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Journal Issue - Volume 15 Issue 4 (April 2006)

Abstract About 30% of proteins require cofactors for their proper folding. The effects of cofactors on the folding reaction have been investigated with α‐lactalbumin as a model protein and metal ions as cofactors. Metal ions accelerate the refolding of α‐lactalbumin by lessening the energy barrier between the molten globule state and the transition state, mainly by decreasing the difference of entropy between the two states. These...

Abstract Phosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP‐dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild‐type...

Abstract Nuclear magnetic resonance (NMR) studies of large membrane‐associated proteins are limited by the difficulties in preparation of stable protein–detergent mixed micelles and by line broadening, which is typical of these macroassemblies. We have used the 68‐kDa homotetrameric KcsA, a thermostable N‐terminal deletion mutant of a bacterial potassium channel from Streptomyces lividans, as a model system for applying NMR methods to membrane...

Abstract Severe acute respiratory syndrome coronavirus (SARS‐CoV) 3C‐like protease (3CLpro) mediates extensive proteolytic processing of replicase polyproteins, and is considered a promising target for anti‐SARS drug development. Here we present a rapid and high‐throughput screening method to study the substrate specificity of SARS‐CoV 3CLpro. Six target amino acid positions flanking the SARS‐CoV 3CLpro cleavage site were investigated. Each...

Abstract The mammalian α/β T cell receptor (TCR) repertoire plays a pivotal role in adaptive immunity by recognizing short, processed, peptide antigens bound in the context of a highly diverse family of cell‐surface major histocompatibility complexes (pMHCs). Despite the extensive TCR–MHC interaction surface, peptide‐independent cross‐reactivity of native TCRs is generally avoided through cell‐mediated selection of molecules with...

Abstract HXMS (hydrogen/deuterium exchange mass spectrometry) of the glucocorticoid receptor ligand‐binding domain (GR LBD) complexed with the agonist dexamethasone and the antagonist RU‐486 is described. Variations in the rates of exchange were observed in regions consistent with the published crystal structures of GR LBD complexed with RU‐486 when compared with the GR dexamethasone complex. We also report the HXMS results for...

Abstract In the double‐stranded DNA containing bacteriophages, hundreds of copies of capsid protein subunits polymerize to form icosahedral shells, called procapsids, into which the viral genome is subsequently packaged to form infectious virions. High assembly fidelity requires the assistance of scaffolding protein molecules, which interact with the capsid proteins to insure proper geometrical incorporation of subunits into the...

Abstract Protein folding, natural conformational changes, or interaction between partners involved in recognition phenomena brings about differences in the solvent‐accessible surface area (SASA) of the polypeptide chain. This primary event can be monitored by the differential chemical reactivity of functional groups along the protein sequence. Diazirine (DZN), a photoreactive gas similar in size to water, generates methylene carbene...

Abstract It is an open question whether nature has utilized all possible protein folds. For a simple protein architecture, the helical repeats, we report a method to address this question based on a mapping between the set of repetitive curves and a space of parameters specifying the curve. The exploration of the parameter space for a particular architecture enables a systematic exploration of the fold space for that protein...

Abstract 3‐Hydroxyanthranilic acid 3,4‐dioxygenase (3HAO) is a non‐heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes the conversion of 3‐hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an endogenous neurotoxin, via the activation of N‐methyl‐D‐aspartate (NMDA) receptors and the precursor of NAD+ biosynthesis. The crystal structure of 3HAO from S. cerevisiae at 2.4 Å resolution shows it to be a...

Abstract Methicillin‐resistant Staphylococcus aureus (MRSA) poses a major threat to human health, particularly through hospital acquired infection. The spread of MRSA means that novel targets are required to develop potential inhibitors to combat infections caused by such drug‐resistant bacteria. Thymidylate kinase (TMK) is attractive as an antibacterial target as it is essential for providing components for DNA synthesis. Here, we...

Abstract Previous studies have shown that rat glycine N‐methyltransferase (GNMT) is phosphorylated in vivo, and could be phosphorylated in vitro on serine residues with a significant increase of enzyme activity, but no phosphorylation sites were identified. In this work the identification of the specific phosphorylation sites of rat GNMT is reported. Three different preparations of rat GNMT were analyzed: (1) purified from liver by...

Abstract SH3 domains are small protein modules that are involved in protein–protein interactions in several essential metabolic pathways. The availability of the complete genome and the limited number of clearly identifiable SH3 domains make the yeast Saccharomyces cerevisae an ideal proteomic‐based model system to investigate the structural rules dictating the SH3‐mediated protein interactions and to develop new tools to assist these studies....

Abstract An open question in protein homology modeling is, how well do current modeling packages satisfy the dual criteria of quality of results and practical ease of use? To address this question objectively, we examined homology‐built models of a variety of therapeutically relevant proteins. The sequence identities across these proteins range from 19% to 76%. A novel metric, the difference alignment index (DAI), is developed to...

Abstract A bacterial display methodology was developed for N‐ and C‐terminal display and demonstrated to enable rapid screening of very large peptide libraries with high precision and efficiency. To overcome limitations of insertional fusion display libraries, a new scaffold was developed through circular permutation of the Escherichia coli outer membrane protein OmpX that presents both N and C termini on the external cell surface. Circularly...

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