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Journal Issue - Volume 8 Issue 4 (1999)

Abstract CORA is a suite of programs for multiply aligning and analyzing protein structural families to identify the consensus positions and capture their most conserved structural characteristics (e.g., residue accessibility, torsional angles, and global geometry as described by inter‐residue vectors/contacts). Knowledge of these structurally conserved positions, which are mostly in the core of the fold and of their properties,...

Abstract We describe an extensive test of Geocore, an ab initio peptide folding algorithm. We studied 18 short molecules for which there are structures in the Protein Data Bank; chains are up to 31 monomers long. Except for the very shortest peptides, an extremely simple energy function is sufficient to discriminate the true native state from more than 108 lowest energy conformations that are searched explicitly for each peptide. A high...

Abstract The reoccurrence of water molecules in crystal structures of RNase T1 was investigated. Five waters were found to be invariant in RNase T1 as well as in six other related fungal RNases. The structural, dynamical, and functional characteristics of one of these conserved hydration sites (WAT1) were analyzed by protein engineering, X‐ray crystallography, and 17O and 2H nuclear magnetic relaxation dispersion (NMRD). The position of WAT1...

Abstract The tumor suppressor p53 is conformationally unstable at physiological temperature. Even the activated p53Δ30 variant, which lacks the self‐inhibiting carboxy terminal domain, has a half‐life of only 8 min at 37°C in vitro. We have developed a genetic approach to identify p53 variants that stabilize the active conformation. The human p53Δ30 gene was randomly mutated, and the resulting library was expressed in Escherichia coli under...

Abstract The effects of a number of cryoprotectants on the kinetic and structural properties of glycogen phosphorylase b have been investigated. Kinetic studies showed that glycerol, one of the most commonly used cryoprotectants in X‐ray crystallographic studies, is a competitive inhibitor with respect to substrate glucose‐1‐P with an apparent Ki value of 3.8% (v/v). Cryogenic experiments, with the enzyme, have shown that glycerol binds at the catalytic...

Abstract In the past few years, a new generation of fold recognition methods has been developed, in which the classical sequence information is combined with information obtained from secondary structure and, sometimes, accessibility predictions. The results are promising, indicating that this approach may compete with potential‐based methods (Rost B et al., 1997, J Mol Biol 270:471–480). Here we present a systematic study of the different...

Abstract Phage‐display peptide library analysis of an anti‐F actin polyclonal antibody identified 12 amino acid residues of actin that appear, in its X‐ray crystal structure, to be grouped together in a surface accessible conformational epitope. Phage epitope mapping was carried out by isolating immune complexes containing members of the J404 nonapeptide phage‐display library formed in diluted antiserum and isolated on a protein A...

Abstract We describe the results of a procedure for maximizing the number of sequences that can be reliably linked to a protein of known three‐dimensional structure. Unlike other methods, which try to increase sensitivity through the use of fold recognition software, we only use conventional sequence alignment tools, but apply them in a manner that significantly increases the number of relationships detected. We analyzed 11 genomes...

Abstract The 2.5 Å crystal structure of the full length human placental isoform of the Gly12 to Val mutant Cdc42 protein (Cdc42(G12V)) bound to both GDP/Mg2+ and GDPNH2 (guanosine‐5′‐diphospho‐β‐amidate) is reported. The crystal contains two molecules in the asymmetric unit, of which one has bound GDP/Mg2+, while the other has bound GDPNH2 without a Mg2+ ion. Crystallization of the protein was induced via hydrolysis of the Cdc42 · GppNHp...

Abstract We have investigated the solution conformation of the functionally relevant C‐terminal extremes of α‐ and β‐tubulin, employing the model recombinant peptides RL52a3 and RL33b6, which correspond to the amino acid sequences 404‐451(end) and 394–445(end) of the main vertebrate isotypes of α‐ and β‐tubulin, respectively, and synthetic peptides with the α‐tubulin(430–443) and β‐tubulin(412–431) internal sequences. α(404–451) and...

Abstract The relative orientations of adjacent structural elements without many well‐defined NOE contacts between them are typically poorly defined in NMR structures. For apo‐S100B(ββ) and the structurally homologous protein calcyclin, the solution structures determined by conventional NMR exhibited considerable differences and made it impossible to draw unambiguous conclusions regarding the Ca2+‐induced conformational change...

Abstract Members of the Ly‐6/uPAR protein family share one or several repeat units of the Ly‐6/uPAR domain that is defined by a distinct disulfide bonding pattern between 8 or 10 cysteine residues. The Ly‐6/uPAR protein family can be divided into two subfamilies. One comprises GPI‐anchored glycoprotein receptors with 10 cysteine residues. The other subfamily includes the secreted single‐domain snake and frog cytotoxins, and differs...

Abstract The structural origins of the specificity of the neurophysin hormone‐binding site for an aromatic residue in peptide position 2 were explored by analyzing the binding of a series of peptides in the context of the crystal structure of liganded neurophysin. A new modeling method for describing the van der Waals surface of binding sites assisted in the analysis. Particular attention was paid to the unusually large (5 kcal/mol)...

Abstract The effect of methylurea, N,N'‐dimethylurea, ethylurea, and butylurea as well as guanidine hydrochloride (GuHCl), urea and pH on the thermal stability, structural properties, and preferential solvation changes accompanying the thermal unfolding of ribonuclease A (RNase A) has been investigated by differential scanning calorimetry (DSC), UV, and circular dichroism (CD) spectroscopy. The results show that the thermal...

Abstract The objective of this study was to evaluate the suitability of the WW domain as a desirable model system to understand the folding and stability of an isolated three‐stranded antiparallel β‐sheet structure. The WW domain was subjected to thermal and chaotropic denaturation/reconstitution utilizing a variety of biophysical methods. This three‐stranded sheet folds reversibly and cooperatively utilizing both urea and GdnHCl as...

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