet ; CD ; NMR ; ultracentrifugation ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The acid-unfolded state of equine β-lactoglobulin was characterized by means of circular dichroism, nuclear magnetic resonance, analytical gel-filtration chromatography, and analytical centrifugation. The acid-unfolded state of equine β-lactoglobulin has a substantial secondary structure as shown by the far-ultraviolet circular dichroism spectrum but lacks persistent tertiary packing of the side chains as indicated by the near-ultraviolet circular dichroism and nuclear magnetic resonance spectra. It is nearly as compact as the native conformation as shown by the gel filtration and sedimentation experiments, and it has the exposed hydrophobic surface as indicated by its tendency to aggregate. All of these characteristics indicate that the acid-unfolded state of equine β-lactoglobulin is a molten globule state. The α helix content in the acid-unfolded state, which has been estimated from the circular dichroism spectrum, is larger than that in the native state, suggesting the presence of nonnative α helices in the molten globule state. This result suggests the generality of the intermediate with nonnative α helices during the folding of proteins having the β-clam fold. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 6 Ill.
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  • 154
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): 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
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 155
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): docking ; correlation ; DFT ; grid-method ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 156
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): protonation equilibrium ; protein conformation ; continuum electrostatics ; potential of mean force ; force fields ; mean field theory ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 8 Ill.
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  • 157
    Digitale Medien
    Digitale Medien
    Prediction of the structure of the replication initiator protein DnaA (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 1-9 
    Details
    ISSN: 0887-3585
    Schlagwort(e): ATP binding ; DNA-binding protein ; helix-loop-helix motif ; open twisted α/β structure ; P-loop ; sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The secondary structure of DnaA protein and its interaction with DNA and ribonucleotides has been predicted using biochemical, biophysical techniques, and prediction methods based on multiple-sequence alignment and neural networks. The core of all proteins from the DnaA family consists of an “open twisted α/β structure,” containing five α-helices alternating with five β-strands. In our proposed structural model the interior of the core is formed by a parallel β-sheet, whereas the α-helices are arranged on the surface of the core. The ATP-binding motif is located within the core, in a loop region following the first β-strand. The N-terminal domain (80 aa) is composed of two α-helices, the first of which contains a potential leucine zipper motif for mediating protein-protein interaction, followed by a β-strand and an additional α-helix. The N-terminal domain and the α/β core region of DnaA are connected by a variable loop (45-70 aa); major parts of the loop region can be deleted without loss of protein activity. The C-terminal DNA-binding domain (94 aa) is mostly α-helical and contains a potential helix-loop-helix motif. DnaA protein does not dimerize in solution; instead, the two longest C-terminal α-helices could interact with each other, forming an internal “coiled coil” and exposing highly basic residues of a small loop region on the surface, probably responsible for DNA backbone contacts. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 158
    Digitale Medien
    Digitale Medien
    Gas phase hydrogen/deuterium exchange reactions of peptide ions in a quadrupole ion trap mass spectrometer (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 53-58 
    Details
    ISSN: 0887-3585
    Schlagwort(e): ion/molecule reactions ; hydrogen/deuterium exchange ; ion trap ; MALDI ; peptide ions ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Hydrogen/deuterium exchange reactions of protonated and sodium cationized peptide molecules have been studied in the gas phase with a MALDI/quadrupole ion trap mass spectrometer. Unit-mass selected precursor ions were allowed to react with deuterated ammonia introduced into the trap cell by a pulsed valve. The reactant gas pressure, reaction time, and degree of the internal excitation of reactant ions were varied to explore the kinetics of the gas phase isotope exchange. Protonated peptide molecules exhibited a high degree of reactivity, some showing complete exchange of all labile hydrogen atoms. On the contrary, peptide molecules cationized with sodium exhibited only very limited reactivity, indicating a vast difference between the gas phase structures of the two ions. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 5 Ill.
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  • 159
    Digitale Medien
    Digitale Medien
    The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 41-52 
    Details
    ISSN: 0887-3585
    Schlagwort(e): type II topoisomerase ; gyrase ; coumarin inhibitor ; clorobiocin ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Coumarin antibiotics, such as clorobiocin, novobiocin, and coumermycin A1, inhibit the supercoiling activity of gyrase by binding to the gyrase B (GyrB) subunit. Previous crystallographic studies of a 24-kDa N-terminal domain of GyrB from E. coli complexed with novobiocin and a cyclothialidine analogue have shown that both ligands act by binding at the ATP-binding site. Clorobiocin is a natural antibiotic isolated from several Streptomyces strains and differs from novobiocin in that the methyl group at the 8 position in the coumarin ring of novobiocin is replaced by a chlorine atom, and the carbamoyl at the 3′ position of the noviose sugar is substituted by a 5-methyl-2-pyrrolylcarbonyl group. To understand the difference in affinity, in order that this information might be exploited in rational drug design, the crystal structure of the 24-kDa GyrB fragment in complex with clorobiocin was determined to high resolution. This structure was determined independently in two laboratories, which allowed the validation of equivalent interpretations. The clorobiocin complex structure is compared with the crystal structures of gyrase complexes with novobiocin and 5′-adenylyl-β,γ-imidodiphosphate, and with information on the bound conformation of novobiocin in the p24-novobiocin complex obtained by heteronuclear isotope-filtered NMR experiments in solution. Moreover, to understand the differences in energetics of binding of clorobiocin and novobiocin to the protein, the results from isothermal titration calorimetry are also presented. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 8 Ill.
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  • 160
    Digitale Medien
    Digitale Medien
    Curious structure in “canonical” alanine-based peptides (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 59-71 
    Details
    ISSN: 0887-3585
    Schlagwort(e): π helix ; i,i+5 hydrogen bonding ; molecular dynamics simulations ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We have performed all atom simulations of blocked peptides of the form (AAXAA)3, where X = Gln, Asn, Glu, Asp, Arg, and Lys with explicit water molecules to examine the interactions between side chains spaced i,i-5 in the sequence. Although side chains in this i,i-5 arrangement are commonly believed to be noninteracting, we have observed the formation of unusual i,i-5 main chain hydrogen bonding in such sequences with positively charged residues (Lys) as well as polar uncharged groups (Gln). Our results are consistent with the unusual percentage of hydrogen bonding curves produced by amide exchange measurements on the well-studied sequence acetyl-(AAQAA)3-amide in water (Shalongo, W., Dugad, L., Stellwagen, E. J. Am. Chem. Soc. 116:8288-8293, 1994). Analysis of our simulations indicated that the glutamine side chain showed the greatest propensity to support π helix formation and that the i,i-5 intramolecular hydrogen bonds were stabilized by water-bridging side chain interactions. This intermittent formation of the unusual π helix structure was observed for up to 23% of the total simulation time in some residues in (AAQAA)3. Control studies on peptides with glutamine side chains spaced i,i-3, i,i-4, and i,i-6 did not reveal similar unique structures, providing stronger evidence for the unique role side chain interactions with i,i-5 spacing. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 11 Ill.
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  • 161
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 162
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 163
    Digitale Medien
    Digitale Medien
    Crystallization and preliminary x-ray analysis of Escherichia coli peptidyl-tRNA hydrolase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 135-136 
    Details
    ISSN: 0887-3585
    Schlagwort(e): crystallization ; X-ray structure ; peptidyl-tRNA hydrolase ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Peptidyl-tRNA hydrolase from Escherichia coli, a monomer of 21 kDa, was overexpressed from its cloned gene pth and crystallized by using polyethylene glycol as precipitant. The crystals are orthorhombic and have unit cell parameters a = 47.24 Å, b = 63.59 Å, and c = 62.57 Å. They belong to space group P212121 and diffract to better than 1.2 Å resolution. The structure is being solved by multiple isomorphous replacement. © 1997 Wiley-Liss Inc.
    Materialart: Digitale Medien
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  • 164
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): collision theory ; protein-protein association ; electrostatic interactions ; dipole steering ; barnase-barstar complex ; rotational-translational entropy ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
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  • 165
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): D-xylose isomerase ; protein crystallography ; enzyme kinetics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 5 Ill.
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  • 166
    Digitale Medien
    Digitale Medien
    Ligand-based protein alignment and isozyme specificity of glutathione S-transferase inhibitors (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 202-216 
    Details
    ISSN: 0887-3585
    Schlagwort(e): analogues ; model compounds ; bound ligands ; isozymes ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Glutathione S-transferases (GST, E.C.2.5.1.18) comprise a family of detoxification enzymes. Elevated levels of specific GST isozymes in tumor cells are thought responsible for resistance to chemotherapeutics, which renders selective GST inhibitors potentially useful pharmaceutical agents. We discuss the development of a structure activity model that rationalizes the isozyme selectivity observed in a series of 12 glutathione (GSH) analogues. Enzymatic activity data was determined for human P1-1, A1-1, and M2-2 isozymes, and these data were then considered in light of structural features of these three GST proteins. A survey of all GST structures in the PDB revealed that GSH binds to these proteins in a single “bioactive” conformation. To focus on differences between binding sites, we exploited our finding of a common GSH conformation and aligned the GST x-ray structures using bound ligands rather than the backbones of the different proteins. Once aligned, binding site lipophilicity and electrostatic potentials were computed, visualized, and compared. Docking and energy minimization exercises provided additional refinements to a model of selectivity developed initially by visual analysis. Our results suggest that binding site shape and lipophilic character are key determinants of GST isozyme selectivity for close GSH analogues. Proteins 28:202-216, 1997. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 6 Ill.
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  • 167
    Digitale Medien
    Digitale Medien
    Structural trees for protein superfamilies (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 241-260 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein structure comparison ; protein modeling ; stepwise folding ; structural motif ; structural similarity ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Structural trees for large protein superfamilies, such as β proteins with the aligned β sheet packing, β proteins with the orthogonal packing of α helices, two-layer and three-layer α/β proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of α helices and/or β strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for α helices to be packed in α-helical layers and β strands in β layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of α helices and/or β strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold. Proteins 28:241-260, 1997. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 5 Ill.
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  • 168
    Digitale Medien
    Digitale Medien
    Knowledge-based modeling of a bacterial dichloromethane dehalogenase (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 217-226 
    Details
    ISSN: 0887-3585
    Schlagwort(e): homology modeling ; theta class ; glutathione S-transferase ; DM11 ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A three-dimensional structural model of the dichloromethane dehalogenase (DCMD) from Methylophilus sp. DM11 is constructed based on sequence similarities to the glutathione S-transferases (GSTs). To maximize sequence identity and minimize gaps in the alignment, a hybrid approach is used that takes advantage of the increased homology found between DM11 and domain I of the sheep blowfly θ class GST (residues 1-79) and domain II of the human α class GST (residues 81-222). The resulting structure has Cα root mean square deviations of 1.16 Å in domain I and 1.83 Å in domain II from the template GSTs, which compare well to those seen in other GST interclass comparisons. The model is further applied to explore the structural basis for substrate binding and catalysis. A conserved network of hydrogen bonds is described that binds glutathione to the G site, placing the thiol group in a suitable location for nucleophilic attack of dichloromethane. A mechanism is proposed that involves activation through a hydrogen bond interaction between Ser12 and glutathione, similar to that found in the θ-GSTs. The model also demonstrates how aromatic residues in the hydrophobic site (H site) could play a role in promoting catalysis: His116 and Trp117 are ideally situated to accept a growing negative charge on a chlorine of dichloromethane, stabilizing displacement. This scheme is consistent with experimental results of single-point mutations and comparisons with other GST structures and mechanisms. Proteins 28:217-226, 1997. © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 6 Ill.
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  • 169
    Digitale Medien
    Digitale Medien
    Studies of the unfolding of an unstable mutant of staphylococcal nuclease: Evidence for low temperature unfolding and compactness of the high temperature unfolded state (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 227-240 
    Details
    ISSN: 0887-3585
    Schlagwort(e): cold unfolding ; protein folding ; heat capacity change ; fluorescence ; circular dichroism ; size exclusion chromatography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Fluorescence and circular dichroism data as a function of temperature were obtained to characterize the unfolding of nuclease A and two of its less stable mutants. These spectroscopic data were obtained with a modified instrument that enables the nearly simultaneous detection of both fluorescence and CD data on the same sample. A global analysis of these multiple datasets yielded an excellent fit of a model that includes a change in the heat capacity change, ΔCp, between the unfolded and native states. This analysis gives a ΔCp of 2.2 kcal/mol/·K for thermal unfolding of the WT protein and 1.3 and 1.8 kcal/mol/K for the two mutants. These ΔCp values are consistent with significant population of the cold unfolded state at ∼0°C. Independent evidence for the existence of a cold unfolded state is the observation of a separately migrating peak in size exclusion chromatography. The new chromatographic peak is seen near 0°C, has a partition coefficient corresponding to a larger hydrodynamic radius, and shows a red-shifted fluorescence spectrum, as compared to the native protein. Data also indicate that the high-temperature unfolded form of mutant nuclease is relatively compact. Size exclusion chromatography shows the high temperature unfolded form to have a hydrodynamic radius that is larger than that for the native form, but smaller than that for the urea or pH-induced unfolded forms. Addition of chemical denaturants to the high-temperature unfolded form causes a further unfolding of the protein, as indicated by an increase in the apparent hydrodynamic radius and a decrease in the rotational correlation time for Trp140 (as determined by fluorescence anisotropy decay measurements). Proteins 28:227-240, 1997 © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 170
    Digitale Medien
    Digitale Medien
    Role of aromatic amino acids in carbohydrate binding of plant lectins: Laser photo chemically induced dynamic nuclear polarization study of hevein domain-containing lectins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 268-284 
    Details
    ISSN: 0887-3585
    Schlagwort(e): lectins ; agglutinins ; chemically induced dynamic nuclear polarization (CIDNP) ; nuclear magnetic resonance (NMR) ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Carbohydrate recognition by lectins often involves the side chains of tyrosine, tryptophan, and histidine residues. These moieties are able to produce chemically induced dynamic nuclear polarization (CIDNP) signals after laser irradiation in the presence of a suitable radical pair-generating dye. Elicitation of such a response in proteins implies accessibility of the respective groups to the light-absorbing dye. In principle, this technique is suitable to monitor surface properties of a receptor and the effect of ligand binding if CIDNP-reactive amino acids are affected. The application of this method in glycosciences can provide insights into the protein-carbohydrate interaction process, as illustrated in this initial study. It focuses on a series of N-acetylglucosamine-binding plant lectins of increasing structural complexity (hevein, pseudohevein, Urtica dioica agglutinin and wheat germ agglutinin and its domain B), for which structural NMR- or X-ray crystallographic data permit a decision of the validity of the CIDNP method-derived conclusions. On the other hand, the CIDNP data presented in this study can be used for a rating of our molecular models of hevein, pseudohevein, and domain B obtained by various modeling techniques. Experimentally, the shape and intensity of CIDNP signals are determined in the absence and in the presence of specific glycoligands. When the carbohydrate ligand is bound, CIDNP signals of side chain protons of tyrosine, tryptophan, or histidine residues are altered, for example, they are broadened and of reduced intensity or disappear completely. In the case of UDA, the appearance of a new tryptophan signal upon ligand binding was interpreted as an indication for a conformational change of the corresponding indole ring. Therefore, CIDNP represents a suitable tool to study protein-carbohydrate interactions in solution, complementing methods such as X-ray crystallography, high-resolution multidimensional nuclear magnetic resonance, transferred nuclear Overhauser effect experiments, and molecular modeling. Proteins 28:268-284, 1997 © 1997 Wiley-Liss Inc.
    Zusätzliches Material: 9 Ill.
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  • 171
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): SRP ; SRP receptor ; GTPase ; expression ; crystallization ; x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 1 Ill.
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  • 172
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): chloramphenicol acetyltransferase ; protein structure ; x-ray crystallography ; antibiotic resistance ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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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  • 173
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): protein structure prediction ; protein fold recognition ; empirical energy function ; protein folding force field ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 9 Ill.
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  • 174
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): scorpion ; toxin ; NMR ; structure ; hydrophobic potentials ; electrostatic potentials ; CSαβ motif ; sodium channel ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
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  • 175
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): serine esterase ; enantiomeric inhibition ; stochastic dynamics ; ab initio calculations ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 10 Ill.
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  • 176
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): molecular recognition ; automated docking ; protein domains ; secondary structure elements ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
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  • 177
    Digitale Medien
    Digitale Medien
    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
    Schlagwort(e): 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
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: 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.
    Zusätzliches Material: 7 Ill.
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  • 178
    Digitale Medien
    Digitale Medien
    Crystals of cytochrome c-553 from Bacillus pasteurii show diffraction to 0.97 å resolution (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 580-585 
    Details
    ISSN: 0887-3585
    Schlagwort(e): B. pasteurii ; gram positive ; cytochrome c553 ; purification ; electron transfer ; crystallization ; x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We report here the purification and characterization of a c-type cytochrome present in the soluble fraction of the gram-positive, alkaliphilic, and highly ureolytic soil bacterium Bacillus pasteurii. The cytochrome is acidic (pI = 3.3), has a molecular mass of 9.5 kDa, and appears to dimerize in 150 mM ionic strength solution. The electronic spectrum is typical of a low-spin hexa-coordinated heme iron. Crystals of the protein in the oxidized state were grown by vapor diffusion at pH 5, by using 3.2 M ammonium sulfate as precipitant. Diffraction data at ultrahigh resolution (0.97 Å) and completeness (99.9%) have been collected under cryogenic conditions, by using synchrotron radiation. The crystals belong to the orthorhombic space group P212121, with cell constants a = 37.14, b = 39.42, c = 44.02 Å, and one protein monomer per asymmetric unit. Attempts to solve the crystal structure by ab initio methods are in progress. Proteins 28:580-585, 1997 © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
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  • 179
    Digitale Medien
    Digitale Medien
    Preliminary crystallographic characterization of ricin agglutinin (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 586-589 
    Details
    ISSN: 0887-3585
    Schlagwort(e): ribosome inactivating protein ; RIP ; ricin ; dimer formation ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The quaternary structure of ricin agglutinin (RCA) has been determined by x-ray crystallography. The refined structure of ricin proved to be a successful search model using the molecular replacement method of phase determination. RCA forms an elongated molecule of dimensions 120 Å × 60 Å × 40 Å with two A chains at the center and a B chain at each end. The A chains are covalently associated via a disulfide bridge between Cys 156 of both chains. Additional contacts at residues 114-115 stabilize the dimer interface. The covalent association of RCA A chains was confirmed by gel filtration under reducing and nonreducing conditions. Proteins 28:586-589, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 180
    Digitale Medien
    Digitale Medien
    Crystallization of the RNA-binding domain of the transcriptional antiterminator protein sacy from Bacillus subtilis (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 590-594 
    Details
    ISSN: 0887-3585
    Schlagwort(e): SacY ; antiterminator ; RNA-binding motif ; crystallization ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: SacY is the antiterminator protein involved in the induction by sucrose of the expression of the levansucrase gene (sacB) of Bacillus subtilis. In the presence of sucrose, SacY is activated and prevents premature termination of transcription by binding to a RNA-antiterminator (RAT) sequence partially overlapping with the terminator sequence. SacY consists of a RNA-binding N-terminal domain, SacY(1-55), and a regulatory domain, SacY(56-280), sensitive to the sucrose concentration. SacY(1-55) is in itself capable of binding to the RAT sequence and preventing termination independently of the sucrose concentration. In this paper we describe the overexpression, the purification, and the crystallization of SacY(1-55). We obtained six different crystal forms, some of them diffracting to high resolution (〉1.5 Å). Self rotation function calculations indicated the presence of a dimer in the asymmetric unit, which is in agreement with a proposed oligomeric state in solution as observed by high-resolution NMR measurements. The crystallization of some site-directed cysteine mutants opens the way of solving the structure by multiple isomorphous replacement. Proteins 28:590-594, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
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  • 181
    Digitale Medien
    Digitale Medien
    Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 1-14 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein architecture ; hinge-bending ; lactoferrin ; hexokinase ; actin ; human tissue factor ; human growth factor ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The activity of many proteins induces conformational transitions by hinge-bending, which involves the movement of relatively rigid parts of a protein about flexible joints. We present an algorithm to identify and visualize the movements of rigid domains about common hinges in proteins. In comparing two structures, the method partitions a protein into domains of preserved geometry. The domains are extracted by an adaptive selection procedure using least-squares fitting. The user can maintain the spatial connectivity of the domains and filter significant structural differences (domain movements) from noise in the compared sets of atomic coordinates. The algorithm subsequently characterizes the relative movements of the found domains by effective rotation axes (hinges). The method is applied to several known instances of domain movements in protein structures, namely, in lactoferrin, hexokinase, actin, the extracellular domains of human tissue factor, and the receptor of human growth factor. The results are visualized with the molecular graphics package VMD (Humphrey et al., J. Mol. Graphics 14(1):33-38, 1996). Applications of the algorithm to the analysis of conformational changes in proteins and to biomolecular docking are discussed. Proteins 29:1-14, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 13 Ill.
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  • 182
    Digitale Medien
    Digitale Medien
    Crystallization and preliminary cryogenic X-ray diffraction analyses of protein L-isoaspartyl O-methyltransferase from human fetal brain (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 457-460 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein L-isoaspartyl methyltransferase ; macroseeding ; S-adenosine-L-homocysteine ; protein crystallization ; L-S-adenosyl methionine ; cryocrystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recombinant human fetal brain protein L-isoaspartyl O-methyltransferase, EC 2.1.1.77, was crystallized in PEG 8000 with adenosine homocysteine by a macroseeding technique. The space group was P21 with a = 47.4 Å, b = 53.9 Å, c = 48.7 Å and β = 116.4° for cryofrozen crystals at 90 K. The crystals diffracted to 2.1 Å and have one molecule per asymmetric unit. Proteins 28:457-460, 1997. © 1997 Wiley-Liss, Inc.
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  • 183
    Digitale Medien
    Digitale Medien
    Crystallization and preliminary X-ray diffraction analysis of bovine seminal plasma PDC-109, a protein composed of two fibronectin type II domains (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 454-456 
    Details
    ISSN: 0887-3585
    Schlagwort(e): bull seminal plasma ; fibronectin type II module ; PDC-109 ; heparin-binding protein ; phosphorylcholine-binding protein ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: PDC-109 is a 13 kDa glycoprotein and the major phosphorylcholine- and heparin-binding protein of bull seminal plasma. It is built by an acidic 23-residue N-terminal sequence followed by a tandem of fibronectin type II domains. Full-length PDC-109 was crystallized in complex with o-phosphorylcholine by vapor diffusion in sitting drops. Crystals grew to maximal size of 0.5 × 0.3 × 0.2 mm3, diffract x-rays beyond 2.6 Å resolution, and belong to space group P321 with unit cell dimensions a = b = 93.6 Å, c = 52.7 Å. Proteins 28:454-456, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Tab.
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  • 184
    Digitale Medien
    Digitale Medien
    Are there dominant membrane protein families with a given number of helices? (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 465-466 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 185
    Digitale Medien
    Digitale Medien
    Dichroic statistical model for prediction and analysis of peptide helicity (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 467-480 
    Details
    ISSN: 0887-3585
    Schlagwort(e): peptide helix prediction ; statistical model ; circular dichroism ; residue statistical weights ; peptide bond ellipticity ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Traditional statistical models for the prediction of peptide helicity are written in terms of the mean fractional helicity of the peptide residues. Far ultraviolet circular dichroic measurements of peptide solutions are converted to mean fractional helicity by partitioning the observed ellipticity between that of a perfect helix and a random coil. This partition does not adequately represent the ensemble of peptide molecules present in solution that populate imperfect helical conformations of quite variable lengths. A new dichroic statistical model has been written in terms of ellipticity rather than fractional helical content that recognizes (1) the source of ellipticity, peptide bond adsorption; (2) the differential ellipticity of peptide bonds in the terminal and interior helical turns; and (3) the contributions of each participant in a conformational ensemble to the observed ellipticity. Comparative analyses of host/guest peptides indicates that significant differences are obtained between residue w and n weights and ellipticity values using the traditional and dichroic statistical models. Proteins 28:467-480, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 186
    Digitale Medien
    Digitale Medien
    Simulation of protein crystal nucleation (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 515-521 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein crystallization ; space group symmetry ; protein-protein contacts ; aggregation ; critical nuclei ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: To attempt to understand the physical principles underlying protein crystallization, an algorithm is described for simulating the crystal nucleation event computationally. The validity of the approach is supported by its ability to reproduce closely the well-known preference of proteins for particular space group symmetries. The success of the algorithm supports a recent argument that protein crystallization is limited primarily by the entropic effects of geometric restrictions imposed during nucleation, rather than particular energetic factors. These simulations provide a new tool for attacking the problem of protein crystallization by allowing quantitative evaluation of new ideas such as the use of racemic protein mixtures. Proteins 28:515-521, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
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  • 187
    Digitale Medien
    Digitale Medien
    Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 494-514 
    Details
    ISSN: 0887-3585
    Schlagwort(e): potential of mean force ; molecular recognition ; protein interfaces ; salt bridges ; hydrophobic interaction ; protein crystallization ; contact patches ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A survey was compiled of several characteristics of the intersubunit contacts in 58 oligomeric proteins, and of the intermolecular contacts in the lattice for 223 protein crystal structures. The total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contact patches are frequently smaller than patches involved in oligomer interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acids at oligomer interfaces. Arginine is the only amino acid prominent in both types of interfaces. Potentials of mean force for residue-residue contacts at both crystal and oligomer interfaces were derived from comparison of the number of observed residue-residue interactions with the number expected by mass action. They show that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. They also suggest that complex salt bridges with certain amino acid compositions might be important in oligomer formation. For a protein that is recalcitrant to crystallization, substitution of lysine residues with arginine or glutamine is a recommended strategy. Proteins 28:494-514, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
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  • 188
    Digitale Medien
    Digitale Medien
    Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: Crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 113-125 
    Details
    ISSN: 0887-3585
    Schlagwort(e): bactericidal antibody ; crystal structure ; Neisseria meningitidis ; peptide-fluorescein conjugate ; PorA outer membrane protein ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Class 1 outer membrane protein PorA of Neisseria meningitidis is a vaccine candidate against bacterial meningitis. Antibodies against PorA are able to induce complement-mediated bacterial killing and thereby play an important role in protection against meningococcal disease. Bactericidal antibodies are all directed against variable regions VR1 and VR2 of the PorA sequence, corresponding to loops 1 and 4 of a two-dimensional topology model of the porin with eight extracellular loops. We have determined the crystal structure to 2.6 Å resolution of the Fab fragment of bactericidal antibody MN12H2 against meningococcal PorA in complex with a linear fluorescein-conjugated peptide TKDTNNNL derived from the VR2 sequence of sero-subtype P1.7,16 (residues 180-187) from meningococcal strain H44/76. The peptide folds deeply into the binding cavity of the Fab molecule in a type I β-turn, with the minimal P1.16 epitope DTNNN virtually completely buried. The structure reveals H-bonds and van der Waals interactions with all minimal epitope residues and one essential salt bridge between Asp-182 of the peptide and His-31 of the MN12H2 light chain. The key components of the recognition of PorA epitope P1.16 by bactericidal antibody MN12H2 correspond well with available thermodynamic data from binding studies. Furthermore, they indicate the structural basis of an increased endemic incidence of infection by group B meningococci in England and Wales since 1981 associated with the occurrence of an Neisseria meningitidis escape mutant (strain MC58). The observed three-dimensional conformation of the peptide provides a rationale for the development of a synthetic peptide vaccine against meningococcal disease. Proteins 29:113-125, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 189
    Digitale Medien
    Digitale Medien
    Backbone entropy of loops as a measure of their flexibility: Application to a Ras protein simulated by molecular dynamics (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 127-140 
    Details
    ISSN: 0887-3585
    Schlagwort(e): loops ; proteins ; backbone entropy ; flexibility ; Molecular Dynamics ; Ras protein ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The flexibility of surface loops plays an important role in protein-protein and protein-peptide recognition; it is commonly studied by Molecular Dynamics or Monte Carlo simulations. We propose to measure the relative backbone flexibility of loops by the difference in their backbone conformational entropies, which are calculated here with the local states (LS) method of Meirovitch. Thus, one can compare the entropies of loops of the same protein or, under certain simulation conditions, of different proteins. These loops should be equal in size but can differ in their sequence of amino acids residues. This methodology is applied successfully to three segments of 10 residues of a Ras protein simulated by the stochastic boundary molecular dynamics procedure. For the first time estimates of backbone entropy differences are obtained, and their correlation with B factors is pointed out; for example, the segments which consist of residues 60-65 and 112-117 have average B factors of 67 and 18 Å2, respectively, and entropy difference T ΔS = 5.4 ± 0.1 kcal/mol at T = 300 K. In a large number of recent publications the entropy due to the fast motions (on the ps-ns time scale) of N-H and C-H vectors has been obtained from their order parameter, measured in nuclear magnetic resonance spin relaxation experiments. This enables one to estimate differences in the entropy of protein segments due to folding-unfolding transitions, for example. However, the vectors are assumed to be independent, and the effect of the neglected correlations is unknown; our method is expected to become an important tool for assessing this approximation. The present calculations, obtained with the LS method, suggest that the errors involved in experimental entropy differences might not be large; however, this should be verified in each case. Potential applications of entropy calculations to rational drug design are discussed. Proteins 29:127-140, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Ill.
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  • 190
    Digitale Medien
    Digitale Medien
    Variations on a theme by Debye and Waller: From simple crystals to proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 153-160 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein dynamics ; molecular dynamics ; crambin ; X-ray ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Debye and Waller showed how to adjust scattering intensities in diffraction experiments for harmonic motions of atoms about an average, static reference configuration. However, many motions, particularly in biological molecules as compared to simple crystals, are far from harmonic. We show how, using a variety of simple anharmonic, multiconformational models, it is possible to construct a variety of Generalized Debye-Waller Factors, and understand their meaning. A central result for these cases is that, in principle, intensity factors cannot be obtained from true total mean square displacements of the atoms. We make the distinction between the intensity factors for unimodal quasiharmonic motions and those for the anharmonic, multimodal (valley hopping) motions. Only the former affect the conventional B factors. Proteins 29:153-160, 1997. Published 1997 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
    Zusätzliches Material: 4 Ill.
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  • 191
    Digitale Medien
    Digitale Medien
    VL:VH domain rotations in engineered antibodies: Crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 161-171 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein ; antibody humanization ; quaternary structure ; complementarity-determining region ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The crystal structures of two pairs of Fab fragments have been determined. The pairs comprise both a murine and an engineered human form, each derived from the antitumor antibodies A5B7 and CTM01. Although antigen specificity is maintained within the pairs, antigen affinity varies. A comparison of the hypervariable loops for each pair of antibodies shows their structure has been well maintained in grafting, supporting the canonical loop model. Detailed structural analysis of the binding sites and domain arrangements for these antibodies suggests the differences in antigen affinity observed are likely to be due to inherent flexibility of the hypervariable loops and movements at the VL:VH domain interface. The four structures provide the first opportunity to study in detail the effects of protein engineering on specific antibodies. Proteins 29:161-171, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 192
    Digitale Medien
    Digitale Medien
    Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): Implications for substrate gating and component interactions (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 141-152 
    Details
    ISSN: 0887-3585
    Schlagwort(e): nonheme iron enzyme ; dinuclear iron center ; leucine gate ; reductase binding site ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The crystal structure of the nonheme iron-containing hydroxylase component of methane monooxygenase hydroxylase (MMOH) from Methylococcus capsulatus (Bath) has been solved in two crystal forms, one of which was refined to 1.7 Å resolution. The enzyme is composed of two copies each of three subunits (α2β2γ2), and all three subunits are almost completely α-helical, with the exception of two β hairpin structures in the α subunit. The active site of each α subunit contains one dinuclear iron center, housed in a four-helix bundle. The two iron atoms are octahedrally coordinated by 2 histidine and 4 glutamic acid residues as well as by a bridging hydroxide ion, a terminal water molecule, and at 4°C, a bridging acetate ion, which is replaced at -160°C with a bridging water molecule. Comparison of the results for two crystal forms demonstrates overall conservation and relative orientation of the domain structures. The most prominent structural difference identified between the two crystal forms is in an altered side chain conformation for Leu 110 at the active site cavity. We suggest that this residue serves as one component of a hydrophobic gate controlling access of substrates to and products from the active site. The leucine gate may be responsible for the effect of the B protein component on the reactivity of the reduced hydroxylase with dioxygen. A potential reductase binding site has been assigned based on an analysis of crystal packing in the two forms and corroborated by inhibition studies with a synthetic peptide corresponding to the proposed docking position. Proteins 29:141-152, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 10 Ill.
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  • 193
    Digitale Medien
    Digitale Medien
    Understanding the recognition of protein structural classes by amino acid composition (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 172-185 
    Details
    ISSN: 0887-3585
    Schlagwort(e): non-bonded contacts ; coordination of amino acids ; Kirchhoff matrices ; lattice models ; singular value decomposition ; secondary structure content prediction ; contact patterns ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Knowledge of amino acid composition, alone, is verified here to be sufficient for recognizing the structural class, α, β, α+β, or α/β of a given protein with an accuracy of 81%. This is supported by results from exhaustive enumerations of all conformations for all sequences of simple, compact lattice models consisting of two types (hydrophobic and polar) of residues. Different compositions exhibit strong affinities for certain folds. Within the limits of validity of the lattice models, two factors appear to determine the choice of particular folds: 1) the coordination numbers of individual sites and 2) the size and geometry of non-bonded clusters. These two properties, collectively termed the distribution of non-bonded contacts, are quantitatively assessed by an eigenvalue analysis of the so-called Kirchhoff or adjacency matrices obtained by considering the non-bonded interactions on a lattice. The analysis permits the identification of conformations that possess the same distribution of non-bonded contacts. Furthermore, some distributions of non-bonded contacts are favored entropically, due to their high degeneracies. Thus, a competition between enthalpic and entropic effects is effective in determining the choice of a distribution for a given composition. Based on these findings, an analysis of non-bonded contacts in protein structures was made. The analysis shows that proteins belonging to the four distinct folding classes exhibit significant differences in their distributions of non-bonded contacts, which more directly explains the success in predicting structural class from amino acid composition. Proteins 29:172-185, 1997. Published 1997 Wiley-Liss, Inc.This article is a US Goverment work and, as such, is in the public domain in the United States of America.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 194
    Digitale Medien
    Digitale Medien
    Studies on the inhibitor-binding site of porcine aldehyde reductase: Crystal structure of the holoenzyme-inhibitor ternary complex (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 186-192 
    Details
    ISSN: 0887-3585
    Schlagwort(e): aldo-keto reductase ; diabetic complications ; drug design ; site-directed mutagenesis ; α/β-barrel ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Aldehyde reductase is an enzyme capable of metabolizing a wide variety of aldehydes to their corresponding alcohols. The tertiary structures of aldehyde reductase and aldose reductase are similar and consist of an α/β-barrel with the active site located at the carboxy terminus of the strands of the barrel. We have determined the X-ray crystal structure of porcine aldehyde reductase holoenzyme in complex with an aldose reductase inhibitor, tolrestat, at 2.4 Å resolution to obtain a picture of the binding conformation of inhibitors to aldehyde reductase. Tolrestat binds in the active site pocket of aldehyde reductase and interacts through van der Waals contacts with Arg 312 and Asp 313. The carboxylate group of tolrestat is within hydrogen bonding distance with His 113 and Trp 114. Mutation of Arg 312 to alanine in porcine aldehyde reductase alters the potency of inhibition of the enzyme by aldose reductase inhibitors. Our results indicate that the structure of the inhibitor-binding site of aldehyde reductase differs from that of aldose reductase due to the participation of nonconserved residues in its formation. A major difference is the participation of Arg 312 and Asp 313 in lining the inhibitor-binding site in aldehyde reductase but not in aldose reductase. Proteins 29:186-192, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 195
    Digitale Medien
    Digitale Medien
    A molecular dynamics simulation study of segment B1 of protein G (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 193-202 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein G ; molecular dynamics ; protein folding ; NMR spectroscopy and x-ray crystallography ; bound water ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The immunoglobulin binding protein, segment B1 of protein G, has been studied experimentally as a paradigm for protein folding. This protein consists of 56 residues, includes both β sheet and α helix and contains neither disulfide bonds nor proline residues. We report an all-atom molecular dynamics study of the native manifold of the protein in explicit solvent. A 2-ns simulation starting from the nuclear magnetic resonance (NMR) structure and a 1-ns control simulation starting from the x-ray structure were performed. The difference between average structures calculated over the equilibrium portion of trajectories is smaller than the difference between their starting conformations. These simulation averages are structurally similar to the x-ray structure and differ in systematic ways from the NMR-determined structure. Partitioning of the fluctuations into fast (〈20 ps) and slow (〈20 ps) components indicates that the β sheet displays greater long-time mobility than does the α helix. Clore and Gronenborn [J. Mol. Biol. 223:853-856, 1992] detected two long-residence water molecules by NMR in a solution structure of segment B1 of protein G. Both molecules were found in the fully exposed regions and were proposed to be stabilized by bifurcated hydrogen bonds to the protein backbone. One of these long-residence water molecules, found near an exposed loop region, is identified in both of our simulations, and is seen to be involved in the formation of a stable water-mediated hydrogen bond bridge. The second water molecule, located near the middle of the α helix, is not seen with an exceptional residence time in either as a result of the conformation being closer to the x-ray structure in this region of the protein. Proteins 29:193-202, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 196
    Digitale Medien
    Digitale Medien
    Structure of the LAV6 peptide: A nucleation site for the correct receptor-induced refolding of the CD4-binding domain of HIV1 gp 120 (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 203-211 
    Details
    ISSN: 0887-3585
    Schlagwort(e): peptide folding ; NMR ; gp 120 ; CD4 binding domain ; inverse γ-turn ; nucleation site ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: LAV44 and LAV15 (lymphadenopathy-associated virus) peptides of the CD4-binding region of gp 120 per se bind to the CD4 receptor (Reed and Kinzel, Biochemistry 30:4521-4528, 1991; Lasky et al., Cell 50:975-985, 1987). Depending on the environment, the LAV peptides exhibit the ability to switch cooperatively between β-sheet and helical conformation when solvent polarity is changed past a critical point. This property, which is dependent on the amino acid sequence LPCR, is crucial for receptor binding (Reed and Kinzel, Proc. Natl. Acad. Sci. U.S.A. 90:6761-6765, 1993). Structure determination with 2D-NMR-spectroscopy reveals that LAV6 peptide (sequence: TLPCRI) has a well-defined structure, partially exhibiting inverse γ-turn conformation in aqueous solution. Quantitative evaluation of the NMR data discloses 90% trans-conformation for the peptide bond between leucine and proline. The Ψ- and Φ-angles fall into the typical range for amino acids located in turns. On the other hand, the amino acid sequence C-terminal to the LPCR tetrad has been shown to fold atypically in the absence of these residues. All these results show that the short sequence of LAV6 peptide, with the central amino acids LPCR, displays a matrix-independent structure and may, therefore, act as a conformational template for forming secondary structure in the intact CD4-binding domain of gp 120. Proteins 29:203-211, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 197
    Digitale Medien
    Digitale Medien
    Refolding simulations of an isolated fragment of barnase into a native-like β hairpin: Evidence for compactness and hydrogen bonding as concurrent stabilizing factors (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 212-227 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; compactness ; hydrogen bonding ; peptide conformation ; β hairpin ; Molecular Dynamics simulations ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Experimental evidence and theoretical models both suggest that protein folding is initiated within specific fragments intermittently adopting conformations close to that found in the protein native structure. These folding initiation sites encompassing short portions of the protein are ideally suited for study in isolation by computational methods aimed at peering into the very early events of folding. We have used Molecular Dynamics (MD) technique to investigate the behavior of an isolated protein fragment formed by residues 85 to 102 of barnase that folds into a β hairpin in the protein native structure. Three independent MD simulations of 1.3 to 1.8 ns starting from unfolded conformations of the peptide portrayed with an all-atom model in water were carried out at gradually decreasing temperature. A detailed analysis of the conformational preferences adopted by this peptide in the course of the simulations is presented. Two of the unfolded peptide conformations fold into a hairpin characterized by native and a larger bulk of nonnative interactions. Both refolding simulations substantiate the close relationship between interstrand compactness and hydrogen bonding network involving backbone atoms. Persistent compactness witnessed by side-chain interactions always occurs concomitantly with the formation of backbone hydrogen bonds. No highly populated conformations generated in a third simulation starting from the remotest unfolded conformer relative to the native structure are observed. However, nonnative long-range and medium-range contacts with the aromatic moiety of Trp94 are spotted, which are in fair agreement with a former nuclear magnetic resonance study of a denaturing solution of an isolated barnase fragment encompassing the β hairpin. All this lends reason to believe that the 85-102 barnase fragment is a strong initiation site for folding. Proteins 29:212-227, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 198
    Digitale Medien
    Digitale Medien
    Report on the 1997 Johns Hopkins protein folding meeting (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 259-263 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 199
    Digitale Medien
    Digitale Medien
    Prediction of protein conformational freedom from distance constraints (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 240-251 
    Details
    ISSN: 0887-3585
    Schlagwort(e): molecular dynamics ; essential dynamics ; protein dynamics ; NMR ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD simulation. Although detailed aspects of dynamical mechanisms are not covered and the extent of variations are only estimated in a relative sense, applications to an IgG-binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins. The method may be used to support the design of mutants, when structural fluctuations for a large number of mutants are to be screened. The results suggest that motional freedom in proteins is ruled largely by a set of simple geometric constraints. Proteins 29:240-251, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 200
    Digitale Medien
    Digitale Medien
    SAmBA: An interactive software for optimizing the design of biological macromolecules crystallization experiments (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 252-257 
    Details
    ISSN: 0887-3585
    Schlagwort(e): software ; crystallization ; experimental design ; JAVA ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http://igs-server.cnrs-mrs.fr. Proteins 29:252-257, 1997. © 1997 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Ill.
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