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Journal Issue - Volume 10 Issue 12 (December 2001)

Abstract Sorcin is a 22 kD calcium‐binding protein that is found in a wide variety of cell types, such as heart, muscle, brain and adrenal medulla. It belongs to the penta‐EF‐hand (PEF) protein family, which contains five EF‐hand motifs that associate with membranes in a calcium‐dependent manner. Prototypic members of this family are the calcium‐binding domains of calpain, such as calpain dVI. Full‐length human sorcin has been...

Abstract Translation initiation factor 1A (aIF‐1A) from the archaeon Methanococcus jannaschii was expressed in Escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional NMR methods. The protein was found to be a member of the OB‐fold family of RNA‐associated proteins, containing a barrel of five beta‐strands, a feature that is shared with the homologous eukaryotic translation initiation factor...

Abstract To elucidate the role of amino acid residues adjacent to the catalytic site of pepsin‐like enzymes, we analyzed and compared the crystal structures of these enzymes, their complexes with inhibitors, and zymogens in the active site area (a total of 82 structures). In addition to the water molecule (W1) located between the active carboxyls and playing a role of the nucleophile during catalytic reaction, another water molecule...

Abstract The solution structure of oxidized bovine microsomal cytochrome b5 mutant (E48, E56/A, D60/A) has been determined through 1524 meaningful nuclear Overhauser effect constraints together with 190 pseudocontact shift constraints. The final family of 35 conformers has rmsd values with respect to the mean structure of 0.045±0.009 nm and 0.088±0.011 nm for backbone and heavy atoms, respectively. A characteristic of this mutant is that of ...

  • Motif‐based fold assignment

  • Łukasz Salwiński, David Eisenberg
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1110/ps.14401 (p 2460-2469)

Abstract Conventional fold recognition techniques rely mainly on the analysis of the entire sequence of a protein. We present an MBA method to improve performance of any conventional sequence‐based fold assignment. The method uses sequence motifs, such as those defined in the Prosite database, and the SwissProt annotation of the fold library. When combined with a simple SDP method, the coverage of MBA is comparable to the results...

Abstract Defensins are cationic and cysteine‐rich peptides that play a crucial role in the host defense against microorganisms of many organisms by their capability to permeabilize bacterial membranes. The low sequence similarity among the members of the large mammalian β‐defensin family suggests that their antimicrobial activity is largely independent of their primary structure. To investigate to what extent these defensins share a...

Abstract We have calculated the stability of decoy structures of several proteins (from the CASP3 models and the Park and Levitt decoy set) relative to the native structures. The calculations were performed with the force field–consistent ES/IS method, in which an implicit solvent (IS) model is used to calculate the average solvation free energy for snapshots from explicit simulations (ESs). The conformational free energy is...

Abstract It has been shown previously that some membrane proteins have a conserved core of amino acid residues. This idea not only serves to orient helices during model building exercises but may also provide insight into the structural role of residues mediating helix–helix interactions. Using experimentally determined high‐resolution structures of α‐helical transmembrane proteins we show that, of the residues within the...

Abstract The structures and dynamics of the native states of two mutational variants of human lysozyme, I56T and D67H, both associated with non‐neuropathic systemic amyloidosis, have been investigated by NMR spectroscopy. The 1H and 15N main‐chain amide chemical shifts of the I56T variant are very similar to those of the wild‐type protein, but those of the D67H variant are greatly altered for 28 residues in the β‐domain. This finding is...

Abstract Par‐4 is a 38‐kD protein pivotal to the apoptotic pathways of various cell types, most notably prostate cells and neurons, where it has been linked to prostate cancer and various neurodegenerative disorders including Alzheimer's and Huntington's diseases and HIV encephalitis. The C‐terminal region of Par‐4 is responsible for homodimerization and the ability of Par‐4 to interact with proposed effector molecules. In this...

Abstract The HypF N‐terminal domain has been found to convert readily from its native globular conformation into protein aggregates with the characteristics of amyloid fibrils associated with a variety of human diseases. This conversion was achieved by incubation at acidic pH or in the presence of moderate concentrations of trifluoroethanol. Electron microscopy showed that the fibrils grown in the presence of trifluoroethanol were...

Abstract IMP‐1 β‐lactamase is a zinc metallo‐enzyme encoded by the transferable blaIMP‐1 gene, which confers resistance to virtually all β‐lactam antibiotics including carbapenems. To understand how IMP‐1 recognizes and hydrolyzes β‐lactam antibiotics it is important to determine which amino acid residues are critical for catalysis and which residues control substrate specificity. We randomized 27 individual codons in the blaIMP‐1 gene to...

Abstract It is generally accepted that enzymes evolved via gene duplication of existing proteins. But duplicated genes can serve as a starting point for the evolution of a new function only if the protein they encode happens to exhibit some activity towards this new function. Although the importance of such catalytic promiscuity in enzyme evolution has been proposed, little is actually known regarding how common promiscuous...

Abstract Biotin protein ligase of Escherichia coli, the BirA protein, catalyses the covalent attachment of the biotin prosthetic group to a specific lysine of the biotin carboxyl carrier protein (BCCP) subunit of acetyl‐CoA carboxylase. BirA also functions to repress the biotin biosynthetic operon and synthesizes its own corepressor, biotinyl‐5′‐AMP, the catalytic intermediate in the biotinylation reaction. We have previously ...

Abstract A model is suggested for the complex between the biotin repressor of Escherichia coli, BirA, and BCCP, the biotin carboxyl carrier protein to which BirA transfers biotin. The model is consistent with prior physical and biochemical studies. Measurement of transfer rates for variants of BirA with single‐site mutations in the proposed BirA:BCCP interface region also provides support. The unique feature of the proposed interaction between...

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