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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 28-37 
    ISSN: 0887-3585
    Keywords: protein evolution ; structure prediction ; information theory ; amino acid substitution ; multiple sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 336-344 
    ISSN: 0887-3585
    Keywords: hydrophobicity ; molecular evolution ; local propensities ; reverse hydrophobic effect ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To investigate how the properties of individual amino acids result in proteins with particular structures and functions, we have examined the correlations between previously derived structure-dependent mutation rates and changes in various physical-chemical properties of the amino acids such as volume, charge, α-helical and β-sheet propensity, and hydrophobicity. In most cases we found the ΔG of transfer from octanol to water to be the best model for evolutionary constraints, in contrast to the much weaker correlation with the ΔG of transfer from cyclohexane to water, a property found to be highly correlated to changes in stability in site-directed mutagenesis studies. This suggests that natural evolution may follow different rules than those suggested by results obtained in the laboratory. A high degree of conservation of a surface residue's relative hydrophobicity was also observed, a fact that cannot be explained by constraints on protein stability but that may reflect the consequences of the reverse-hydrophobic effect. Local propensity, especially α-helical propensity, is rather poorly conserved during evolution, indicating that non-local interactions dominate protein structure formation. We found that changes in volume were important in specific cases, most significantly in transitions among the hydrophobic residues in buried locations. To demonstrate how these techniques could be used to understand particular protein families, we derived and analyzed mutation matrices for the hypervariable and framework regions of antibody light chain V regions. We found a surprisingly high conservation of hydrophobicity in the hypervariable region, possibly indicating an important role for hydrophobicity in antigen recognition. Proteins 27:336-344, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 461-466 
    ISSN: 0887-3585
    Keywords: protein folding ; molecular evolution ; lattice models ; fitness landscapes ; neutral networks ; spin-glass theory ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non self-averaging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process. Proteins 29:461-466, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0887-3585
    Keywords: type II topoisomerase ; gyrase ; coumarin inhibitor ; clorobiocin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Coumarin antibiotics, such as clorobiocin, novobiocin, and coumermycin A1, inhibit the supercoiling activity of gyrase by binding to the gyrase B (GyrB) subunit. Previous crystallographic studies of a 24-kDa N-terminal domain of GyrB from E. coli complexed with novobiocin and a cyclothialidine analogue have shown that both ligands act by binding at the ATP-binding site. Clorobiocin is a natural antibiotic isolated from several Streptomyces strains and differs from novobiocin in that the methyl group at the 8 position in the coumarin ring of novobiocin is replaced by a chlorine atom, and the carbamoyl at the 3′ position of the noviose sugar is substituted by a 5-methyl-2-pyrrolylcarbonyl group. To understand the difference in affinity, in order that this information might be exploited in rational drug design, the crystal structure of the 24-kDa GyrB fragment in complex with clorobiocin was determined to high resolution. This structure was determined independently in two laboratories, which allowed the validation of equivalent interpretations. The clorobiocin complex structure is compared with the crystal structures of gyrase complexes with novobiocin and 5′-adenylyl-β,γ-imidodiphosphate, and with information on the bound conformation of novobiocin in the p24-novobiocin complex obtained by heteronuclear isotope-filtered NMR experiments in solution. Moreover, to understand the differences in energetics of binding of clorobiocin and novobiocin to the protein, the results from isothermal titration calorimetry are also presented. © 1997 Wiley-Liss Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 22 (1995), S. 413-418 
    ISSN: 0887-3585
    Keywords: protein folding ; lattice models ; protein energetics ; local interactions ; spin-glass theory ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lattice models of proteins were used to examine the role of local propensities in stabilizing the native state of a protein, using techniques drawn from spin-glass theory to characterize the free-energy landscapes. In the strong evolutionary limit, optimal conditions for folding are achieved when the contributions from local interactions to the stability of the native state is small. Further increasing the local interactions rapidly decreases the foldability. © 1995 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 38-47 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; Bayesian statistics ; amino acid substitution ; information theory ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We introduce a novel Bayesian probabilistic method for predicting the solvent accessibilities of amino acid residues in globular proteins. Using single sequence data, this method achieves prediction accuracies higher than previously published methods. Substantially improved predictions - comparable to the highest accuracies reported in the literature to date - are obtained by representing alignments of the example proteins and their homologs as strings of residue substitution classes, depending on the side chain types observed at each alignment position. These results demonstrate the applicability of this relatively simple Bayesian approach to structure prediction and illustrate the utility of the classification methodology previously developed to extract information from aligned sets of structurally related proteins. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 289-295 
    ISSN: 0887-3585
    Keywords: molecular evolution ; protein evolution ; mutation matrices ; Metropolis kinetics ; Boltzmann statistics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: New computational models of natural site mutations are developed that account for the different selective pressures acting on different locations in the protein. The number of adjustable parameters is greatly reduced by basing the models on the underlying physical-chemical properties of the amino acids. This allows us to use our method on small data sets built of specific protein types. We demonstrate that with this approach we can represent the evolutionary patterns in HIV envelope proteins far better than with more traditional methods. Proteins 32:289-295, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 240-252 
    ISSN: 0887-3585
    Keywords: protein folding ; Monte Carlo ; simulated annealing ; genetic algorithm ; β-strands ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe an improved algorithm for protein structure prediction, assuming that the location of secondary structural elements is known, with particular focus on prediction for proteins containing β-strands. Hydrogen bonding terms are incorporated into the potential function, supplementing our previously developed residue-residue potential which is based on a combination of database statistics and an excluded volume term. Two small mixed α/β proteins, 1-CTF and BPTI, are studied. In order to obtain native-like structures, it is necessary to allow the β-strands in BPTI to distort substantially from an ideal geometry, and an automated algorithm to carry this out efficiently is presented. Simulated annealing Monte Carlo methods, which contain a genetic algorithm component as well, are used to produce an ensemble of low-energy structures. For both proteins, a cluster of structures with low RMS deviation from the native structure is generated and the energetic ranking of this cluster is in the top 2 or 3 clusters obtained from simulations. These results are encouraging with regard to the possibility of constructing a robust procedure for tertiary folding which is applicable to β-strand containing proteins. Proteins 33:240-252, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 222-227 
    ISSN: 0006-3592
    Keywords: γ-poly(glutamate) ; γ-PGA ; Bacillus licheniformis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Bacillus licheniformis ATCC 9945A was grown on Medium E in batch fermentations in which the pH was maintained at 5.5., 6.5, 7.4, and 8.25. The effects of pH on cell growth, carbon source utilization, and γ-polyglutamic acid (γ-PGA) production, molecular weight, and polymer stereochemistry were determined. The γ-PGA yield was highest (15 g/L, 96 h growth time) at pH 6.5. The increase in γ-PGA formation at pH 6.5 corresponded with a relatively high specific production rate at high γ-PGA concentration (0.09 h-1, ∼15 g/L γ-PGA). In contrast, the specific γ-PGA production rates at fermentor pH values of 5.5 and 7.4 decreased significantly for γ-PGA fermentor yields 〉∼5 g/L. Interestingly, alteration of the medium pH had little to no significant effects on the product quality as measured by stereochemical composition and molecular weight. While glutamate and glycerol utilization were similar as a function of pH, citrate consumption increased at pH 6.5, indicating that the formation of γ-PGA from citrate at pH 6.5 was of increased importance. The effect of aeration was evaluated by increasing the agitation speed (250 to 800 rpm) and aeration rate (0.5 to 2.0 L/min) at pH 6.5, the pH of maximal γ-PGA production. Increased aeration resulted in doubling of the cell dry weights (2 to 4 g/L), increasing γ-PGA yields (6.3 to 23 g/L by 48 h) and increasing in the maximum γ-PGA-specific production rate (0.09 to 0.11 h-1). Other effects of increased agitation included a rapid depletion of glutamate and citrate (by 50 h) and a decrease in product molecular weight. Despite the increase in agitation and aeration, oxygen limitation of the culture was not avoided, because the partial pressure decreased to 〈1.0% by 29 h. © 1996 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 430-437 
    ISSN: 0006-3592
    Keywords: glucose ; glycerol ; γ-poly(glutamic acid) ; Bacillus licheniformis ATCC 9945a ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Bacillus licheniformis ATCC 9945a is one of the bacterial strains that produce γ-poly(glutamic acid) (γ-PGA). The use of carbohydrate medium components for γ-PGA production was explored. Cells were grown in shake flasks or in controlled pH fermentors using medium formulations that contain different carbon sources. During the cultivations, aliquots were removed to monitor cell growth, carbon utilization, polymer production, and polymer molecular weight. Glucose was a better carbon source than glycerol for cell growth. Furthermore, glucose was utilized at a faster rate than glycerol, citrate, or glutamate. However, by using mixtures of glucose and glycerol in medium formulations, the efficiency of γ-PGA production increased. For example, by increasing the glycerol in medium formulations from 0 to 40 g/L, the γ-PGA broth concentration after 96 h increased from 5.7 to 20.5 g/L. Considering that glycerol utilization was low for the glucose/glycerol mixtures studied, it was unclear as to the mechanism by which glycerol leads to enhanced product formation. Cell growth and concomitant γ-PGA production (12 g/L) at pH 6.5 was possible using glucose as a carbon source if trace amounts (0.5 g/L each) of citrate and glutamate were present in the medium. We suggested that citrate and glutamate were useful in preventing salt precipitation from the medium. In addition, glutamate may be preferred relative to ammonium chloride as a nitrogen source. The conversion of glucose to γ-PGA by the strain ATCC 9945a was believed to occur by glycolysis of glucose to acetyl-CoA and tricarboxylic acid (TCA) cycle intermediates that were then metabolized via the TCA cycle to form α-ketoglutarate, which is a direct glutamate precursor. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 430-437, 1998.
    Additional Material: 9 Ill.
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