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Journal Issue - Volume 13 Issue 2 (February 2004)

Abstract The myoglobin protein binds oxygen and catalyzes NO oxidation. As a key model protein, its dynamics have been well studied by spectroscopy and by crystallography as well as by simulation. Nonetheless, visualization of the mechanism of movement of ligands within myoglobin has been difficult. Coordinates of the A1 and A3 taxonomic spectral states of myoglobin from the 1 Å crystal structure (1a6g) are generated as consistent...

Abstract The fully reduced hen egg white lysozyme (HEWL), which is a good model of random coil structure, has been converted to highly organized amyloid fibrils at low pH by adding ethanol. In the presence of 90% (v/v) ethanol, the fully reduced HEWL adopts β‐sheet secondary structure at pH 4.5 and 5.0, and an α‐to‐β transition is observed at pH 4.0. A red shift of the Congo red absorption spectrum caused by the precipitation of the...

Abstract Alpha‐Lytic protease (αLP) is an extracellular bacterial pro‐protease marked by extraordinary conformational rigidity and a highly cooperative barrier to unfolding. Although these properties successfully limit its proteolytic destruction, thereby extending the functional lifetime of the protease, they come at the expense of foldability (t1/2 = 1800 yr) and thermodynamic stability (native αLP is less stable than the unfolded species)....

Abstract The α‐crystallins, αA and αB, are major lens structural proteins with chaperone‐like activity and sequence homology to small heat‐shock proteins. As yet, their crystal structures have not been determined because of the large size and heterogeneity of the assemblies they form in solution. Because α‐crystallin chaperone activity increases with temperature, understanding structural changes of α‐crystallin as it is heated may...

Abstract Cold shock proteins (Csps) are assumed to play a central role in the regulation of gene expression under cold shock conditions. Acting as single‐stranded nucleic acid‐binding proteins, they trigger the translation process and are therefore involved in the compensation of the influence of low temperatures (cold shock) upon the cell metabolism. However, it is unknown so far how Csps are switched on and off as a function of...

Abstract A model for prediction of α‐helical regions in amino acid sequences has been tested on the mainly‐α protein structure class. The modeling represents the construction of a continuous hypothetical α‐helical conformation for the whole protein chain, and was performed using molecular mechanics tools. The positive prediction of α‐helical and non‐α‐helical pentapeptide fragments of the proteins is 79%. The model considers only...

Abstract Amino acid residue–solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction‐energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid–solvent interactions by introducing a contrast parameter for the hydrophobicity, Cs, and a mean attraction parameter for the amino acids, ω. Changes in...

Abstract The preparation of proteins for structural and functional analysis using the Escherichia coli expression system is often hampered by the formation of insoluble intracellular protein aggregates (inclusion bodies). Transferring those proteins into their native states by in vitro protein folding requires screening for the best buffer conditions and suitable additives. However, it is difficult to assess the success of such a screen if no...

Abstract Like most extracellular bacterial proteases, Streptomyces griseus protease B (SGPB) and α‐lytic protease (αLP) are synthesized with covalently attached pro regions necessary for their folding. In this article, we characterize the folding free energy landscape of SGPB and compare it to the folding landscapes of αLP and trypsin, a mammalian homolog that folds independently of its zymogen peptide. In contrast to the thermodynamically...

Abstract The conformations of loops are determined by the water‐mediated interactions between amino acid residues. Energy functions that describe the interactions can be derived either from physical principles (physical‐based energy function) or statistical analysis of known protein structures (knowledge‐based statistical potentials). It is commonly believed that statistical potentials are appropriate for coarse‐grained...

Abstract Structure prediction on a genomic scale requires a simplified energy function that can efficiently sample the conformational space of polypeptide chains. A good energy function at minimum should discriminate native structures against decoys. Here, we show that a recently developed, residue‐specific, all‐atom knowledge‐based potential (167 atomic types) based on distance‐scaled, finite ideal‐gas reference state...

Abstract Dipeptidyl peptidase IV (DPPIV) is a member of the prolyl oligopeptidase family of serine proteases. DPPIV removes dipeptides from the N terminus of substrates, including many chemokines, neuropeptides, and peptide hormones. Specific inhibition of DPPIV is being investigated in human trials for the treatment of type II diabetes. To understand better the molecular determinants that underlie enzyme catalysis and substrate...

Abstract The PLUNC family of human proteins are candidate host defense proteins expressed in the upper airways. The family subdivides into short (SPLUNC) and long (LPLUNC) proteins, which contain domains predicted to be structurally similar to one or both of the domains of bactericidal/permeability‐increasing protein (BPI), respectively. In this article we use analysis of the human, mouse, and rat genomes and other sequence data to...

Abstract The Ca2+ binding 70–80 loop of factor X (fX) contains one basic (Arg71) and three acidic (Glu74, Glu76, and Glu77) residues whose contributions to the zymogenic and enzymatic properties of the protein have not been evaluated. We prepared four Ala substitution mutants of fX (R71A, E74A, E76A, and E77A) and characterized their activation kinetics by the factor VIIa and factor IXa in both the absence and presence of cofactors. Factor VIIa...

Abstract The increasing volume of genomic data opens new possibilities for analysis of protein function. We introduce a method for automated selection of residues that determine the functional specificity of proteins with a common general function (the specificity‐determining positions [SDP] prediction method). Such residues are assumed to be conserved within groups of orthologs (that may be assumed to have the same specificity) and...

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