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Journal Issue - Volume 18 Issue 12 (December 2009)

  • In This Issue

  • Published in Wiley Interscience on Nov 24, 2009
  • DOI: 10.1002/pro.293 (p n/a-n/a)

Abstract Agrin is a multidomain heparan sulfate proteoglycan involved in postsynaptic differentiation at the neuromuscular junction. Binding of agrin to synaptic basal lamina is mediated by the N‐terminal agrin (NtA) domain. The NtA domain of agrin is followed by a tandem of nine follistatin‐like (FS) domains forming a rod‐like spacer to the laminin G‐like domains of the molecule. Here we report that the most C‐terminal cysteine residue of NtA...

Abstract We present the crystal structure determination of an anti‐HIV‐1 gp120 single‐chain variable fragment antibody variant, 3B3, at 2.5 Å resolution. This 3B3 variant was derived from the b12 antibody, using phage display and site‐directed mutagenesis of the variable heavy chain (VH) complementary‐determining regions (CDRs). 3B3 exhibits enhanced binding affinity and neutralization activity against several cross‐clade primary...

Abstract Purification and in vitro protein‐folding schemes were developed to produce monodisperse samples of the mature wild‐type HIV‐2 protease (PR2), enabling a comprehensive set of biochemical and biophysical studies to assess the dissociation of the dimeric protease. An E37K substitution in PR2 significantly retards autoproteolytic cleavage during expression. Furthermore, it permits convenient measurement of the dimer...

Abstract The effect of the Y108V mutation of human glutathione S‐transferase P1‐1 (hGST P1‐1) on the binding of the diuretic drug ethacrynic acid (EA) and its glutathione conjugate (EASG) was investigated by calorimetric, spectrofluorimetric, and crystallographic studies. The mutation Tyr 108 → Val resulted in a 3D‐structure very similar to the wild type (wt) enzyme, where both the hydrophobic ligand binding site (H‐site) and...

Abstract Eps15 homology (EH)‐domain containing proteins are regulators of endocytic membrane trafficking. EH‐domain binding to proteins containing the tripeptide NPF has been well characterized, but recent studies have shown that EH‐domains are also able to interact with ligands containing DPF or GPF motifs. We demonstrate that the three motifs interact in a similar way with the EH‐domain of EHD1, with the NPF motif having the...

Abstract Rhodaneses/sulfurtransferases are ubiquitous enzymes that catalyze the transfer of sulfane sulfur from a donor molecule to a thiophilic acceptor via an active site cysteine that is modified to a persulfide during the reaction. Here, we present the first crystal structure of a triple‐domain rhodanese‐like protein, namely YnjE from Escherichia coli, in two states where its active site cysteine is either unmodified or present as a...

Abstract Ubiquitin‐like modifications are important mechanisms in cellular regulation, and are carried out through several steps with reaction intermediates being thioester conjugates of ubiquitin‐like proteins with E1, E2, and sometimes E3. Despite their importance, a thorough characterization of the intrinsic stability of these thioester intermediates has been lacking. In this study, we investigated the intrinsic stability by...

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Abstract Caspases are vital to apoptosis and exist in the cell as inactive zymogens. Dimerization is central to procaspase activation because the active sites are comprised of loops from both monomers. Although initiator procaspases are stable monomers until activated on cell death scaffolds, the effector caspases, such as procaspase‐3, are stable dimers. The activation mechanisms are reasonably well understood in terms of...

Abstract Quantitative measurement of small molecules with high spatiotemporal resolution provides a solid basis for correct understanding and accurate modeling of metabolic regulation. A promising approach toward this goal is the FLIP (fluorescent indicator protein) nanosensor based on bacterial periplasmic binding proteins (PBPs) and fluorescence resonance energy transfer (FRET) between the yellow and cyan variants of green...

Abstract S100B and S100A10 are dimeric, EF‐hand proteins. S100B undergoes a calcium‐dependant conformational change allowing it to interact with a short contiguous sequence from the actin‐capping protein CapZ (TRTK12). S100A10 does not bind calcium but is able to recruit the N‐terminus of annexin A2 important for membrane fusion events, and to form larger multiprotein complexes such as that with the cation channel proteins TRPV5/6....

Abstract Recombinant expression of eukaryotic proteins in Escherichia coli is often limited by poor folding and solubility. To address this problem, we employed a recently developed genetic selection for protein folding and solubility based on the bacterial twin‐arginine translocation (Tat) pathway to rapidly identify properly folded recombinant proteins or soluble protein domains of mammalian origin. The coding sequences for 29 different...

Abstract Quantitative prediction of protein–protein binding affinity is essential for understanding protein–protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein–protein binding affinity. The potential is obtained by statistically analyzing X‐ray structures of protein–protein complexes in the Protein Data Bank. This approach...

Abstract True catalases are tyrosine‐liganded, usually tetrameric, hemoproteins with subunit sizes of ∼55–84 kDa. Recently characterized hemoproteins with a catalase‐related structure, yet lacking in catalatic activity, include the 40–43 kDa allene oxide synthases of marine invertebrates and cyanobacteria. Herein, we describe the 1.8 Å X‐ray crystal structure of a 33 kDa subunit hemoprotein from Mycobacterium avium ssp....

Abstract Purified preparations of the recombinant b′x domain fragment of human protein‐disulphide isomerase (PDI), which are homogeneous by mass spectrometry and sodium dodecyl sulfate polyacrylamide gel electrophoresis, comprise more than one species when analyzed by ion‐exchange chromatography and nondenaturing polyacrylamide gel electrophoresis. These species were resolved and shown to be monomer and dimer by analytical ...

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