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Journal Issue - Volume 7 Issue 2 (February 1998)

  • Thank you, Hans!

  • Ralph A. Bradshaw, David S. Eisenberg, Mark A. Hermodson, Joseph J. Villafranca, Brian W. Matthews, Robert T. Sauer
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560070201 (p 231-232)

Abstract A consensus approach for the assignment of structural domains in proteins is presented. The approach combines a number of previously published algorithms, and takes advantage of the elevated accuracy obtained when assignments from the individual algorithms are in agreement. The consensus approach is tested on a data set of 55 protein chains, for which domain assignments from four automated methods were known, and for which...

Abstract A novel class of synthetic, multisite‐directed thrombin inhibitors, known as hirunorms, has been described recently. These compounds were designed to mimic the binding mode of hirudin, and they have been proven to be very strong and selective thrombin inhibitors. Here we report the crystal structure of the complex formed by human α‐thrombin and hirunorm V, a 26‐residue polypeptide containing non‐natural amino acids,...

Abstract A DNA/protein sequence comparison is a popular computational tool for molecular biologists. Finding a good alignment implies an evolutionary and/or functional relationship between proteins or genomic loci. Sequential similarity between two proteins indicates their structural resemblance, providing a practical approach for structural modeling, when structure of one of these proteins is known. The first step in the homology...

Abstract Prostate specific antigen (PSA) and human glandular kallikrein 2 (hK2), produced essentially by the prostate gland, are 237‐amino acid monomeric proteins, with 79% identity in primary structure. Twenty‐five anti‐PSA monoclonal antibodies (Mabs) were studied for binding to a large array of synthetic linear peptides selected from computer models of PSA and hK2, as well as to biotinylated peptides covering the entire PSA...

Abstract Calcium sensor proteins translate transient increases in intracellular calcium levels into metabolic or mechanical responses, by undergoing dramatic conformational changes upon Ca2+ binding. A detailed analysis of the calcium binding‐induced conformational changes in the representative calcium sensors calmodulin (CaM) and troponin C was performed to obtain insights into the underlying molecular basis for their response to ...

Abstract Crotalus adamanteus snake venom adamalysin II is the structural prototype of the adamalysin or ADAM family comprising proteolytic domains of snake venom metalloproteinases, multimodular mammalian reproductive tract proteins, and tumor necrosis factor α convertase, TACE, involved in the release of the inflammatory cytokine, TNFα. The structure of adamalysin II in noncovalent complex with two small‐molecule right‐hand side...

Abstract C. glutamicum meso‐diaminopimelate dehydrogenase is an enzyme of the L‐lysine biosynthetic pathway in bacteria. The binding of NADPH and diaminopimelate to the recombinant, overexpressed enzyme has been analyzed using hydrogen/deuterium exchange and electrospray ionization/mass spectrometry. NADPH binding reduces the extent of deuterium exchange, as does the binding of diaminopimelate. Pepsin digestion of the deuterated...

Abstract The mutation Ala28 to serine in human immunodeficiency virus, type 1, (HIV‐1) protease introduces putative hydrogen bonds to each active‐site carboxyl group. These hydrogen bonds are ubiquitous in pepsin‐like eukaryotic aspartic proteases. In order to understand the significance of this difference between HIV‐1 protease and homologous, eukaryotic aspartic proteases, we solved the three‐dimensional structure of A28S mutant...

Abstract As a first step to determine the folding pathway of a protein with an α/β doubly wound topology, the 1H, 13C, and 15N backbone chemical shifts of Azotobacter vinelandii holoflavodoxin II (179 residues) have been determined using multidimensional NMR spectroscopy. Its secondary structure is shown to contain a five‐stranded parallel β‐sheet (β2‐βl‐β3‐β4‐β5) and five α‐helices. Exchange rates for the individual amide protons of...

Abstract Bryodin 1 (BD1) is a type I ribosome‐inactivating protein (RIP) with low inherent animal toxicity. It has been cloned recently and the recombinant protein (rBDl) has been produced and crystallized. To gain insight into the relationship of rBDl structure and function, we investigated the role of sequences in a region (residues 128‐156) that exhibits homology with membrane interactive sequences and is not part of the...

Abstract The role of interhelical turns in determining protein structure has been investigated previously in relatively simple four‐helix‐bundle proteins using combinatorial mutagenesis coupled with screening for functional variants. To assess the tolerance to sequence substitution of a short, interhelical turn in a larger, more complicated protein, we have exploited a more sensitive in vivo selection for catalytic activity....

Abstract Apolipophorin‐III (apoLp‐III) from the insect, Manduca sexta, is a 166‐residue exchangeable apolipoprotein that plays a critical role in the dynamics of plasma lipoprotein interconversions. Our previous work indicated that a 36‐residue C‐terminal peptide fragment, generated by cyanogen bromide digestion of apoLp‐III, was unable to bind to lipid surfaces (Narayanaswami V, Kay CM, Oikawa K, Ryan RO, 1994, Biochemistry 33:13312‐13320),...

Abstract The colicin El channel polypeptide was shown to be organized anisotropically in membranes by solid‐state NMR analysis of samples of uniformly 15N‐labeled protein in oriented planar phospholipid bilayers. The 190 residue C‐terminal colicin E1 channel domain is the largest polypeptide to have been characterized by 15N solid‐state NMR spectroscopy in oriented membrane bilayers. The 15N‐NMR spectra of the colicin E1 show that: (1) the...

Abstract A pentasaccharide (PS) fragment of heparin capable of activating antithrombin (AT) markedly accelerates the inhibition of factor Xa by AT, but has insignificant effect on inhibition of thrombin. For inhibition of thrombin, the bridging function of a longer polysaccharide chain is required to accelerate the reaction. To study the basis for the similar reactivity of thrombin with the native or heparin‐activated conformers of...

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