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Journal Issue - Volume 17 Issue 11 (November 2008)

Abstract The regulatory mechanism of Src tyrosine kinases includes conformational activation by a change in the catalytic domain tertiary structure and in domain–domain contacts between the catalytic domain and the SH2/SH3 regulatory domains. The kinase is activated when tyrosine phosphorylation occurs on the activation loop, but without phosphorylation of the C‐terminal tail. Activation also occurs by allostery when contacts...

Abstract Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for...

Abstract The C3–inhibitory domain of Staphylococcus aureus extracellular fibrinogen‐binding protein (Efb‐C) defines a novel three‐helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb‐C bound to its cognate subdomain of human C3 (C3d) identified Arg‐131 and Asn‐138 of Efb‐C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces ...

Abstract Receptor activity‐modifying protein (RAMP) 1 forms a heterodimer with calcitonin receptor‐like receptor (CRLR) and regulates its transport to the cell surface. The CRLR·RAMP1 heterodimer functions as a specific receptor for calcitonin gene‐related peptide (CGRP). Here, we report the crystal structure of the human RAMP1 extracellular domain. The RAMP1 structure is a three‐helix bundle that is stabilized by three disulfide...

Abstract Nodulation formation efficiency D (NfeD) is a member of a class of membrane‐anchored ClpP‐class proteases. There is a second class of NfeD homologs that lack the ClpP domain. The genes of both NfeD classes usually are part of an operon that also contains a gene for a prokaryotic homolog of stomatin. (Stomatin is a major integral‐membrane protein of mammalian erythrocytes.) Such NfeD/stomatin homolog gene pairs are present...

Abstract We designed a simple position‐specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly, clustering, target selection, refinement, and consensus, all in one process. Our initial implementation of this theory converges to within 6 Å of the native structures for 100% of decoys on all six standard benchmark proteins used...

Abstract Enzymes of the glyoxylate shunt are important for the virulence of pathogenic organisms such as Mycobacterium tuberculosis and Candida albicans. Two isoforms have been identified for malate synthase, the second enzyme in the pathway. Isoform A, found in fungi and plants, comprises ∼530 residues, whereas isoform G, found only in bacteria, is larger by ∼200 residues. Crystal structures of malate synthase isoform G from Escherichia coli...

Abstract Effector molecules such as calmodulin modulate the interactions of membrane‐associated guanylate kinase homologs (MAGUKs) and other scaffolding proteins of the membrane cytoskeleton by binding to the Src homology 3 (SH3) domain, the guanylate kinase (GK) domain, or the connecting HOOK region of MAGUKs. Using surface plasmon resonance, we studied the interaction of members of all four MAGUK subfamilies—synapse‐associated...

Abstract We report a very fast and accurate physics‐based method to calculate pH‐dependent electrostatic effects in protein molecules and to predict the pK values of individual sites of titration. In addition, a CHARMm‐based algorithm is included to construct and refine the spatial coordinates of all hydrogen atoms at a given pH. The present method combines electrostatic energy calculations based on the Generalized Born...

Abstract Flavonoids are the major functional components of many herbal and insect preparations and demonstrate varied pharmacological functions including antibacterial activity. Here by enzymatic assay and crystal structure analysis, we studied the inhibition of three flavonoids (quercetin, apigenin, and (S)‐sakuranetin) against the β‐hydroxyacyl‐acyl carrier protein dehydratase from Helicobacter pylori (HpFabZ). These three...

Abstract Pax3, a member of the paired class homeodomain family of transcription factors, is essential for early skeletal muscle development. Previously, others and we have shown that the stability of Pax3 is regulated on a post‐translational level. Evidence in the literature and from our laboratory suggests that phosphorylation, a common form of regulation, may play a role. However, at present, the sites of Pax3 phosphorylation are...

Abstract Many recombinant eukaryotic proteins tend to form insoluble aggregates called inclusion bodies, especially when expressed in Escherichia coli. We report the first application of the technique of three‐phase partitioning (TPP) to obtain correctly refolded active proteins from solubilized inclusion bodies. TPP was used for refolding 12 different proteins overexpressed in E. coli. In each case, the protein refolded by TPP gave either...

Abstract The human kallikrein‐related peptidases (KLKs) comprise 15 members (KLK1–15) and are the single largest family of serine proteases. The KLKs are utilized, or proposed, as clinically important biomarkers and therapeutic targets of interest in cancer and neurodegenerative disease. All KLKs appear to be secreted as inactive pro‐forms (pro‐KLKs) that are activated extracellularly by specific proteolytic release of their...

Abstract The prokaryotic lectin cyanovirin‐N (CV‐N) is a potent inhibitor of HIV envelope‐mediated cell entry, and thus is a leading candidate among a new class of potential anti‐HIV microbicides. The activity of CV‐N is a result of interactions with the D1 arm of high‐mannose oligosaccharides on the viral glycoprotein gp120. Here, we present computationally refined models of CV‐N recognition of the di‐ and trisaccharides that...

Abstract The X‐ray structure of the homodimeric chaperone CesT is the only structure among the type three secretion system (TTSS) chaperones that shows a domain swap. This swap has potential importance for the mechanism of effector translocation through a TTSS. Here we present two nuclear magnetic resonance strategies exploiting pre‐existing structural models and residual dipolar couplings (RDCs), which reveal the unswapped 35.4‐kDa...