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Journal Issue - Volume 11 Issue 2 (February 2002)

Abstract Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising when one considers that binding is a dynamic process with populations in equilibrium and that the shape of the binding site is strongly influenced by the molecular partner. It derives implicitly from the concept of populations....

Abstract EF‐hand Ca2+‐binding proteins participate in both modulation of Ca2+ signals and direct transduction of the ionic signal into downstream biochemical events. The range of biochemical functions of these proteins is correlated with differences in the way in which they respond to the binding of Ca2+. The EF‐hand domains of calbindin D9k and calmodulin are homologous, yet they respond to the binding of calcium ions in a drastically different manner. A...

Abstract Streptococcal protein G (SpG) is a bacterial cell surface receptor exhibiting affinity to both human immunoglobulin (IgG) and human serum albumin (HSA). Interestingly, the serum albumin and immunoglobulin‐binding activities have been shown to reside at functionally and structurally separated receptor domains. The binding domain of the HSA‐binding part has been shown to be a 46‐residue triple α‐helical structure, but the...

Abstract Knowledge of the structural properties of linker histones is important to the understanding of their role in higher‐order chromatin structure and gene regulation. Here we study the conformational properties of the peptide Ac‐EKTPVKKKARKAAGGAKRKTSG‐NH2 (NE‐1) by circular dichroism and 1H‐NMR. This peptide corresponds to the positively charged region of the N‐terminal domain, adjacent to the globular domain, of mouse histone H1e...

Abstract Crystal structures have shown that the HIV‐1 protease flaps, domains that control access to the active site, are closed when the active site is occupied by a ligand. Although flap structures ranging from closed to semi‐open are observed in the free protease, crystal structures reveal that even the semi‐open flaps block access to the active site, indicating that the flaps are mobile in solution. The goals of this paper are...

Abstract An automatic sequence search and analysis protocol (DomainFinder) based on PSI‐BLAST and IMPALA, and using conservative thresholds, has been developed for reliably integrating gene sequences from GenBank into their respective structural families within the CATH domain database ( http://www.biochem.ucl.ac.uk/bsm/cath_new). DomainFinder assigns a new gene sequence to a CATH homologous superfamily provided that PSI‐BLAST...

Abstract The three‐dimensional structure of huwentoxin‐II (HWTX‐II), an insecticidal peptide purified from the venom of spider Selenocosmia huwena with a unique disulfide bond linkage as I‐III, II‐V, and IV‐VI, has been determined using 2D 1H‐NMR. The resulting structure of HWTX‐II contains two β‐turns (C4‐S7 and K24‐W27) and a double‐stranded antiparallel β‐sheet (W27‐C29 and C34‐K36). Although the C‐terminal double‐stranded β‐sheet cross‐linked by two...

Abstract The redox protein flavodoxin has been shown earlier to be reduced by the pyruvate‐oxidoreductase (POR) enzyme complex of Helicobacter pylori, and also was proposed to be involved in the pathogenesis of gastric mucosa‐associated lymphoid‐tissue lymphoma (MALToma). Here, we report its X‐ray structure, which is similar to flavodoxins of other bacteria and cyanobacteria. However, H. pylori flavodoxin has an alanine residue near the isoalloxazine ring...

Abstract The first report of the full‐length structure of the collagen‐like polypeptide [(Pro‐Pro‐Gly)10]3 is given. This structure was obtained from crystals grown in a microgravity environment, which diffracted up to 1.3 Å, using synchrotron radiation. The final model, which was refined to an Rfactor of 0.18, is the highest‐resolution description of a collagen triple helix reported to date. This structure provides clues regarding a series of...

Abstract The binding sites for the two cations essential for the catalytic function of 5‐phospho‐d‐ribosyl α‐1‐diphosphate (PRPP) synthases have been identified from the structure of the Bacillus subtilis phosphoribosyldiphosphate synthetase (PRPPsase) with bound Cd2+. The structure determined from X‐ray diffraction data to 2.8‐Å resolution reveals the same hexameric arrangement of the subunits that was observed in the complexes of the enzyme with the...

Abstract The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio prediction of association of two independently determined protein structures usually fail when they are applied to a large set of complexes, mostly because of inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface...

Abstract The FAD‐dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R‐mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction—the enantiospecific formation of α‐hydroxynitriles—is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme‐mediated C–C bond formation. Starting from the recently determined X‐ray crystal structure,...

Abstract The amino acid composition and architecture of all β‐barrel membrane proteins of known three‐dimensional structure have been examined to generate information that will be useful in identifying β‐barrels in genome databases. The database consists of 15 nonredundant structures, including several novel, recent structures. Known structures include monomeric, dimeric, and trimeric β‐barrels with between 8 and 22...

Abstract A prerequisite for structural genomics and related projects is to standardize the process of gene overexpression and protein solubility screening to enable automation for higher throughput. We have tested a methodology to rapidly subclone a large number of human genes and screen these for expression and protein solubility in Escherichia coli. The methodology, which can be partly automated, was used to compare the effect of six...

Abstract Modeling side‐chain conformations on a fixed protein backbone has a wide application in structure prediction and molecular design. Each effort in this field requires decisions about a rotamer set, scoring function, and search strategy. We have developed a new and simple scoring function, which operates on side‐chain rotamers and consists of the following energy terms: contact surface, volume overlap, backbone dependency,...

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