Library

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • 1995-1999  (1,976)
  • 1996  (1,976)
  • Biochemistry and Biotechnology  (1,203)
  • Cell & Developmental Biology  (458)
  • Analytical Chemistry and Spectroscopy  (226)
  • Nuclear reactions
  • Numerical Methods and Modeling
Material
Years
  • 1995-1999  (1,976)
Year
Keywords
  • 101
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 237-252 
    ISSN: 0887-3585
    Keywords: cotranslational folding ; protein secondary structure ; ribosome ; reading frame ; neural network ; computer-prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 102
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 103
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 261-264 
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; calcium-binding myristoylation ; noncrystallographic symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Neurocalcins are novel brain-specific proteins that belong to a new subclass of the EF-hand super-family of calcium binding proteins, defined by the photoreceptor cell-specific protein recoverin (Terasawa et al., J. Biol. Chem. 267:19596-19599, 1992). Here we report the purification and crystallization of unmyristoylated recombinant bovine neurocalcin δ from Escherichia coli. Crystals of a bovine neurocalcin δ have been grown by macro-seeding at room temperature through vapor phase equilibration using the hanging drop technique with ammonium sulfate as the precipitating agent. The crystals diffract to at least 2.5 Å resolution and belong to monoclinic space group P2I with unit cell dimensions a = 42.734 Å, b = 94.343 Å, c = 50.696 Å, and β = 98.37°. The asymmetric unit contains two molecules, with corresponding crystal volume per protein mass (Vm) of 2.29 Å3/Da and solvent fraction of 45% by volume, exhibiting an approximate 222 point symmetry. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 104
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 286-299 
    ISSN: 0887-3585
    Keywords: lattice model of proteins ; Monte Carlo method ; mirror image fold ; multiple mutations ; hydrophobic core repacking ; turn handedness modification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In solution, the B domain of protein A from Staphylococcus aureus (B domain) possesses a three-helix bundle structure. This simple motif has been previously reproduced by Kolinski and Skolnick (Proteins 18: 353-366, 1994) using a reduced representation lattice model of proteins with a statistical interaction scheme. In this paper, an improved version of the potential has been used, and the robustness of this result has been tested by folding from the random state a set of three-helix bundle proteins that are highly homologous to the B domain of protein A. Furthermore, an attempt to redesign the B domain native structure to its topological mirror image fold has been made by multiple mutations of the hydrophobic core and the turn region between helices I and II. A sieve method for scanning a large set of mutations to search for this desired property has been proposed. It has been shown that mutations of native B domain hydrophobic core do not introduce significant changes in the protein motif. Mutations in the turn region were also very conservative; nevertheless, a few mutants acquired the desired topological mirror image motif. A set of all atom models of the most probable mutant was reconstructed from the reduced models and refined using a molecular dynamics algorithm in the presence of water. The packing of all atom structures obtained corroborates the lattice model results. We conclude that the change in the handedness of the turn induced by the mutations, augmented by the repacking of hydrophobic core and the additional burial of the second helix N-cap side chain, are responsible for the predicted preferential adoption of the mirror image structure. © 1996 Wiley-Liss, Inc.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 105
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 315-334 
    ISSN: 0887-3585
    Keywords: particle mesh Ewald ; cutoff ; periodic box ; shell ; root mean square deviation ; atomic fluctuation ; order parameters ; force field ; aqueous solution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Soc. 106:765-784, 1984; J. Comput. Chem. 7:230-252, 1986) vs. Cornell et al. (J. Am. Chem. Soc. 117:5179-5197, 1995)], different treatments of the long-range electrostatic interaction (8 Å cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent-accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N-H backbone vectors.With the Cornell et al. force field and a periodic box model, the simulated structures stay much closer to the experimental X-ray structure than with the older Weiner et al. force field. A further improvement of the simulation is found when the electrostatic interaction is evaluated with the particle mesh Ewald method; after 1.2 ns of simulation the backbone RMSD amounts to only 1.13 Å. The analysis of the dynamic parameters shows that this good structural agreement is not due to a damping of internal motion in the protein.For a given length of simulation time, the shell models achieve an agreement between simulated and experimental structures that is comparable to the best models that employ a periodic box of solvent models. However, compared with the box models, the fluctuations of the protein atoms in the shell models are smaller, and only with simulation times as long as 2 ns do they become of comparable size to the experimental ones. © 1996 Wiley-Liss, Inc.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 106
    ISSN: 0887-3585
    Keywords: structure-based drug design ; ligand-protein recognition ; binding landscapes ; docking funnels ; stochastic search ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Energy landscapes of molecular recognition are explored by performing “semi-rigid” docking of FK-506 and rapamycin with the Fukisawa binding protein (FKBP-12), and flexible docking simulations of the Ro-31-8959 and AG-1284 inhibitors with HIV-1 protease by a genetic algorithm. The requirements of a molecular recognition model to meet thermodynamic and kinetic criteria of ligand-protein docking simultaneously are investigated using a family of simple molecular recognition energy functions. The critical factor that determines the success rate in predicting the structure of ligand-protein complexes is found to be the roughness of the binding energy landscape, in accordance with a minimal frustration principle. The results suggest that further progress in structure prediction of ligand-protein complexes can be achieved by designing molecular recognition energy functions that generate binding landscapes with reduced frustration. © 1996 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 107
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 366-378 
    ISSN: 0887-3585
    Keywords: hydration/solvation ; Kohlrausch-Williams-Watts relaxation ; diffusion ; residence time ; Voronoi polyhedra ; ubiquitin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system containing the globular protein ubiquitin and 4,197 water molecules has been used for the analysis of the influence exerted by a protein on solvent dynamics in its vicinity. Using Voronoi polyhedra, the solvent has been divided into three subsets, i.e., the first and second hydration shell, and the remaining bulk, which is hardly affected by the protein. Translational motion in the first shell is retarded by a factor of 3 in comparison to bulk. Several molecules in the first shell do not reach the diffusive regime within 100 ps. Shell-averaged orientational autocorrelation functions, which are also subject to a retardation effect, cannot be modeled by a single exponential time law, but are instead well-described by a Kohlrausch-Williams-Watts (KWW) function. The underlying distribution of single-molecule rotational correlation times is both obtained directly from the simulation and derived theoretically. The temperature dependence of reorientation is characterized by a strongly varying correlation time, but a virtually temperature-independent KWW exponent. Thus, the coupling of water structure relaxation with the respective environment, which is characteristic of each solvation shell, is hardly affected by temperature. In other words, the functional form of the distributions of single-molecule rotational correlation times is not subject to a temperature effect. On average, a correlation between reorientation and lifetimes of neighborhood relations is observed. © 1996 Wiley-Liss, Inc.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 108
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 379-388 
    ISSN: 0887-3585
    Keywords: protein modeling ; lattice approximation error ; adjusting of energy functions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lattice models of proteins can approximate off-lattice structures to arbitrary precision with RMS (root mean squared) deviations roughly equal to half the lattice spacing (Rykunov et al., Proteins 22:100-109, 1995; Reva et al., J. Comp. Biol., 1996). However, even small distortions in the positions of chain links lead to significant errors in lattice-based energy calculations (Reva et al., J. Comp. Chem., 1996). These errors arise mainly from rigid interactions (such as steric repulsion) which change their energies considerably at a range which is much smaller than the usual accuracy of lattice modeling (〉1.0 Å). To reduce this error, we suggest a procedure of adjusting energy functions to a given lattice. The general approach is illustrated with energy calculations based on pairwise potentials by Kolinski et al. (J. Chem. Phys. 98:1-14, 1993). At all the lattice spacings, from 0.5-3.8 Å, the lattice-adjusted potentials improve the accuracy of lattice-based energy calculations and Increase the correlations between off-lattice and lattice energies. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 109
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 1-8 
    ISSN: 0887-3585
    Keywords: lattice models of proteins ; self-consistent field optimization ; self-avoiding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present an algorithm to build self-avoiding lattice models of chain molecules with low RMS deviation from their actual 3D structures. To find the optimal coordinates for the lattice chain model, we minimize a function that consists of three terms: (1) the sum of squared deviations of link coordinates on a lattice from their off-lattice values, (2) the sum of “short-range” terms, penalizing violation of chain connectivity, and (3) the sum of “long-range” repulsive terms, penalizing chain self-intersections. We treat this function as a chain molecule “energy” and minimize it using self-consistent field (SCF) theory to represent the pairwise link repulsions as 3D fields acting on the links. The statistical mechanics of chain molecules enables computation of the chain distribution in this field on the lattice. The field is refined by iteration to become self-consistent with the chain distribution, then dynamic programming is used to find the optimal lattice model as the “lowest-energy” chain pathway in this SCF. We have tested the method on one of the coarsest (and most difficult) lattices used for model building on proteins of all structural types and show that the method is adequate for building self-avoiding models of proteins with low RMS deviations from the actual structures. © 1996 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 110
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 42-54 
    ISSN: 0887-3585
    Keywords: cell surface receptors ; hematopoietic factors ; cytokines ; structure prediction ; homology modeling ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Stem-cell factor (SCF) is a noncovalent homodimeric cytokine that exhibits profound biological function in the early stages of hematopoiesis by binding to a cell surface tyrosine kinase receptor that is encoded by the c-Kit proto-oncogene. The results obtained from a combined implementation of homology-based molecular modeling and computational simulations in the study of species-specific SCF/c-Kit interactions are reported. The structural models of the human and rat SCF ligands are based on the close structural similarity to the cytokine M-CSF, whose Cα structure has recently become available. The constant domains of the human Fc fragment are used as a template for the ligand binding domains of the c-Kit receptor. The factors responsible for the stabilization of the SCF quaternary structure and the molecular determinants for ligand recognition and ligand specificity have been identified by assessing the conformational, topographical, and dynamic features of the isolated ligands and of the ligand-receptor complexes. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 111
    ISSN: 0887-3585
    Keywords: α/β structure ; β barrel ; electrostatic potential ; flavin adenine dinucleotide ; flavin mononucleotide ; pyridine nucleotide ; structure refinement ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic properties on the protein surface were examined on the basis of the crystal structure of NADH-cytochrome b5 reductase refined to a crystallographic R factor of 0.223 at 2.1 Å resolution and of the other three flavin-dependent reductases. A structural comparison of NADH-cytochrome b5 reductase with the other flavin-dependent reductases, ferredoxin-NADP+ reductase, phthalate dioxygenase reductase, and nitrate reductase, showed that the α/β structure is the common motif for binding pyridine nucleotide. Although the amino acid residues associated with pyridine nucleotide-binding are not conserved, the electrostatic properties and the location of the pyridine nucleotide-binding pockets of NADH-requiring reductases were similar to each other. The electrostatic potential of the surface near the flavin-protruding side (dimethylbenzene end of the flavin ring) of NADH-cytochrome b5 reductase was positive over a wide area while that of the surface near the heme-binding site of cytochrome b5 was negative. This implied that the flavin-protruding side of NADH-cytochrome b5 reductase is suitable for interacting with its electron-transfer partner, cytochrome b5. This positive potential area is conserved among four flavin-dependent reductases. A comparison of the electron-transfer partners of four flavin-dependent reductases showed that there are significant differences in the distribution of electrostatic potential between inter-molecular and inter-domain electron-transfer reactions. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 112
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 66-71 
    ISSN: 0887-3585
    Keywords: BPTI ; folding ; unfolding ; disulfide ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure and folding of basic pancreatic trypsin inhibitor (BPTI) has been studied extensively by experimental means. We report a computer simulation study of the structural stability of various disulfide mutants of BPTI, involving eight 250-psec molecular dynamics simulations of the proteins in water, with and without a phosphate counterion. The presence of the latter alters the relative stability of the single disulfide species [5-55] and [30-51]. This conclusion can explain results of mutational studies and the conservation of residues in homologues of BPTI, and suggests a possible role of ions in stabilizing one intermediate over another in unfolding or folding processes. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 113
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 114
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No Abstracts.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 115
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 116
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 134-145 
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; supercoiling ; structure prediction ; hemagglutinin ; mannose-binding protein ; protein engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The discontinuities found in heptad repeats of α-helical coiled-coil proteins have been characterized. A survey of 40 α-fibrous proteins reveals that only two classes of heptad breaks are prevalent: the stutter, corresponding to a deletion of three residues, and the newly identified “stammer,” corresponding to a deletion of four residues. This restriction on the variety of insertions/deletions encountered gives support to a unifying structural model, where different degrees of supercoiling accommodate the observed breaks. Stutters in the hemagglutinin coiled-coil region have previously been shown to produce an underwinding of the supercoil, and we show here how, in other cases, stammers would lead to overwinding. An analysis of main-chain structure also indicates that the mannose-binding protein, as well as hemagglutinin, contains an underwound coiled-coil region. In contrast to knobs-into-holes packing, these models give rise to non-close-packed cores at the sites of the heptad phase shifts. We suggest that such non-close-packed cores may function to terminate certain coiled-coil regions, and may also account for the flexibility observed in such long α-fibrous molecules as myosin. The local underwinding or overwinding caused by these specific breaks in the heptad repeat has a global effect on the structure and can modify both the assembly of the protein and its interaction properties. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 117
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 352-358 
    ISSN: 0887-3585
    Keywords: peptide ; phage displayed library ; tumor-associated antigen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Peptide ligands for tumor-associated TAG72 antigen were identified by screening a large, diverse decapeptide library expressed on the surface of filamentous phages. Fifty-eight clones of phages were selected from the eluates after the third round of biopanning and their DNA inserts were sequenced. A dominant decapeptide HYVSIELPDH (14/58) was found with the binding reactivity for TAG72 antigen in the TAG72-binding ELISA and Western dot blotting. It also showed a preferential binding to colonic adenocarcinomatous cells expressing the TAG72 antigen in the histochemical study. Therefore, this anti-TAG72 decapeptide may be useful in serving as the starting point with regard to further designing peptidomimetics for potential pharmaceuticals.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 118
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 227-237 
    ISSN: 0887-3585
    Keywords: computer simulation ; metalloenzymes ; protein/ligand interactions ; rational drug design ; substrate docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We used molecular dynamics computer simulation to “fly” a small flexible ligand, L-leucine hydroxamic acid, into the active site of thermolysin. The potential, which imposed no constraints between protein and ligand, produced conformations close to the crystallographically determined one. The calculations made use of the combined molecular mechanics/grid method of Luty et al. (J. Comp. Chem. 16:454-464, 1995), in which atoms of the active site are free to move whereas the rest of the protein, assumed to be rigid, is represented as points of a grid, and which also includes an implicit solvation model. The method is sufficiently fast that large sets of simulations could be carried out, enabling statistical sampling and exploration of the effect of initial position and conformation of the ligand on the probability of successful docking. In a charged catalytic Glu/uncharged ligand regime, when the initial position of the ligand was determined by random translations and rotations that kept the center of mass within 8.0 Å of the crystal one, none of the 20 runs placed the ligand correctly. In a second set with uncharged Glu and zwitterionic ligand, 3 of 24 similarly placed random structures flew the ligand in successfully. In a third set with the same protonation scheme as the second the starting positions had randomly determined conformations but kept the hydroxyamate oxygens within 4.0 Å of the zinc; in this case 22 of 25 runs reoriented correctly. A diverse set of energetic, structural, and dynamic criteria was used for evaluation of the calculations. The results indicate the method to be a promising tool for the rational drug design process.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 119
    ISSN: 0887-3585
    Keywords: nucleotide dependent enzymes ; pyrophosphotransferase ; allostery ; substrate-effector complexes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacillus subtilis phosphoribosylpyrophosphate (PRPP) synthetase has been expressed to high levels in an Escherichia coli host strain devoid of endogenous PRPP synthetase. A rapid and efficient purification protocol has been developed allowing production of enzyme preparations with purity conforming to the stringent criteria required for crystallization. Crystallization experiments, in combination with dynamic light scattering studies, have led to the production of three crystal forms of the enzyme. These forms include the free enzyme, the enzyme in a binary complex with the substrate adenosine triphosphate (ATP), and the enzyme in a quaternary complex with the substrate analog α, β-methylene adenosine triphosphate (mATP), the substrate ribose-5-phosphate (Rib-5-P), and the allosteric inhibitor adenosine diphosphate (ADP). Diffraction data showed that all three crystal forms are suitable for structure determination. They crystallize in the same hexagonal space group, P63, with virtually identical unit cell dimensions of a = b = 115.6 Å c = 107.8 Å, and with two molecules in the asymmetric unit. The self-rotation function showed the existence of a non-crystallographic twofold axis perpendicular to the c axis. The availability of the different complexes should allow questions regarding the molecular mechanisms of catalysis and allostery in PRPP synthetase to be addressed.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 120
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 247-252 
    ISSN: 0887-3585
    Keywords: atomic force microscopy ; canavalin ; satellite tobacco mosaic virus ; dislocation ; two-dimensional nuclei ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In the course of time-lapse video and atomic force microscopy (AFM) investigations of macromolecular crystal growth, we frequently observed the sedimentation of microcrystals and three-dimensional nuclei onto the surfaces of much larger, growing protein or virus crystals. This was followed by the direct incorporation over time of the smaller crystals into the bulk of the larger crystals. In some cases, clear indications were present that upon absorption of the small crystal onto the surface of the larger, there was proper alignment of the respective lattices, and consolidation proceeded without observable defect formation, i.e., the two lattices knitted together without discontinuity. In the case of at least one virus crystal, cubic satellite tobacco mosaic virus (STMV), addition of three-dimensional nuclei and subsequent expansion provided the principal growth mechanism at high supersaturation. This process has not been reported for growth from solution of conventional crystals. In numerous other instances, the lattices of the small and larger crystals were obviously misaligned, and incorporation occurred with the formation of some defect. This phenomenon of small crystals physically embedded in larger crystals could only degrade the overall diffraction and materials properties of macromolecular crystals.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 121
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 253-258 
    ISSN: 0887-3585
    Keywords: glycosylasparaginase ; crystallization ; protein purification ; lysosomes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Aspartylglucosaminidase (AGA) is a lysosomal asparaginase that takes part in the ordered degradation of glycoproteins and a deficiency of which results in a lysosomal accumulation disease aspartylglucosaminuria in human. The mature enzyme consists of 24-kDa and 17-kDa subunits, which are both heterogeneously glycosylated. Activation of the enzyme from a single precursor polypeptide into two subunits is accomplished in the endoplasmic reticulum (ER). The relative lack of this proteolytic capacity in several tested high-producing expression systems has complicated the production of active recombinant enzyme in high quantities, which would be an alternative for purification of this molecule for crystallization. Consequently, the AGA enzyme has to be purified directly from cellular or tissue sources for crystallographic analysis. Here we describe a large-scale purification method to produce milligram amounts of homogeneous AGA from human leukocytes. The purified AGA enzyme represents a heterogeneous pool of molecules not only due to glycosylation, but also heterogeneity at the polypeptide level, as demonstrated here. We were able to isolate a homogeneous polypeptide pool that was successfully crystallized and preliminary X-ray data collected from the crystals. The crystals diffract well to 2.0 Å and are thus suitable for determination of the crystal structure of AGA.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 122
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 263-265 
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; POU-domain ; transcription factor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The POU domain, representing an approximately 150 amino acid conserved region, serves as the DNA-recognition domain for a large number of eukaryotic transcription factors. Bipartite in nature, the POU domain is comprised of a N-terminal POU-specific domain connected by a linker of variable length to a C-terminal homeodomain. We report here co-crystals of pituitary-specific factor Pit-1 POU domain bound as a dimer to a 28 bp DNA fragment. The crystals diffract to at least 2.3 Å in resolution and belong to space group P1 with unit cell dimensions of a = 42.5 Å, b = 50.1 Å, c = 55.8 Å, α = 76.7°, β = 79.3°, and γ = 67.2°.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 123
    ISSN: 0887-3585
    Keywords: coiled-coil ; extracellular matrix ; thrombospondin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cartilage oligomeric matrix protein (COMP) is a pentameric glycoprotein of the thrombospondin family found in cartilage and tendon. Self-association of COMP is achieved through the formation of a five-stranded α-helical bundle that involves 64 N-terminal residues (from 20 to 83). The complex is further stabilized by the interchain disulfide bonds between cysteines 68 and 71. We have prepared, by expression in Escherichia coli, several peptides of different lengths from the N-terminal region of COMP and studied their amenability to crystallization. Crystals of the best quality were obtained with a peptide spanning COMP residues 28-72. This peptide forms disulfide linked pentamers with 87% of α-helical structure. Crystals were grown by the hanging drop vapor diffusion method, using polyethylene glycol 1500 as a precipitant. The crystals belong to space group P21 with unit cell dimensions a = 38.47 Å, b = 49.47 Å, c = 54.98 Å, β = 103.84° and contain one pentamer per asymmetric unit. They diffract strongly to at least 1.8 Å resolution.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 124
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 266-268 
    ISSN: 0887-3585
    Keywords: polyamines ; group IV decarboxylases ; pyridoxal phosphate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of truncated (Δ425-461) pyridoxal-5′-phosphate (PLP)-dependent mouse ornithine decarboxylase (mOrnDC′) have been obtained that diffract to 2.2 Å resolution (P21212, a = 119.5 Å, b = 74.3 Å, c = 46.1 Å). OrnDC produces putrescine, which is the precursor for the synthesis of polyamines in eukaryotes. Regulation of activity and understanding of the mechanism of action of this enzyme may aid in the development of compounds against cancer. mOrnDC is a member of group IV PLP-dependent decarboxylases, for which there are no known representative structures.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 125
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 269-271 
    ISSN: 0887-3585
    Keywords: Archaea ; hyperthermophiles ; histone fold ; X-ray diffraction ; anomalous dispersion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: HMfA and HMfB are histone proteins from the thermophilic archaeon Methanothermus fervidus. They wrap DNA into nucleosome-like structures and appear to represent the basic core histone fold. HMfA was crystallized in space groups P42212 and P212121. HMfB crystallized in space group P21212, while a selenomethionine-substituted variant, SeMet-HMfB, yielded crystals in C2221. In all crystal forms HMfA, HMfB, or SeMet-HMfB may be present as homodimers.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 126
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 127
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 128
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 272-273 
    ISSN: 0887-3585
    Keywords: polyamines ; pyridoxal phosphate ; drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Trypanosoma brucei ornithine decarboxylase, expressed and purified from E. coli, has been crystallized by the vapor diffusion method using PEG 3350 as a precipitant. The crystals belong to the monoclinic space group P21 and have cell constants of a = 66.3 Å, b = 151.8 Å, c = 83.7 Å, and β = 101.2°. While larger crystals are twinned, smaller crystals (0.4 × 0.3 × 0.05 mm3) are single.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 129
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 275-291 
    ISSN: 0887-3585
    Keywords: homology modeling ; 5-lipoxygenases ; 12-lipoxygenases ; 15-lipoxygenases ; side chain placement ; arachidonic acid metabolism ; leukotrienes ; lipoxins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lipoxygenases are a class of non-heme iron dioxygenases which catalyze the hydroperoxidation of fatty acids for the biosynthesis of leukotrienes and lipoxins. The structure of the 839-residue soybean lipoxygenase-1 was used as a template to model human 5-, 12-, and 15-lipoxygenases. A distance-based algorithm for placing side chains in a low homology environment (only the four iron ligands were fixed during side chain placement) was devised. Twenty-six of the 56 conserved lipoxygenase residues were grouped in four distinct regions of the enzyme. These regions were analyzed to discern whether the side chain interactions could be duplicated in the models or whether alternate conformers should be considered. The effects of site directed mutagenesis variants were rationalized using the models of the human lipoxygenases. In particular, variants which shifted positional specificity between 12- and 15-lipoxygenase activity were analyzed. Analysis of active site residues produced a model which accounts for observed lipoxygenase positional specificity and stereospecificity.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 130
    ISSN: 0887-3585
    Keywords: protein structure determination by NMR ; distance geometry ; structure calculation with DIANA ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using “realistic” potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 131
    ISSN: 0887-3585
    Keywords: catalysis ; mechanism ; phosphotransfer ; X-ray diffraction ; crystal ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a ternary complex of pig muscle phosphoglycerate kinase (PGK) containing 3-phosphoglycerate (3-PG) and manganese adenylylimidodiphosphate (Mn AMP-PNP) has been determined and refined at 2.0 A resolution. The complex differs from the true substrate ternary complex only in the presence of an imido- rather than an oxylink between β- and γ-phosphates of the bound nucleotide. The 3-PG is bound in a similar manner to that observed in binary complexes. The nucleotide is bound in a similar manner to Mg ADP except that the metal ion is coordinated by all three α-, β-, and γ-phosphates, but not by the protein. The γ-phosphate, which is transferred in the reaction, is not bound by the protein. One further characteristic of the ternary complex is that Arg-38 moves to a position where its guanidinium group makes a triple interaction with the N-terminal domain, the C-terminal domain, and the 1-carboxyl group of the bound 3-PG.Although a hinge-bending conformation change is seen in the ternary complex, it is no larger than that observed in the 3-PG binary complex. To reduce that distance between two bound substrates to a value consistent with the direct in-line transfer known to occur in PGK, we modeled the closure of a pronounced cleft in the protein structure situated between the bound substrates. This closure suggested a mechanism of catalysis that involves the “capture” of the γ-phosphate by Arg-38 and the N-terminus of helix-14, which has a conserved Gly-Gly-Gly phosphate binding motif. We propose that nucleophilic attack by the 1-carboxyl group of the 3-PG on the γ-phosphorus follows the capture of the γ-phosphate, leading to a pentacoordinate transition state that may be stabilized by hydrogen bonds donated by the NH groups in the N-terminus of helix 14 and the guanidinium group of Arg-38. During the course of the reaction the metal ion is proposed to migrate to a position coordinating the α- and β-phosphates and the carboxyl group of Asp-374. The mechanism is consistent with the structural information from binary and ternary substrate complexes and much solution data, and gives a major catalytic role to Arg-38, as indicated by site-directed mutagenesis.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 132
    ISSN: 0887-3585
    Keywords: X-ray protein crystallography ; structure determination ; anomalous scattering ; protein-porphyrin interaction ; metalloporphyrin demetalation ; multiple alignment ; structural comparison ; ferritin and bacterioferritin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystallographic studies of L-chain horse spleen apoferritin (HSF) co-crystallized with Pt-hematoporphyrin IX and Sn-protoporphyrin IX have brought significant new insights into structure-function relationships in ferritins. Interactions of HSF with porphyrins are discussed. Structural results show that the nestling properties into HSF are dependent on the porphyrin moiety. (Only protoporphyrin IX significantly interacts with the protein, whereas hematoporphyrin IX does not.) These studies additionally point out the L-chain HSF ability to demetalate metalloporphyrins, a result which is of importance in looking at the iron storage properties of ferritins. In both compound investigated (whether the porphyrin reaches the binding site or not), the complexation appears to be concomitant with the extraction of the metal from the porphyrin.To analyze further the previous results, a three-dimensional alignment of ferritin sequences based on available crystallographic coordinates, including the present structures, is given. It confirms a high degree of homology between these members of the ferritin family and thus allows us to emphasize observed structural differences: 1) unlike L-chain HSF, H-chain human ferritin presents no preformed binding site; and 2) despite the absence of axial ligands, and due to the demetalation, L-chain HSF is able to host protoporphyrin at a similar location to that naturally found in bacterioferritin.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 133
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 322-334 
    ISSN: 0887-3585
    Keywords: aspartic proteinases ; catalysis ; Hartree-Fock calculations ; substrate binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have performed ab initio Hartree-Fock self-consistent field calculations on the active site of endothiapepsin. The active site was modeled as a formic acid/formate anion moiety (representing the catalytic aspartates, Asp-32 and -215) and a bound water molecule. Residues Gly-34, Ser-35, Gly-217, and Thr-218, which all form hydrogen bonds to the active site, were modeled using formamide and methanol molecules. The water molecule, which is generally believed to function as the attacking nucleophile in catalysis, was allowed to bind to the active site in four distinct configurations. The geometry of each configuration was optimized using two basis sets (4-31G and 4-31G*). The results indicate that in the native enzyme the nucleophilic water is bound in a catalytically inert configuration. However, by rotating the carboxyl group of Asp-32 by about 90° the water molecule can be reorientated to attack the scissile bond of the substrate. A model of the bound enzyme-substrate complex was constructed from the crystal structure of a difluorostatone inhibitor complexed with endothiapepsin. This model suggests that the substrate itself initiates the reorientation of the nucleophilic water immediately prior to catalysis by forcing the carboxyl group of Asp-32 to rotate. The theoretical results predict that the active site of endothiapepsin undergoes a large distortion during substrate binding and this observation has been used to explain some of the kinetics results which have been reported for mutant aspartic proteinases.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 134
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 506-509 
    ISSN: 0887-3585
    Keywords: MAD phasing ; mutagenesis ; auto-digestion ; replication ; dimerization ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of both native and mutant Escherichia coli UmuD′ protein were obtained using the hanging drop method. Soaking the native crystals in solutions of heavy metal ions failed to produce good isomorphous derivatives, and selenomethionine substituted wild-type protein did not crystallize under conditions that gave native crystals. Site-directed mutagenesis was used to change the penultimate residue, a methionine amino acid, to either a valine or a threonine amino acid. Crystals were subsequently obtained from these mutant proteins with and without selenomethionine Incorporation. Crystals of the native, the mutant, and the selenomethionine Incorporated protein were all similar, crystallizing in the P41212 space group. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 135
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 514-516 
    ISSN: 0887-3585
    Keywords: D-amino acid ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The gene encoding the meso-diaminopimelate dehydrogenase (DAPDH) from Corynebacterium glutamicum was overexpressed and purified to homogeneity. Crystals of the binary DAPDH-NADP+ complex were obtained from solutions of polyethylene glycol 8000, 100 mM sodium cacodylate, pH 6.5, and 150-300 mM Mg(OAc)2. The crystals diffract to 2.2 Å, belong to the orthorhombic space group P21, and contain two molecules per asymmetric unit. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 136
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 137
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 138
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 420-424 
    ISSN: 0887-3585
    Keywords: serpin ; β-sheet rearrangement ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A growing body of experimental evidence demonstrates that the serpin antichymotrypsin plays a regulatory role in Alzheimer plaque physiology by interacting with the 42 residue β-amyloid protein, and we have used molecular modeling and energy minimization techniques to study this interaction. Based on the unique plasticity of β-sheet elements in antichymotrypsin (as well as other serpins), we conclude that the interaction of the two proteins is mediated by insertion of the N-terminus of β-amyloid into β-sheet C of antichymotrypsin as a pseudo-strand s1C. This β-strand insertion requires the displacement of native antichymotrypsin strand s1C, which is known to occur partially or completely at different stages of serpin function. Thus, the association of the two proteins in vivo may be facilitated by a particular functional state of the serpin, e.g., the native or protease-complexed state. © 1996 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 139
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 438-445 
    ISSN: 0887-3585
    Keywords: random energy model ; protein-ligand complexes ; docking ; specific recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Random Energy Model of statistical physics is applied to the problem of the specificity of recognition between two biological (macro)molecules forming a non-covalent complex. In this model, the native mode of association is separated by an energy gap from a large body of non-native modes. Whereas the native mode is unique, the non-native modes form an energy spectrum which is approximated by a gaussian distribution. Specificity can then be estimated by writing the partition function and calculating the ratio r of non-native to native modes at thermodynamic equilibrium. We examine three situations: (i) recognition in the absence of a competitor; (ii) recognition in the presence of a competing ligand; (iii) recognition in a heterogeneous mixture. We derive the dependence of the ratio r on temperature and on the concentration of competing ligands, and we estimate the effect of a local perturbation such as can result from a point mutation. Cases (i) and (iii) are modeled by docking experiments in the computer. In case (iii), which is representative of a wide variety of biological situations, we show that Increasing the heterogeneity of a mixture affects the specificity of recognition, even when the concentration of competing species is kept constant. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 140
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 446-455 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; GROMOS ; high pressure ; unfolding ; denaturation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have performed a 800 ps molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) in water coupled to a pressure bath at 1, 10,000, 15,000, and 20,000 bar. The simulation reproduces quite well the experimental behavior of the protein under high pressure. The protein keeps its globular form, but adopts a different conformation with a very small reduction in volume. Some residues in the hydrophobic core become exposed to water and a large part of the secondary structure of the protein, (60% of the sheet structure and 40% of the helical structure) is denatured between 10 and 15 kbar. This is in good agreement with experimental data (Goossens, K., et al. Eur. J. Biochem, 236:254-262, 1996) that show denaturation of BPTI between 8 and 14 kbar. A further Increase of the pressure results in a freezing of the protein as deduced from the large decrease of the mobility of the residues. During the simulation, the normal structure of water changes from an ice Ih-like to an ice VI-like structure, while keeping the liquid state. The driving force of the high pressure induced conformational transition seems be the higher compressibility of the water compared with the protein. This produces a change in the solvent properties and leads to penetration of the solvent into the hydrophobic core. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 141
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 473-485 
    ISSN: 0887-3585
    Keywords: site-directed mutagenesis ; active-site serine ; tyrosine ; glutamic acid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Serine β-lactamases contribute widely to the β-lactam resistance phenomena. Unfortunately, the intimate details of their catalytic mechanism remain elusive and subject to some controversy even though many “natural” and “artificial” mutants of these different enzymes have been isolated.This paper is essentially focused on class C β-lactamases, which contain a Tyr (Tyr150) as the first residue of the second conserved element, in contrast to their class A counterparts, in which a Ser is found in the corresponding position. We have modified this Tyr residue by site-directed mutagenesis. On the basis of the three-dimensional structure of the Enterobacter cloacae P99 enzyme, it seemed that residues Glu272 and His314 might also be important. They were similarly substituted. The modified enzymes were isolated and their catalytic properties determined.Our results indicated that His314 was not required for catalysis and that Glu272 did not play an important role in acylation but was involved to a small extent in the deacylation process. Conversely, Tyr150 was confirmed to be central for catalysis, at least with the best substrates.On the basis of a comparison of data obtained for several class C enzyme mutants and in agreement with recent structural data, we propose that the phenolate anion of Tyr150, in conjunction with the alkyl ammonium of Lys315, acts as the general base responsible for the activation of the active-site Ser64 during the acylation step and for the subsequent activation of a water molecule in the deacylation process.The evolution of the important superfamily of penicillin-recognizing enzymes is further discussed in the light of this proposed mechanism. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 142
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 486-500 
    ISSN: 0887-3585
    Keywords: protein-DNA interaction ; DNA bending ; helix-turn-helix ; Poisson-Boltzmann electrostatics ; docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method is presented to predict overall conformations of protein-DNA complexes on the basis of the known three-dimensional structures of the proteins. The method is restricted to proteins with a common twofold symmetry axis, which show only minor conformational changes upon binding to DNA. The method uses a numerical finite difference solution of the linearized Poisson-Boltzmann equation and subsequent energy minimization cycles. Structural parameters - the rotation angle of the DNA relative to the protein around the common symmetry axis, the protein-DNA distance, and intermolecular hydrogen-bonding contacts - are presented for two test cases, DNA bound to CAP (catabolite gene activator protein) and to the Cro-repressor of bacteriophage 434. The DNA curvature in the starting model of the docking procedure was chosen as a smoothed approximation of the conformation found in the X-ray structures of these complexes. The method is further used to predict the unknown structure of the complex between the factor for inversion stimulation (FIS) and DNA, which is bent upon binding to FIS. In contrast to the test cases, the unknown curvature of the starting model is derived from a calibration of electrostatic precalculations for different proteins according to crystallographically observed DNA bending. The results of the modeling are in good accordance with the experimentally observed overall structure of protein-DNA complexes for the two test cases; for FIS, they correspond to several of the experimentally proposed protein-DNA contacts. © 1996 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 143
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 510-513 
    ISSN: 0887-3585
    Keywords: Leishmania ; parasite metabolism ; selenomethionine ; x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Adenine phosphoribosyltransferase from the protozoan parasite Leishmania donovani has been crystallized in the presence of the substrate Mg2+-α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) or the product adenosine-5-monophosphate, as well as in the absence of ligand. These crystals belong to the space group P6122 or its enantiomorph P6522, with unit cell dimensions of a = b = 64.0 Å, c = 240.5 Å, α = β = 90°, and γ = 120°. The crystals diffract to 1.9 Å. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 144
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 145
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 517-522 
    ISSN: 0887-3585
    Keywords: Hsp (heat shock protein) ; Saccharomyces cerevisiae ; crystallization ; overexpression ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Expression of the Saccharomyces cerevisiae Hsp82 chaperone in a pep4-3- and hsc82-deficient strain of S. cerevisiae yielded over 25% of the total cell protein as intact Hsp82. Similarly, the amino-terminal domain (residues 1-220) of Hsp82 was expressed to 18% of the total cell protein. Crystals of the intact Hsp82 were readily obtained. The crystals were very fragile, suggesting a high solvent content, and diffracted to approximately 8 Å. Tetragonal bipyrimidal crystals of the amino-terminal domain of Hsp82 were readily obtained under a variety of different conditions. The crystals have primitive tetragonal space group (P422, P4122, or its enantiomorph P4322) with unit cell dimensions of a = 75.1 Å and c = 111.3 Å, contain 60% by volume solvent, and diffract to 2.5 Å resolution. Addition of 25% glycerol to the mother liquor gave rise to large rod-shaped crystals. The crystals diffract to 2.8 Å resolution, have an orthorhombic space group (P2221, P21212, or P212121) with cell dimensions of a = 45.2 Å, b = 115.4 Å, and c = 116.9 Å, and a solvent content of 58% by volume. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 146
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 9-31 
    ISSN: 0887-3585
    Keywords: structure prediction ; homology modeling ; conformational search ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present results of structural modeling of the variable fragment of Mα2,3, an antibody capable of neutralizing all short snake toxins. Three different methods were used to model the hypervariable loops: the conformational search algorithm CONGEN (Bruccoleri and Karplus, Biopolymers 26:137-168, 1987), high-temperature molecular dynamics (Bruccoleri and Karplus, Biopolymers 29:1847-1862, 1990), and a combined knowledge-based and energy-based algorithm (Martin et al., Proc. Natl. Acad. Sci. USA 86:9268-9272, 1989). Ninety plausible conformations were generated and were clustered into 13 classes. The clustering results indicate that there was little overlap of the conformational space explored by the different methods. Canonical loop structures were found by all methods for two of the loops, in agreement with previously established empirical modeling criteria. Nine of the 13 classes of structure were rejected on the ground of their lacking common features of antibody combining-site structure. The remaining four models were refined using restrained molecular dynamics. It was found that interconversion between the four resulting structures is possible with no significant energy barriers, suggesting that they are in thermodynamic equilibrium at 300 K. Features of the combining-site structure likely to be particularly important for antigen binding are discussed. © 1996 Wiley-Liss, Inc.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 147
    ISSN: 0887-3585
    Keywords: avian lysozyme ; anti-protein Fab ; antibody-antigen complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The HyHEL-5 antibody has more than a thousandfold lower affinity for bobwhite quail lysozyme (BWQL) than for hen egg-white lysozyme (HEL). Four sequence differences exist between BWQL and HEL, of which only one is involved in the interface with the Fab. The structure of bobwhite quail lysozyme has been determined in the uncomplexed state in two different crystal forms and in the complexed state with HyHEL-5, an anti-hen egg-white lysozyme Fab. Similar backbone conformations are observed in the three molecules of the two crystal forms of uncomplexed BWQL, although they show considerable variability in side-chain conformation. A relatively mobile segment in uncomplexed BWQL is observed to be part of the HyHEL-5 epitope. No major backbone conformational differences are observed in the lysozyme upon complex formation, but side-chain conformational differences are seen in surface residues that are involved in the interface with the antibody. The hydrogen bonding in the interface between BWQL and HyHEL-5 is similar to that in previously determined lysozyme-HyHEL-5 complexes. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 148
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 95-107 
    ISSN: 0887-3585
    Keywords: yeast ; cross-interface substitutions ; phagemid ; missense mutations ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cassette mutagenesis was used to produce a library of mutations at the interface of the N- and C-terminal helices of Saccharomyces cerevisiae iso-1-cytochrome c. The library is random and comprises 〉98% mutations. Over 11,000 candidates were assayed for function by selecting for the ability of yeast, with the mutated gene as their sole cytochrome c source, to grow on nonfermentable carbon sources. We estimate that ≈0.5% of the 160,000 total amino acid combinations at these four residues result in a functional cytochrome c. Significant correlations are found between the phenotype of yeast harboring the alleles and both the Dayhoff mutation matrix and transfer free energies (cyclohexane-to-water and n-octanol-to-water). Similar correlations are observed with respect to growth rate. Finally, sequences that are consistent with function follow a binary amino acid pattern. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 149
    ISSN: 0887-3585
    Keywords: crystallization ; interferon-γ ; receptor complex ; purification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray diffraction quality crystals have been obtained from a complex between interferon γ and the extracellular domain of its high-affinity cell surface receptor. The crystals were obtained from interferon γ/interferon γ receptor complexes purified by size exclusion chromatography. Diffraction quality crystals required analyzing these complex samples by isoelectric focusing gels to select purified complex fractions devoid of unbound interferon γ. These studies used interferon γ receptor engineered with an eight amino acid N-terminal deletion to eliminate heterogeneity generated due to proteolytic cleavage. In addition, the receptor was expressed in an E. coli secretion cell line which eliminated the need to refold the protein. Hexagonal crystals were grown from 1.6 M ammonium phosphate solutions and belong to a spacegroup of P6522 with unit cell dimensions a = 145.9 Å and c = 180.3 Å. These crystals diffract to at least 2.9 Å resolution when exposed to synchrotron radiation. SDS PAGE analysis of the crystals demonstrated that both interferon γ and the receptor were present. Analysis of the x-ray diffraction data revealed that the crystals contain complexes with a stoichiometry of 2:1 receptor: ligand within the crystallographic asymmetric unit and consist of approximately 55% solvent. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 150
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 115-117 
    ISSN: 0887-3585
    Keywords: dapD ; protein structure ; succinyl-transferase ; X-ray crystallography ; THDP ; hexapeptide repeat ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of tetrahydrodipicolinate-N-succinyltransferase have been obtained from solutions containing 2-propanol and polyethylene glycol 4,000. These crystals belong to the monoclinic space group P21, diffract X-rays to a resolution of 2.2 Å, and contain one trimer per asymmetric unit. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 151
    ISSN: 0887-3585
    Keywords: Protein crystallization ; X-ray crystallography ; methanogenic Archaea ; hyperthermophilic enzymes ; halophilic enzymes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Formylmethanofuran:tetrahydromethanopterin formyltransferase from the hyperthermophilic methanogenic Archaeon Methanopyrus kandleri (growth temperature optimum 98°C) was crystallized by vapor diffusion methods. Crystal form M obtained with 2-methyl-2,4-pentanediol as precipitant displayed the space group P21 with unit cell parameters of a = 87.0 Å, b = 75.4 Å, c = 104.7 Å, and β = 113.9° and diffracted better than 2 Å resolution. Crystal form P grown from polyethylene glycol 8000 belonged to the space group I4122 and had unit cell parameters of 157.5 Å and 242.1 Å. Diffraction data to 1.73 Å were recorded. Crystal form S which was crystallized from (NH4)2SO4in the space group I4122 with unit cell parameters of 151.3 Å and 249.5 Å diffracted at least to 2.2 Å resolution. All crystal forms probably have four molecules per asymmetric unit and are suitable for X-ray structure analysis. © 1996 Wiley-Liss, Inc.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 152
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 123-133 
    ISSN: 0887-3585
    Keywords: enthalpy ; thermodynamics ; folding/unfolding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two effects are mainly responsible for the observed enthalpy change in protein unfolding: the disruption of internal interactions within the protein molecule (van der Waals, hydrogen bonds, etc.) and the hydration of the groups that are buried in the native state and become exposed to the solvent on unfolding. In the traditional thermodynamic analysis, the effects of hydration have usually been evaluated using the thermodynamic data for the transfer of small model compounds from the gas phase to water. The contribution of internal interactions, on the other hand, are usually estimated by subtracting the hydration effects from the experimental enthalpy of unfolding. The main drawback of this approach is that the enthalpic contributions of hydration, and those due to the disruption of internal interactions, are more than one order of magnitude larger than the experimental enthalpy value. The enthalpy contributions of hydration and disruption of internal interactions have opposite signs and cancel each other almost completely resulting in a final value that is over 10 times smaller than the individual terms. For this reason, the classical approach cannot be used to accurately predict unfolding enthalpies from structure: any error in the estimation of the hydration enthalpy will be amplified by a factor of 10 or more in the estimation of the unfolding enthalpy. Recently, it has been shown that simple parametric equations that relate the enthalpy change with certain structural parameters, especially changes in solvent accessible surface areas have considerable predictive power. In this paper, we provide a physical foundation to that parametrization and in the process we present a system of equations that explicitly includes the enthalpic effects of the packing density between the different atoms within the protein molecule. Using this approach, the error in the prediction of folding/unfolding enthalpies at 60°C, the median temperature for thermal unfolding, is better than ±3% (standard deviation = 4 kcal/mol). © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 153
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 146-156 
    ISSN: 0887-3585
    Keywords: membrane proteins ; seven-helix proteins ; G-protein-coupled receptors ; R factor ; phase error ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacteriorhodopsin (BR), halorhodopsin (HR), and rhodopsin (Rh) all belong to the class of seven-helix membrane proteins. For BR, a structural model at atomic resolution is available; for HR, diffraction data are available only down to a resolution of 6 Å in the membrane plane, and for Rh, down to 9 Å. BR and HR are closely related proteins with a sequence homology of 34%, while Rh does not share any sequence homology with BR. An atomic model for HR is derived that is based on sequence alignment and the atomic model for BR and is improved by molecular dynamics simulations. The model structure obtained accounts well for the experimentally observed difference between HR and BR in the projection map, where HR exhibits a higher density in the region between helices D and E. The reason for this difference lies partially in the different side chains and partially in slightly different helix tilts. The scattering amplitudes and phases of the model structure are calculated and agree with the experimental data down to a resolution of about 8 Å. If the helix positions are adopted from the projection map for HR and used as input in the model, this number improves to 7 Å. Analogously, an atomic model for Rh is derived based on the atomic model for BR and subjected to molecular dynamics simulations. Optimal agreement with the experimental projection map for Rh is obtained when the entire model structure is rotated slightly about two axes in the membrane plane. The agreement with the experimental projection map is not as satisfactory as for HR, but the results indicate that even for a nonhomologous, but structurally related, protein such as Rh, an acceptable model structure can be derived from the structure of BR. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 154
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 167-171 
    ISSN: 0887-3585
    Keywords: protein folding ; Lattice models ; Contact potentials ; Protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To calculate the tertiary structure of a protein from its amino acid sequence, the thermodynamic approach requires a potential function of sequence and conformation that has its global minimum at the native conformation for many different proteins. Here we study the behavior of such functions for the simplest model system that still has some of the features of the protein folding problem, namely two-dimensional square lattice chain configurations involving two residue types. First we show that even the given contact potential, which by definition is used to identify the folding sequences and their unique native conformations, cannot always correctly select which sequences will fold to a given structure. Second, we demonstrate that the given contact potential is not always able to favor the native alignment of a native sequence on its own native conformation over other gapped alignments of different folding sequences onto that same conformation. Because of these shortcomings, even in this simple model system in which all conformations and all native sequences are known and determined directly by the given potential, we must reexamine our expectations for empirical potentials used for inverse folding and gapped alignment on more realistic representations of proteins. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 155
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 186-191 
    ISSN: 0887-3585
    Keywords: protein folds ; number of fold types ; maximum likelihood estimation ; statistical sampling approach ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Many protein structures have now been determined and reveal that protein molecules can adopt the same fold despite having very different sequences. It has been suggested that, owing to different stereochemical constraints, the number of ways that a sequence can fold may be limited. Therefore, it is reasonable to ask how many fold types exist in nature. Several groups have tackled this problem with very different results. In the present study, a novel statistical sampling approach is used to reestimate this number. The results suggest that the number of protein folds in nature is probably several hundreds. © 1996 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 156
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 236-238 
    ISSN: 0887-3585
    Keywords: NAD+ synthetase ; Bacillus subtilis ; protein crystals ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: NAD+-synthetase is a ubiquitous enzyme catalyzing the last step in the biosynthesis of NAD+. Mutants of NAD+ synthetase with impaired cellular functions have been isolated, indicating a key role for this enzyme in cellular metabolism. Crystals of the enzyme from Bacillus subtilis suitable for x-ray crystallographic investigation have been grown from polyethylene glycol solutions. Investigation on the structural organization of NAD+ synthetase, an enzyme fundamental for NAD+ biosynthesis, and belonging to the recently characterized amidotransferase enzymatic family, will provide more insight into the catalytic mechanism of deamido-NAD+ → NAD+ conversion, a biosynthetic process that is a potential target for the development of antibiotic compounds against Bacillus sp. and related bacteria. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 157
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 204-216 
    ISSN: 0887-3585
    Keywords: horseradish peroxidase ; homology modeling ; 2D NMR assignment ; substrate binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this study, two alternative three-dimensional (3D) models of horseradish peroxidase (HRP-C) - differing mainly in the structure of a long untemplated insertion - were refined, systematically assessed, and used to make predictions that can both guide and be tested by future experimental studies. A key first step in the model-building process was a procedure for multiple sequence alignment based on structurally conserved regions and key conserved residues, including those side chains providing ligands to the two Ca2+ binding sites. The model refinements reported here include (1) optimization of side-chain conformations; (3) addition of structural waters using a template-independent procedure; (2) structural refinement of the untemplated 34 amino acid insertion located between the F and G helices, using both energy criteria and NMR data; (4) unconstrained energy optimization of the refined models. Using these procedures, two refined structures of HRP-C were obtained, differing mainly in the conformation of this long insertion. The presence of residues in this insertion that could potentially interact with bound substrates suggests a functional role that may be related to the general ability of class III peroxidases to form stable 1:1 complexes with a variety of substrates. The structural validity of the models was systematically assessed by a variety of criteria. Most notably, the ProsaII z scores and Profiles 3D scores of the two HRP-C models indicated that they are significantly better than would be obtained by simple amino acid replacement, using any of the known structures as a template. These two 3D HRP-C models, were then used to predict candidate residues for the assignment of NOESY cross-peaks previously noted in 2D-NMR studies. Specifically, the residues known as Ile X, Phe A, Phe B, aliphatic residue Q, and Ile T. Candidate substrate binding sites were also identified and compared with experimentally based predictions. This work is timely because new X-ray structures are anticipated that will facilitate the validation of these procedures. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 158
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 192-203 
    ISSN: 0887-3585
    Keywords: molecular recognition ; myoglobin ; Leu ; Ile ; Val binding protein ; lipase ; lysozyme ; azurin ; triose phosphate isomerase ; carbonic anhydrase ; phosphoglycerate kinase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method for the detection of hydrophobic patches on the surfaces of protein tertiary structures is presented. It delineates explicit contiguous pieces of surface of arbitrary size and shape that consist solely of carbon and sulphur atoms using a dot representation of the solvent-accessible surface. The technique is also useful in detecting surface segments with other characteristics, such as polar patches. Its potential as a tool in the study of protein-protein interactions and substrate recognition is demonstrated by applying the method to myoglobin, Leu/Ile/Val-binding protein, lipase, lysozyme, azurin, triose phosphate isomerase, carbonic anhydrase, and phosphoglycerate kinase. Only the largest patches, having sizes exceeding random expectation, are deemed meaningful. In addition to well-known hydrophobic patches on these proteins, a number of other patches are found, and their significance is discussed. The method is simple, fast, and robust. The program text is obtainable by anonymous ftp. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 159
    ISSN: 0887-3585
    Keywords: vestimentifera ; structure ; cryoelectron microscopy ; frozen-hydrated specimens ; single-particle 3D reconstruction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A frozen-hydrated specimen of the V1 hemoglobin of the hydrothermal vent tube worm Riftia pachyptila was observed in the electron microscope and subjected to three-dimensional reconstruction by the method of random conical tilt series. The 3D volume possesses a D6 point-group symmetry. When viewed along its 6-fold axis the vertices of its upper hexagonal layer are 16° clockwise rotated compared to those of the lower layer. A central linker complex is decorated by 12 hollow globular substructures. The linker complex comprises (i) a central hexagonal toroid, (ii) two internal bracelets onto which the hollow globular substructures are built, and (iii) six structures connecting the two hexagonal layers. The hollow globular substructures, related to the dodecamers of globin chains resulting from the dissociation of the hexagonal bilayer hemoglobin, have a local pseudo 3-fold symmetry and are composed each of three elongated structures visible when the volume is displayed at high threshold. At a resolution of 36 Å, the 3D volumes of the hexagonal bilayer hemoglobins of Riftia pachyptyla and of the leech Macrobdella decora look almost perfectly identical. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 160
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A mixed phage library containing random peptides from four to eight residues in length flanked by cysteine residues was screened using a recombinant soluble, form of human ICAM-1, which included residues 1-453, (ICAM-11-453). Phage bound to immobilized ICAM-11-453 were eluted by three methods: (1) soluble ICAM-11-453, (2) neutralizing murine monoclonal antibody, (anti-ICAM-1, M174F5B7), (3) acidic conditions. After three rounds of binding and elution, a single, unique ICAM-1 binding phage bearing the peptide EWCEYLGGYLRYCA was isolated; the identical phage was selected with each method of elution. Attempts to isolate phage from non-constrained (i.e., not containing cysteines) libraries did not yield a phage that bound to ICAM-1. Phage displaying EWCEYLGGYLRCYA bound to immobilized ICAM-11-453 and to ICAM-11-185, a recombinant ICAM-1, which contains only the two amino-terminal immunoglobulin domains residing within residues 1-185. This is the region of the ICAM-1 that is bound by LFA-1. The phage did not bind to proteins other than ICAM-1. The phage bound to two ICAM-1 mutants, which contained amino acid substitutions that dramatically decreased or eliminated the binding to LFA-1. Studies were also performed with the corresponding synthetic peptide. The linear form of the synthetic EWCEYLGGYLRCYA peptide was found to inhibit LFA-1 binding to immobilized ICAM-11-453 in a protein-protein binding assay. By contrast, the disulfide, cyclized, form of the peptide was inactive. The EWCEYL portion of the sequence is homologous to the EWPEYL sequence found within rhinovirus coat protein 14, a nonintegrin protein that binds to ICAM-1. Taken together, the results suggests that the EWCEYLGGYLRCYA sequence is capable to binding to immobilized ICAM-1. Phage display appears to represent a new approach for the identification of peptides that interfere with ICAM-1 binding to β2 integrins. © 1996 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 161
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 271-287 
    ISSN: 0887-3585
    Keywords: protein folding ; protein thermodynamics ; entropy sampling Monte Carlo ; reduced protein models ; folding intermediates ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: There is considerable experimental evidence that the cooperativity of protein folding resides in the transition from the molten globule to the native state. The objective of this study is to examine whether simplified models can reproduce this cooperativity and if so, to identify its origin. In particular, the thermodynamics of the conformational transition of a previously designed sequence (A. Kolinski, W. Galazka, and J. Skolnick, J. Chem. Phys. 103: 10286-10297, 1995), which adopts a very stable Greek-key β-barrel fold has been investigated using the entropy Monte Carlo sampling (ESMC) technique of Hao and Scheraga (M.-H. Hao and H.A. Scheraga, J. Phys. Chem. 98: 9882-9883, 1994). Here, in addition to the original potential, which includes one body and pair interactions between side chains, the force field has been supplemented by two types of multi-body potentials describing side chain interactions. These potentials facilitate the proteinlike pattern of side chain packing and consequently increase the cooperativity of the folding process. Those models that include an explicit cooperative side chain packing term exhibit a well-defined all-or-none transition from a denatured, random coil state to a high-density, well-defined, nativelike low-energy state. By contrast, models lacking such a term exhibit a conformational transition that is essentially continuous. Finally, an examination of the conformations at the free-energy barrier between the native and denatured states reveals that they contain a substantial amount of native-state secondary structure, about 50% of the native contacts, and have an average root mean square radius of gyration that is about 15% larger than native. © 1996 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 162
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 323-352 
    ISSN: 0887-3585
    Keywords: rotamer prediction ; side chain entropy ; solvent accessibility ; simulated annealing ; Monte-Carlo ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A common approach to protein modeling is to propose a backbone structure based on homology or threading and then to attempt to build side chains onto this backbone. A fast algorithm using the simple criteria of atomic overlap and overall rotamer probability is proposed for this purpose. The method was first tested in the context of exhaustive searches of side chain configuration space in protein cores and was then applied to all side chains in 49 proteins of known structure, using simulated annealing to sample space. The latter procedure obtains the correct rotamer for 57% and the correct χ1 value for 74% of the 6751 residues in the sample. When low-temperature Monte-Carlo simulations are initiated from the results of the simulated-annealing processes, consensus configurations are obtained which exhibit slightly more accurate predictions. The Monte-Carlo procedure also allows converged side chain entropies to be calculated for all residues. These prove to be accurate indicators of prediction reliability. For example, the correct rotamer is obtained for 79% and the correct χ1 value is obtained for 84% of the half of the sample residues exhibiting the lowest entropies. Side chain entropy and predictability are nearly completely uncorrelated with solvent-accessible area. Some precedents for and implications of this observation are discussed. © 1996 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 163
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 1-17 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; modeling ; helix packing ; cyclin box ; Rb ; TFIIB ; evolution ; superfolds ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The smooth progression of the eukaryotic cell cycle relies on the periodic activation of members of a family of cell cycle kinases by regulatory proteins called cyclins. Outside of the cell cycle, cyclin homologs play important roles in regulating the assembly of transcription complexes; distant structural relatives of the conserved cyclin core or “box” can also function as general transcription factors (like TFIIB) or survive embedded in the chain of the tumor suppressor, retinoblastoma protein. The present work attempts the prediction of the canonical secondary, supersecondary, and tertiary fold of the minimal cyclin box domain using a combination of techniques that make use of the evolutionary information captured in a multiple alignment of homolog sequences. A tandem set of closely packed, helical modules are predicted to form the cyclin box domain.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 164
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 18-34 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; secondary structure prediction ; tertiary structure prediction ; cyclin ; cell cycle ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present heuristic-based predictions of the secondary and tertiary structures of the cyclins A, B, and D, representatives of the cyclin superfamily. The list of suggested constraints for tertiary structure assembly was left unrefined in order to submit this report before an announced crystal structure for cyclin A becomes available. To predict these constraints, a master sequence alignment over 270 positions of cyclin types A, B, and D was adjusted based on individual secondary structure predictions for each type. We used new heuristics for predicting aromatic residues at protein-protein interfaces and to identify sequentially distinct regions in the protein chain that cluster in the folded structure. The boundaries of two conjectured domains in the cyclin fold were predicted based on experimental data in the literature. The domain that is important for interaction of the cyclins with cyclin-dependent kinases (CDKs) is predicted to contain six helices; the second domain in the consensus model contains both helices and a β-sheet that is formed by sequentially distant regions in the protein chain. A plausible phosphorylation site is identified. This work represents a blinded test of the method for prediction of secondary and, to a lesser extent, tertiary structure from a set of homologous protein sequences. Evaluation of our predictions will become possible with the publication of the announced crystal structure.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 165
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 35-50 
    ISSN: 0887-3585
    Keywords: protein structure ; protein folding ; protein engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We carry out a statistical analysis of the nonbonded interactions in 10 high-resolution nonhomologous protein structures, using original algorithms. We observe a tendency of nonbonded interactions which contribute significantly (i.e., with an energy lower than the average value, referred to as “strong”) to protein stability, to be concentrated in clusters of residues that are strongly sequence correlated. We characterize this sequence correlation and subsequently define a “system” as the pattern that describes these clusters. In order to study the distribution of the systems in the proteins we build a matrix for each protein and for each term of the empirical potential function used to compute the nonbonded interactions; each ij element is the number of common residues between the systems i and j. The analysis of the matrices shows the presence of compact blocks that define units in the protein structure which concentrate strong and weak interactions inside the unit itself and display relative independence with respect to the rest of the protein. Comparing the blocks defined by the three nonbonded energy components (electrostatic, hydrogen bonds, and van der Waals interactions) we observe a one-to-one correspondence between the blocks of different energy components with an average overlap of 90% of the residues forming each block.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 166
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 51-72 
    ISSN: 0887-3585
    Keywords: Markov chain ; vector projection ; forbidden rule ; accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Based on the sequence-coupled (Markov chain) model and vector-projection principle, a discriminant function method is proposed to predict sites in protein substrates that should be susceptible to cleavage by the HIV-1 protease. The discriminant function is defined by Δ = φ+ - φ-, where φ+ and φ- are the cleavable and noncleavable attributes for a given peptide, and they can be derived from two complementary sets of peptides, S+ and S-, known to be cleavable and noncleavable, respectively, by the enzyme. The rate of correct prediction by the method for the 62 cleavable peptides and 239 noncleavable peptides in the training set are 100 and 96.7%, respectively. Application of the method to the 55 sequences which are outside the training set and known to be cleaved by the HIV-1 protease accurately predicted 100% of the peptides as substrates of the enzyme. The method also predicted all but one of the sites hydrolyzed by the protease in native HIV-1 and HIV-2 reverse transcriptases, where the HIV-1 protease discriminates between nearly identical sequences in a very subtle fashion. Finally, the algorithm predicts correctly all of the HIV-1 protease processing sites in the native gag and gag/pol HIV-1 polyproteins, and all of the cleavage sites identified in denatured protease and reverse transcriptase. The new predictive algorithm provides a novel route toward understanding the specificity of this important therapeutic target.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 167
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 81-91 
    ISSN: 0887-3585
    Keywords: hydrostatic pressure ; secondary ; tertiary ; and quaternary structure ; folding ; molten globule ; protein-nucleic acid interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Many biochemists would regard pressure as a physical parameter mainly of theoretical interest and of rather limited value in experimental biochemistry. The goal of this overview is to show that pressure is a powerful tool for the study of proteins and modulation of enzymatic activity.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 168
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 73-80 
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; flavoenzyme ; drug target ; Trypanosoma cruzi ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of the complex between Trypanosoma cruzi trypanothione reductase (TR) (EC 1.6.4.8) and the antiparasitic drug mepacrine (quinacrine) has been solved at 2.9 Å resolution. Mepacrine is a competitive inhibitor of TR but does not affect human glutathione reductase (GR), a closely related host enzyme. Of particular importance for inhibitor binding are four amino acid residues in the disulfide substrate-binding site of TR that are not conserved in human GR, namely, Glu-18 (Ala-34 in GR), Trp-21 (Arg-37), Ser-109 (Ile-113), and Met-113 (Asn-117).The acridine ring of mepacrine is fixed at the active site close to the hydrophobic wall formed by Trp-21 and Met-113. Specific pairwise interactions between functional groups of the drug and amino acid side chains include the ring nitrogen and Met-113, the chlorine atom and Trp-21, and the oxymethyl group and Ser-109. The alkylamino chain of mepacrine points into the inner region of the active site and is held in position by a solvent-mediated hydrogen bond to Glu-18.The structure of the complex shows for the first time the atomic interactions between TR and an inhibitory ligand. This is a crucial step towards the rational design of inhibitors that might be suited as drugs against Chagas' disease. © 1996 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 169
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 138-140 
    ISSN: 0887-3585
    Keywords: ADP-ribosyl cyclase ; crystals ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: ADP-ribosyl cyclase synthesizes the secondary messenger cyclic ADP-ribose from NAD+. Diffraction quality crystals of the enzyme from ovotestes of Aplysia californica have been obtained. Crystallographic analysis of this enzyme will yield insight into the mode of binding of the novel cyclic nucleotide and the mechanism by which NAD+ is cyclized.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 170
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 134-137 
    ISSN: 0887-3585
    Keywords: lectins ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In the seeds of legume plants a class of sugar-binding proteins can be found, generally called legume lectins. In this paper we present the crystallization of phytohemagglutinin-L (PHA-L), a glycosylated lectin from the seeds of the common bean (Phaseolus vulgaris). Single PHA-L crystals were grown by vapor diffusion, using PEG as precipitant. The protein crystallizes in the monoclinic space group C2, and diffracts to a resolution of 2.7 Å. The unit cell parameters are a = 106.3 Å, b = 121.2 Å, c = 90.8 Å, and β = 93.7°. The asymmetric unit probably contains one PHA-L tetramer. Crystals of a recombinant nonglycosylated form of PHA-L, grown under identical conditions, and crystals of the native PHA-L, grown in the presence of isopropanol, did not survive the mounting process.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 171
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 115-133 
    ISSN: 0887-3585
    Keywords: receptor proteins ; estrogen receptor ; DNA bending ; DNA unwinding ; DNA recognition ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to investigate the binding of the glucocorticoid receptor (GR) dimer to DNA. For this purpose simulations of the complex formed by a DNA segment and a dimer of GR-DNA binding domains (GR-DBD) have been carried out, employing an available X-ray structure. A second set of simulations was based on this structure as well, except that the DNA segment was altered to the consensus glucocorticoid response element (GRE). Simulations of a single GR-DBD and of the uncomplexed GRE served as controls. For the simulations, each system was encapsulated in an ellipsoid of water. Protein-DNA interactions, dimer interactions, and DNA structural parameters were analyzed for each system and compared. The consensus GRE is found to yield more favorable and symmetric interactions between the GR-DBDs and the GRE, explaining the ability of the GR dimer to recognize this DNA segment. Further analysis focused on deformations of the DNA that are induced by the binding of GR. The deformations observed involve a 35° bend of the DNA, an unwinding, and a displacement of the helical axis. These deformations are consistent with a mechanism for transcriptional regulation that involves a change of nucleosome packing upon GR binding. Significant protein-protein and protein-DNA interactions, both direct and water mediated, develop due to the deformations of the GRE and are indicative of an increased recognition achieved through DNA deformation. The interactions include direct interactions between the GRE and glycine-458 and serine-459, side groups which differentiate GR from other members of the nuclear hormone receptor family.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 172
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 92-114 
    ISSN: 0887-3585
    Keywords: phospholipid membranes ; permeation ; antibiotics ; computer simulations ; tryptophan ; water ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The microscopic details of lipid-protein interactions are examined using molecular dynamics simulations of the gramicidin A channel embedded in a fully hydrated dimyristoyl phosphatidylcholine (DMPC) bilayer. A novel construction protocol was used to assemble the initial configurations of the membrane protein complex for the simulations. Three hundreds systems were constructed with different initial lipid placement and conformations. Seven systems were simulated with molecular dynamics. One system was simulated for a total of 600 psec, four were simulated for 300 psec, and two for 100 psec. Analysis of the resulting trajectories shows that the bulk solvent-membrane interface region is much broader than traditionally pictured in simplified continuum theories: its width is almost 15 Å. In addition, lipid-protein interactions are far more varied, both structurally and energetically, than is usually assumed: the total interaction energy between the gramicidin A and the individual lipids varies from 0 to -50 kcal/mol. The deuterium quadrupolar splittings of the lipid acyl chains calculated from the trajectories are in good agreement with experimental data. The lipid chains in direct contact with the GA are ordered but the effect is not uniform due to the irregular surface of the protein. Energy decompositions shows that the most energetically favorable interactions between lipid and protein involve nearly equal contributions from van der Waals and electrostatic interactions. The tryptophans, located near the bulk-membrane interface, appear to be particularly important in mediating both hydrogen bonding interactions with the lipid glycerol backbone and water and also in forming favorable van der Waals contacts with the hydrocarbon chains. In contrast, the interactions of the leucine residues with the lipids, also located near the interface, are dominated by van der Waals interactions with the hydrocarbon lipid chains.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 173
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 174
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. iii 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 175
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 141-142 
    ISSN: 0887-3585
    Keywords: cardiotoxin ; hemolysis ; ion channel toxicology ; mushroom ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Volvatoxin A2, an ion channel disturbed cardiotoxic and hemolytic protein from the edible mushroom, Volvarilla volvacea, has been crystallized by the vapor diffusion method using polyethylene glycol 4000 and ammonium sulfate in sodium acetate buffer pH 4.6. The best crystals belong to the monoclinic space group C2 with unit cell dimensions a = 155.25 Å, b = 58.06 Å, c = 116.92 Å, and β = 119.5°. These crystals diffract to at least 2.2 Å and there are four molecules of molecular weight 24 kDa per asymmetric unit with a solvent content of 48%.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 176
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 145-151 
    ISSN: 0887-3585
    Keywords: protein stability ; protein dynamics ; hydrogen exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: All possible protein folding intermediates exist in equilibrium with the native protein at native as well as non-native conditions, with occupation determined by their free energy level. The study of these forms can illuminate the fundamental principles of protein structure and folding. Hydrogen exchange methods can be used to detect and characterize these partially unfolded forms at native conditions and as a function of mild denaturant and temperature. This information illuminates the requirements that govern the ability of kinetic and equilibrium methods to study folding intermediates.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 177
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 152-157 
    ISSN: 0887-3585
    Keywords: antibody X-ray crystallography ; antibody modeling ; protein structure prediction ; structure comparison ; model evaluation ; prediction accuracy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the BR96 antibody variable regions is compared to two X-ray structures of a BR96-carbohydrate complex, independently determined after the model was built and analyzed. The comparison illustrates the opportunities and limitations of antibody modeling. Encouraging results were obtained for the prediction of single CDR loop conformations and for the outline of the BR96 antigen binding site. The comparison of CDR loop conformations in the two X-ray structures provides a realistic reference frame for the CDR loop predictions. CDR loop prediction accuracy is lower when not only conformational, but also positional criteria are taken into account.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 178
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 165-177 
    ISSN: 0887-3585
    Keywords: sequence data sets ; similarity screening ; redundancy reduction ; signal peptides ; database errors ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: When preparing data sets of amino acid or nucleotide sequences it is necessary to exclude redundant or homologous sequences in order to avoid overestimating the predictive performance of an algorithm. For some time methods for doing this have been available in the area of protein structure prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary threshold value for excluding redundant sequences. The impact of the choice of scoring matrix used in the alignments is examined. We demonstrate that the parameter determining the quality of the correlation is the relative entropy of the matrix, rather than the assumed (PAM or identity) substitution model. Results are presented for the case of prediction of cleavage sites in signal peptides. By inspection of the false positives, several errors in the database were found. The procedure presented may be used as a general outline for finding a problem-specific similarity measure and threshold value for analysis of other functional amino acid or nucleotide sequence patterns.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 179
    ISSN: 0887-3585
    Keywords: NMR ; iron-sulfur proteins ; nuclear Overhauser effect ; paramagnetic relaxation ; relaxation matrix analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have accounted for the effect of paramagnetism on the intensities of NOEs in a 73-residue paramagnetic metalloprotein, the reduced high-potential iron sulfur protein ISO I from Ectothiorhodospira halophila, whose solution structure had been recently solved by us. The paramagnetic effects were dealt with through a suitably modified complete relaxation matrix approach. We have then recalculated the structure through a distance geometry program by minimizing the difference between the sixth roots of the calculated and experimental NOEs.The average RMSD, calculated on residues 4-71, within the structures constituting the two families decreased from 0.67 to 0.46 Å for backbone atoms and from 1.23 to 1.06 Å for all heavy atoms. The structures in the new family are for the most part within the indetermination of the previous, less resolved, family. A few specific differences are detected and related to the presence of non-negligible paramagnetic effects, which are now properly evaluated.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 180
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 195-208 
    ISSN: 0887-3585
    Keywords: protein evolution ; conserved cysteine ; pyridoxal phosphate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: It was previously suggested that the conserved Cys-191 of aspartate aminotransferases (AATases) is conserved, not because it is essential, but because it is frozen in the sequence, with no neutral corridor to traverse to the similar phenotype of Ala-191 (Gloss et al., Biochemistry 31:32-39, 1992). This hypothesis has now been tested by additional mutations. All possible one-base mutations from Cys were made at position 191. All of these variants display kinetic parameters (kcat and kcat/KM values) that differ from the wild-type enzyme by 30% or more. The non-conserved cysteines that are predominantly Ala in other AATase sequences (Cys-82, Cys-192, and Cys-401) were mutated to Ser to test the corollary that a neutral Cys → Ala corridor does exist for these positions. These Cys → Ser mutations yielded enzymes with wild-type-like kinetic parameters. The pKa values of the internal aldimines of the mutants, Cys-191 → Ser, Phe, Tyr, and Trp are higher than that of wild type by 0.6-0.8 pH units. The stabilities to urea denaturation of the Cys-191 mutants are similar to that of wild type, while those of the non-conserved cysteines show greater variation. Examination of the three-dimensional environment of the five cysteines showed that the van der Waals contacts of Cys-191 are more conserved than are those of the non-conserved cysteines. These data provide further support for the above hypothesis.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 181
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 353-357 
    ISSN: 0887-3585
    Keywords: VEGF ; angiogenesis ; tumor vascularization ; inclusion bodies ; cysteine mutants ; X-ray crystallography ; crystals ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vascular endothelial growth factor (VEGF) is a potent angiogenic factor with a unique specificity for vascular endothelial cells. In addition to its role in vasculogenesis and embryonic angiogenesis, VEGF is implicated in pathologic neovascularization associated with tumors and diabetic retinopathy. Four different constructs of a short variant of VEGF sufficient for receptor binding were overexpressed in Escherichia coli, refolded, purified, and crystallized in five different space groups. In order to facilitate the product on of heavy atom derivatives, single cysteine mutants were designed based on the crystal structure of platelet-derived growth factor. A construct consisting of residues 8 to 109 was crystallized in space group P21, with cell parameters a = 55.6 Å, b = 60.4 Å, c = 77.7 Å, β = 90.0°, and four monomers in the asymmetric unit. Native and derivative data were collected for two of the cysteine mutants as well as for wild-type VEGF. © 1996 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 182
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 183
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 358-360 
    ISSN: 0887-3585
    Keywords: allergy ; Bet v 1 ; betula ; birch ; pollen ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 17 kDa protein from Betula verrucosa (White Birch) pollen, Bet v 1, is the clinically most important birch pollen allergen causing immediate Type I IgE-mediated allergy. The three-dimensional structure of Bet v 1 and its IgE-binding epitopes are at present not known. In addition, the biological function of Bet v 1 in birch pollen is not fully established. In this work, Bet v 1 has been expressed in Escherichia coli as a recombinant protein, purified and crystallized. The space group of recombinant Bet v 1 crystals is orthorhombic C2221 with unit cell parameters a = 32.13 Å, b = 74.22 Å, and c = 118.60 Å. There is one Bet v 1 molecule per asymmetric unit and the water content is 41%. Crystals diffract to 2.0 Å resolution and a complete native data set was collected from a single crystal using CuKα X-rays from a rotating anode. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 184
    ISSN: 0887-3585
    Keywords: contact maps ; Monte Carlo dynamics ; protein structure prediction ; contact map energy function ; sequence specificity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We introduce an energy function for contact maps of proteins. In addition to the standard term, that takes into account pair-wise interactions between amino acids, our potential contains a new hydrophobic energy term. Parameters of the energy function were obtained from a statistical analysis of the contact maps of known structures. The quality of our energy function was tested extensively in a variety of ways. In particular, fold recognition experiments revealed that for a fixed sequence the native map is identified correctly in an overwhelming majority of the cases tested. We succeeded in identifying the structure of some proteins that are known to pose difficulties for such tests (BPTI, spectrin, and cro-protein). In addition, many known pairs of homologous structures were correctly identified, even when the two sequences had relatively low sequence homology. We also introduced a dynamic Monte Carlo procedure in the space of contact maps, taking topological and polymeric constraints into account by restrictive dynamic rules. Various aspects of protein dynamics, including high-temperature melting and refolding, were simulated. Perspectives of application of the energy function and the method for structure checking and fold prediction are discussed. Proteins 26:391-410 © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 185
    ISSN: 0887-3585
    Keywords: cutinase ; molecular dynamics simulation ; mutant structures ; comparative structural analysis ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In characterizing mutants and covalently inhibited complexes of Fusarium solani cutinase, which is a 197-residue lipolytic enzyme, 34 variant structures, crystallizing in 8 different crystal forms, have been determined, mostly at high resolution. Taking advantage of this considerable body of information, a structural comparative analysis was carried out to investigate the dynamics of cutinase. Surface loops were identified as the major flexible protein regions, particularly those forming the active-site groove, whereas the elements constituting the protein scaffold were found to retain the same conformation in all the cutinase variants studied. Flexibility turned out to be correlated with thermal motion. With a given crystal packing environment, a high flexibility turned out to be correlated with a low involvement in crystal packing contacts. The high degree of crystal polymorphism, which allowed different conformations with similar energy to be detected, made it possible to identify motions which would have remained unidentified if only a single crystal form had been available. Fairly good agreement was found to exist between the data obtained from the structural comparison and those from a molecular dynamics (MD) simulation carried out on the native enzyme. The crystallographic approach used in this study turned out to be a suitable tool for investigating cutinase dynamics. Because of the availability of a set of closely related proteins in different crystal environments, the intrinsic drawback of a crystallographic approach was bypassed. By combining several static pictures, the dynamics of the protein could be monitored much more realistically than what can be achieved on the basis of static pictures alone. Proteins 26:442-458 © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 186
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 187
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 481-482 
    ISSN: 0887-3585
    Keywords: crystallization ; methylenetetrahydrofolate dehydrogenase ; eukaryotes ; prokaryotic enzymes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Saccharomyces cerevisiae possesses three isozymes of 5,10-methylenetetrahydrofolate dehydrogenase (MTD). The NAD-dependent enzyme is the first monofunctional form found in eukaryotes. Here we report its crystallization in a form suitable for high-resolution structure. The space group is P42212 with cell constants a = b = 75.9, c = 160.0 Å, and there is one 36 kDa molecule in the asymmetric unit. Crystals diffract to 2.9 Å resolution. Proteins 26:481-482 © 1996 Wiley-Liss, Inc.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 188
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 178-194 
    ISSN: 0887-3585
    Keywords: electron transfer ; electrostatic surface ; solvent accessibility ; structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The cytochrome c553 from Desulfovibrio vulgaris (DvH c553) is of importance in the understanding of the relationship of structure and function of cytochrome c due to its lack of sequence homology with other cytochromes, and its abnormally low oxido-reduction potential. In evolutionary terms, this protein also represents an important reference point for the understanding of both bacterial and mitochondrial cytochromes c. Using the recently determined nuclear magnetic resonance (NMR) structure of the reduced protein we compare the structural, dynamic, and functional characteristics of DvH c553 with members of both the mitochondrial and bacterial cytochromes c to characterize the protein in the context of the cytochrome c family, and to understand better the control of oxido-reduction potential in electron transfer proteins.Despite the low sequence homology, striking structural similarities between this protein and representatives of both eukaryotic [cytochrome c from tuna (tuna c)] and prokaryotic [Pseudomonas aeruginosa c551 (Psa c551)] cytochromes c have been recognized. The previously observed helical core is also found in the DvH c553. The structural framework and hydrogen bonding network of the DvH c553 is most similar to that of the tuna c, with the exception of an insertion loop of 24 residues closing the heme pocket and protecting the propionates, which is absent in the DvH c553. In contrast, the Psa c551 protects the propionates from the solvent principally by extending the methionine ligand arm. The electrostatic distribution at the recognized encounter surface around the heme in the mitochondrial cytochrome is reproduced in the DvH c553, and corresponding hydrogen bonding networks, particularly in the vicinity of the heme cleft, exist in both molecules.Thus, although the cytochrome DvH c553 exhibits higher primary sequence homology to other bacterial cytochromes c, the structural and physical homology is significantly greater with respect to the mitochondrial cytochrome c. The major structural and functional difference is the absence of solvent protection for the heme, differentiating this cytochrome from both reference cytochromes, which have evolved different mechanisms to cover the propionates. This suggests that the abnormal redox potential of the DvH c553 is linked to the raised accessibility of the heme and supports the theory that redox potential in cytochromes is controlled by heme propionate solvent accessibility.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 189
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 209-217 
    ISSN: 0887-3585
    Keywords: MCCS ; structural evaluation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The accuracy and reliability of the recently proposed scaling-relaxation method for loop closure were examined by using extensive conformational sampling. For each of the eight heptapeptides chosen to represent a variety of protein conformations, 1,000-2,000 conformations were sampled. Each segment contained 14 rotatable backbone dihedral angles. The average root mean square deviations (RMSDs) between the predicted and the native conformations were 0.7 Å for the backbone and 1.2 Å for the side chain atoms. These predictions were substantially more accurate than the previous predictions (1.1 Å for the backbone and 2.2 Å for the side chain atoms) of the same eight protein segments based on limited conformational sampling (100 conformations for each segment). Large prediction errors mostly occurred at polar and surface side chains that are unlikely to have any meaningful conformation. Moreover, the reliability of seven of the eight predictions was demonstrated with their energy-RMSD and stability-RMSD correlations of the low-energy conformations, where the conformational stability was estimated by using the multiple copy simultaneous sampling method.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 190
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 218-226 
    ISSN: 0887-3585
    Keywords: pentamer ; salt bridges ; axial cavity ; thrombospondin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional structure of the assembly domain of the cartilage oligomeric matrix protein (COMP) has been modeled. The model demonstrates a parallel five-stranded coiled coil and fits well with a large amount of experimental data that describe the oligomerization state, the α-helical conformation, the helix directionality and the properties of the (abcdefg)n repeat sequence containing apolar residues at (a) and (d) positions. Comparison of the pentamer model with the known dimer, trimer, and tetramer coiled coils revealed interactions that could mediate the switch to the formation of the pentamer coiled coil. The most distinctive feature of the pentamer model involves ion pair interactions. Charged side chains of the pentamer can form (f-g), (f-b′), and (e-c′) interhelical ion pairs, which are neither experimentally observed nor modeled in the di-, tri-, and tetramers. A polar glutamine residue could be adopted at an interior (d) position of the modeled structure due to the formation of a symmetrical network of buried hydrogen bonds between five such glutamines. The pentamer model contains an axial cavity that can accept water molecules. Conformational analysis was carried out in an attempt to determine the three-dimensional structure of the disulfide bonded C-terminal region of the pentamer. Recent data on crystallization of the COMP assembly domain (Efimov et al., Proteins 24:259-262, 1996) indicate that the prediction can be tested experimentally in the near future.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 191
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 388-393 
    ISSN: 0887-3585
    Keywords: model compounds ; protein thermodynamics ; convergence temperatures ; polar hydration ; protein packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this article we generalize the use of a relationship based on the occurrence of some characteristic temperatures in protein unfolding, which were originally high-lighted for proteins showing the unfolding enthalpy-entropy convergence. On this basis, we show how to dissect the unfolding Gibbs energy of globular proteins in terms of solid-like and liquid-like contributions, untangling the protein energetics by a scheme which does not suffer from excessive intricacy. We also provide an experimental estimate of unfavorable polar contributions to the protein stability, by which it seems possible to evaluate the number of buried residues in individual proteins. A comparison is assessed with the so-called hard sphere model of globular proteins. Results seem to reconcile the view that the protein interior is liquid-like with the observation that protein organization resembles an assembly of closely packed spheres.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 192
    ISSN: 0887-3585
    Keywords: barnase ; site-specific mutagenesis ; RNAse ; RNA ; poly(A) ; pH-profile ; enzyme kinetics ; electrostatics ; Delphi ; Tanford-Kirkwood ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Barnase, the guanine specific ribonuclease of Bacillus amyloliquefaciens, was subjected to mutations in order to alter the electrostatic properties of the enzyme.Ser-85 was mutated into Glu with the goal to introduce an extra charge in the neighborhood of His-102. A double mutation (Ser-85-Glu and Asp-86-Asn) was introduced with the same purpose but without altering the global charge of the enzyme. A similar set of mutations was made using Asp at position 85. For all mutants the pI was determined using the technique of isoelectric focusing and calculated on the basis of the Tanford-Kirkwood theory.When Glu was used to replace Ser-85, the correlation between the experimental and the calculated values was perfect. However, in the Ser-85-Asp mutant, the experimental pI drop is bigger than the calculated one, and in the double mutant (Ser-85-Asp and Asp-86-Asn) the compensation is not achieved.The effect of the mutations on the pKa of His-102 can be determined from the pH dependence of the kcat/KM for the hydrolysis of dinucleotides, e.g., GpC. The effect can also be calculated using the method of Honig. In this case the agreement is very good for the Glu-mutants and the single Asp-mutant, but less for the double Asp-mutant. The global stability of the Asp-mutants is, however, the same as the wild type, as shown by stability studies using urea denaturation. Molecular dynamics calculations, however, show that in the double Asp-mutant His-102 (H+) swings out of its pocket to make a hydrogen bridge with Gln-104 which should cause an additional pKa rise.The effect of the Glu-mutations was also tested on all the kinetic parameters for GpC and the cyclic intermediate G 〉 p at pH 6.5, for RNA at pH 8.0, and for poly(A) at pH 6.2. The effect of the mutations is rather limited for the dinucleotide and the cyclic intermediate, but a strong increase of the KM is observed in the case of the single mutant (extra negative charge) with polymeric substrates.These results indicate that the extra negative charge has a strong destabilizing effect on the binding of the polymeric substrates in the ground state and the transition state complex. A comparison with the structure of bound tetranucleotides (Buckle, A.M. and Fersht, A.R., Biochemistry 33:1644-1653, 1994) shows that the extra negative charge points towards the P2 site.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 193
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 407-408 
    ISSN: 0887-3585
    Keywords: KDOP synthase ; lipopolysaccharide biosynthesis ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: 3-Deoxy-D-manno-octulosonate-8-phosphate (KDOP) synthase catalyzes the production of KDOP from phosphoenolpyruvate (PEP) and arabinose-5-phosphate (A5P). In gram-negative bacteria KDOP is subsequently dephosphorylated, cytidylylated, and linked to lipid A and is required for lipid A incorporation into the outer membrane (Raetz, Annu. Rev. Biochem. 59:129-170, 1990). We have crystallized two forms of KDOP synthase belonging to space groups I23 or I213, one with a = b = c = 118.0 Å and the other with a = b = c = 233 Å.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 194
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 450-466 
    ISSN: 0887-3585
    Keywords: lactate dehydrogenase ; Rossmann fold ; cotranslational folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics (MD) simulations of N-terminal peptides from lactate dehydrogenase (LDH) with increasing length and individual secondary structure elements were used to study their stability in relation to folding. Ten simulations of 1-2 ns of different peptides in water starting from the coordinates of the crystal structure were performed. The stability of the peptides was compared qualitatively by analyzing the root mean square deviation (RMSD) from the crystal structure, radius of gyration, secondary and tertiary structure, and solvent accessible surface area. In agreement with earlier MD studies, relatively short (〈 15 amino acids) peptides containing individual secondary structure elements were generally found to be unstable; the hydrophobic α1-helix of the nucleotide binding fold displayed a significantly higher stability, however. Our simulations further showed that the first βαβ supersecondary unit of the characteristic dinucleotide binding fold (Rossmann fold) of LDH is somewhat more stable than other units of similar length and that the α2-helix, which unfolds by itself, is stabilized by binding to this unit. This finding suggests that the first βαβ unit could function as an N-terminal folding nucleus, upon which the remainder of the polypeptide chain can be assembled. Indeed, simulations with longer units (βαβα and βαβαββ) showed that all structural elements of these units are rather stable. The outcome of our studies is in line with suggestions that folding of the N-terminal portion of LDH in vivo can be a cotranslational process that takes place during the ribosomal peptide synthesis.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 195
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 485-494 
    ISSN: 0887-3585
    Keywords: static quenching ; tryptophan-disulfide interaction ; lifetimes distribution analysis ; blood coagulation ; factor II ; γ-carboxyglutamic acid domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The wavelength dependent fluorescence decay properties of bovine prothrombin fragment 1 have been investigated employing a picosecond time-correlated single photon counting technique. All observations are discussed with using the crystal structure (Soriano-Garcia et al., Biochemistry 31:2554-2566, 1992). Fluorescence lifetimes distribution and conventional multiexponential analysis, as well as acrylamide quenching studies lead to the identification of six distinguishable tryptophan excited-states. Accessibility to the quencher and the known structure are used to associate a fluorescence decay of the tryptophan present in the Gla domain (Trp42) with two red shifted components (2.3 and 4.9 ns). The two kringle domain tryptophans (Trp90 and Trp126) exhibit four decay times (0.06, 0.24, 0.68, and 2.3 ns), which are blue shifted. The calcium-induced fluorescence quenching is a result of static quenching: the five decay times remain unchanged, whereas the fluorescence intensity of Trp42 is decreased. The static quenching process is a consequence of a ground state interaction between the Cys18-Cys23 disulfide bridge and Trp42. The monomolecular equilibrium constant for this disulfide-π-electron interaction is found as 4.8.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 196
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 514-515 
    ISSN: 0887-3585
    Keywords: ketosteroid isomerase ; crystallization ; protein-steroid interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Δ5-3-ketosteroid isomerase from Pseudomonas putida biotype B has been crystallized. The crystals belong to the space group P212121 with unit cell dimensions of a = 36.48 Å, b = 74.30 Å, c = 96.02 Å, and contain one homodimer per asymmetric unit. Native diffraction data to 2.19 Å resolution have been obtained from one crystal at room temperature indicating that the crystals are quite suitable for structure determination by multiple isomorphous replacement.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 197
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 516-519 
    ISSN: 0887-3585
    Keywords: tRNA ; transglycosylation ; queuosine ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The tRNA modifying enzyme tRNA-guanine transglycosylase (Tgt) catalyzes the exchange of guanine in the first position of the anticodon with the queuine precursor 7-aminomethyl-7-deazaguanine. Tgt from Zymomonas mobilis has been purified by crystallization and further recrystallized to obtain single crystals suitable for x-ray diffraction studies. Crystals were grown by vapor diffusion/gel crystallization methods using PEG 8,000 as precipitant. Macroseeding techniques were employed to produce large single crystals. The crystals of Tgt belong to the monoclinic space group C2 with cell constants a = 92.1 Å, b = 65.1 Å, c = 71.9 Å, and β = 97.5°, and contain one molecule per asymmetric unit. A complete diffraction data set from one native crystal has been obtained at 1.85 Å resolution.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 198
    ISSN: 0887-3585
    Keywords: esterase ; crystallography ; crystallization ; synchrotron radiation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Acetyl xylan esterase from Penicillium purpurogenum, a single-chain 23 kDa member of a newly characterized family of esterases that cleaves side chain ester linkages in xylan, has been crystallized. The crystals diffract to better than 1 Å resolution at the Cornell High Energy Synchrotron Source (CHESS) and are highly stable in the synchrotron radiation. The space group is P212121 and cell dimensions are a = 34.9 Å, b = 61.0 Å, c = 72.5 Å.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 199
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 200
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 12-27 
    ISSN: 0887-3585
    Keywords: protein-membrane interaction ; free energy perturbation ; lipid desolvation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The desolvation of lipid molecules in a complex of the enzyme human synovial phospholipase A2 with a lipid membrane is investigated as a mechanism that enhances the overall activity of the enzyme. For this purpose the interaction of the enzyme phospholipase A2 with a dilauryl-phosphatityl-ethanolamin (DLPE) membrane monolayer surface has been studied by means of molecular dynamics simulations. Two enzyme-membrane complexes, a loose and a tight complex, are considered. For comparison, simulations are also carried out for the enzyme in aqueous solution. The conformation, dynamics, and energetics of the three systems are compared, and the interactions between the protein and lipid molecules are analyzed. Free energies of solvation are calculated for the lipid molecules in the enzyme-membrane interface. Along with the calculated dielectric susceptibility at this interface, the results show the desolvation of lipids in a tightly bound, but not in a loosely bound protein-membrane complex. The desolvated lipids are found to interact mainly with hydrophobic protein residues, Including Leu-2, Val-3, Ala-18, Leu-19, Phe-24, Val-31, and Phe-70. The results also explain why the turnover rate of phospholipase A2 complexed to a membrane is enhanced after a critical amount of negatively charged reaction product is accumulated. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...