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Journal Issue - Volume 18 Issue 10 (October 2009)

  • In this issue

  • Published in Wiley Interscience on Sep 23, 2009
  • DOI: 10.1002/pro.252 (p n/a-n/a)

Abstract We still know very little about how proteins achieve their native three‐dimensional structure in vitro and in the cell. Folding studies as proteins emerge from the mega Dalton‐sized ribosome pose special challenges due to the large size and complicated nature of the ribosome‐nascent chain complex. This work introduces a combination of three‐component analysis of fluorescence depolarization decays (including the presence of two local...

Abstract Identifying conserved pockets on the surfaces of a family of proteins can provide insight into conserved geometric features and sites of protein–protein interaction. Here we describe mapping and comparison of the surfaces of aligned crystallographic structures, using the protein kinase family as a model. Pockets are rapidly computed using two computer programs, FADE and Crevasse. FADE uses gradients of atomic density to...

Abstract Protein structure alignment methods are essential for many different challenges in protein science, such as the determination of relations between proteins in the fold space or the analysis and prediction of their biological function. A number of different pairwise and multiple structure alignment (MStA) programs have been developed and provided to the community. Prior knowledge of the expected alignment accuracy is...

Abstract On the basis of the results of activity studies, previous reports have suggested that vitamin D binding protein (DBP) is significantly or even completely deglycosylated in cancer patients, eliminating the molecular precursor of the immunologically important Gc macrophage activating factor (GcMAF), a glycosidase‐derived product of DBP. The purpose of this investigation was to directly determine the relative degree of...

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Abstract ZntB is the distant homolog of CorA Mg2+ transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn2+ and Cd2+, but not Mg2+. Here, we report the 1.90 Å crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel‐shaped homopentamer that is similar to the full‐length CorA from Thermatoga maritima, but differs from two...

Abstract A general method was developed for the discovery of protease‐activated binding ligands, or proligands, from combinatorial prodomain libraries displayed on the surface of E. coli. Peptide libraries of candidate prodomains were fused with a matrix metalloprotease‐2 substrate linker to a vascular endothelial growth factor‐binding peptide and sorted using a two‐stage flow cytometry screening procedure to isolate proligands that required ...

Abstract Transferases and hydrolases catalyze different chemical reactions and express different dynamic responses upon ligand binding. To insulate the ligand molecule from the surrounding water, transferases bury it inside the protein by closing the cleft, while hydrolases undergo a small conformational change and leave the ligand molecule exposed to the solvent. Despite these distinct ligand‐binding modes, some transferases and...

Abstract The DH‐PH domain tandems of Dbl‐homology guanine nucleotide exchange factors catalyze the exchange of GTP for GDP in Rho‐family GTPases, and thus initiate a wide variety of cellular signaling cascades. Although several crystal structures of complexes of DH‐PH tandems with cognate, nucleotide free Rho GTPases are known, they provide limited information about the dynamics of the complex and it is not clear how accurately they...

Abstract A large number of β‐lactamases have emerged that are capable of conferring bacterial resistance to β‐lactam antibiotics. Comparison of the structural and functional features of this family has refined understanding of the catalytic properties of these enzymes. An arginine residue present at position 244 in TEM‐1 β‐lactamase interacts with the carboxyl group common to penicillin and cephalosporin antibiotics and thereby...

Abstract The effects of temperature and urea denaturation (6M urea) on the dominant structures of the 20‐residue Trp‐cage mini‐protein TC5b are investigated by molecular dynamics simulations of the protein at different temperatures in aqueous and in 6M urea solution using explicit solvent degrees of freedom and the GROMOS force‐field parameter set 45A3. In aqueous solution at 278 K, TC5b is stable throughout the 20 ns of MD simulation and the...

Abstract Coiled‐coils are widespread protein–protein interaction motifs typified by the heptad repeat (abcdefg)n in which “a” and “d” positions are hydrophobic residues. Although identification of likely coiled‐coil sequences is robust, prediction of strand order remains elusive. We present the X‐ray crystal structure of a short form (residues 583–611), “Q1‐short,” of the coiled‐coil assembly specificity domain from the voltage‐gated potassium...

Abstract Plasmodium falciparum FK506‐binding protein 35 (PfFKBP35) that binds to FK506 contains a conserved tetratricopeptide repeat (TPR) domain. Several known TPR domains such as Hop, PPP5, CHIP, and FKBP52 are structurally conserved and are able to interact with molecular chaperones such as Hsp70/Hsp90. Here, we present the crystal structure of PfFKBP35‐TPR and demonstrate its interaction with Hsp90 C‐terminal pentapeptide...

Abstract In this study we introduce a computationally‐driven enzyme redesign workflow for altering cofactor specificity from NADPH to NADH. By compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or BLOSUM62 scores of the residues populating the cofactor binding site. Instead, we find that...

Abstract The D1‐D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, QA and QB, the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of QB binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in...

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