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Journal Issue - Volume 2 Issue 10 (October 1993)

Abstract An understanding of the forces that contribute to stability is pivotal in solving the protein‐folding problem. Classical theory suggests that disulfide bonds stabilize proteins by reducing the entropy of the denatured state. More recent theories have attempted to expand this idea, suggesting that in addition to configurational entropic effects, enthalpic and native‐state effects occur and cannot be neglected. Experimental...

Abstract Three crystal structures, representing two distinct conformational states, of the mammalian catalytic subunit of cAMP‐dependent protein kinase were solved using molecular replacement methods starting from the refined structure of the recombinant catalytic subunit ternary complex (Zheng, J., et al., 1993a, Biochemistry 32, 2154–2161). These structures correspond to the free apoenzyme, a binary complex with an iodinated inhibitor...

Abstract A β‐bulge is a region of irregularity in a β‐sheet involving two β‐strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand. These irregularities in β‐sheets were identified and classified automatically, extending the definition of β‐bulges given by Richardson et al. (Richardson, J.S., Getzoff, E.D., & Richardson, D.C., 1978, Proc. Natl. Acad. Sci. USA...

Abstract The three‐dimensional solution structure is reported for ω‐conotoxin GVIA, which is a potent inhibitor of presynaptic calcium channels in vertebrate neuromuscular junctions. Structures were generated by a hybrid distance geometry and restrained molecular dynamics approach using interproton distance, torsion angle, and hydrogen‐bonding constraints derived from 1H NMR data. Conformations of GVIA with low constraint violations converged...

Abstract A single aspartate residue has been placed at various positions in individual peptides for which the alanine‐based reference peptide is electrically neutral, and the helix contents of the peptides have been measured by circular dichroism. The dependence of peptide helix content on aspartate position has been used to determine the helix propensity (s‐value). Both the charged (Asp−) and uncharged (Asp0) forms of the aspartate residue are...

Abstract Creatinase (creatine amidinohydrolase, EC 3.5.3.3) from Pseudomonas putida is a homodimer of 45 kDa subunit molecular mass, the three‐dimensional structure of which is known at 1.9 Å resolution. Three point mutants, A109V, V355M, and V182I, as well as one double mutant combining A109V and V355M, and the triple mutant with all three replacements, were compared with wild‐type creatinase regarding their physical and enzymological...

Abstract α‐Glucan phosphorylases are characterized by considerable difference in substrate specificities, even though the primary structures are well conserved among the enzymes from microorganisms, plants, and animals. The higher plant phosphorylase isozyme designated as type L exhibits low affinity for a large, highly branched glucan (glycogen), presumably due to steric hindrance caused by a unique 78‐residue insertion located...

Abstract The three‐dimensional structures of d‐Phe‐Pro‐Arg‐chloromethyl ketone‐inhibited thrombin in complex with Tyr‐63‐sulfated hirudin55–65 (ternary complex) and of thrombin in complex with the bifunctional inhibitor d‐Phe‐Pro‐Arg‐Pro‐(Gly)4‐hirudin54–65 (CGP 50, 856, binary complex) have been determined by X‐ray crystallography in crystal forms different from those described by Skrzypczak‐Jankun et al. (Skrzypczak‐Jankun, E., Carperos, V.E.,...

Abstract Electrostatic interactions are among the key factors determining the structure and function of proteins. Here we report experimental results that illuminate the functional importance of local dipoles to these interactions. The refined 1.7‐Å X‐ray structure of the liganded form of the sulfate‐binding protein, a primary sulfate active transport receptor of Salmonella typhimurium, shows that the sulfate dianion is completely buried and...

Abstract We have determined the major sites responsible for isoaspartate formation during in vitro aging of bovine brain calmodulin under mild conditions. Protein l‐isoaspartyl methyltransferase (EC 2.1.1.77) was used to quantify isoaspartate by the transfer of methyl‐3H from S‐adenosyl‐l‐[methyl‐3H]methionine to the isoaspartyl (α‐carboxyl) side chain. More than 1.2 mol of methyl‐acceptor sites per mol of calmodulin accumulated...

Abstract Recombinant human brain‐derived neurotrophic factor (BDNF) is now under extensive investigation because of its potential clinical applications. Radioactively labeled proteins are usually required to study receptor binding and pharmacokinetic properties of proteins. This study was undertaken to see if iodination affects the biological and conformational properties of a recombinant BDNF. BDNF was iodinated using a...

Abstract NADPH is a system in phagocytic cells that generates O2− and hydrogen peroxide in the endocytic vacuole, both of which are important for killing of the engulfed microbe. Dysfunction of this oxidase results in the syndrome of chronic granulomatous disease, characterized by a profound predisposition to bacterial and fungal infections. A flavocytochrome b is the site of most of the mutations causing this syndrome. The FAD and NADPH...

Abstract We describe a confidence test for branching order that can aid protein phylogeny reconstruction as well as the evaluation of the optimal tree. It is proposed that the process resulting in the observed amino acid residue differences, which is the basis for the identification of the order and relative times of divergence events, is appropriately described by a modification of the negative binomial distribution. The relative...

Abstract An algorithm is proposed for the conversion of a virtual‐bond polypeptide chain (connected Cα atoms) to an all‐atom backbone, based on determining the most extensive hydrogen‐bond network between the peptide groups of the backbone, while maintaining all of the backbone atoms in energetically feasible conformations. Hydrogen bonding is represented by aligning the peptide‐group dipoles. These peptide groups are not contiguous in the...

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