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Journal Issue - Volume 12 Issue 8 (August 2003)

Abstract The identification of protein biochemical functions based on their three‐dimensional structures is strongly required in the post‐genome‐sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique...

Abstract The use of spectroscopy in the study of fatty acids binding to bovine β‐lactoglobulin (BLG) appears to be a difficult task, as these acid compounds, assumed as the protein natural ligands, do not exhibit favorable optical response such as, for example, absorption or fluorescence. Therefore, the BLG fatty‐acid equilibrium has been tackled by exploiting the competition between fatty acids and ANS, a widely used fluorescent...

Abstract The explosion of biological data resulting from genomic and proteomic research has created a pressing need for data analysis techniques that work effectively on a large scale. An area of particular interest is the organization and visualization of large families of protein sequences. An increasingly popular approach is to embed the sequences into a low‐dimensional Euclidean space in a way that preserves some predefined...

Abstract The interactions of wild‐type (WT) and AV77 tryptophan repressor (TR) with several operators have been studied using surface plasmon resonance. The use of this real‐time method has been able to settle several outstanding issues in the field, in a way that has heretofore not been possible. We resolve the issue of the super‐repressor status of the AV77 aporepressor and find that in contrast to early studies, which found no...

Abstract The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of TT1542 are present in a wide range of organisms. The TT1542 homologs in eukaryotes, PIG‐L in mammals, and GPI12 in yeast and protozoa, have N‐acetylglucosaminylphosphatidylinositol (GlcNAc‐PI) de‐N‐acetylase activity. Although most of the...

Abstract Despite their clinical importance, the mechanism of action of the class C β‐lactamases is poorly understood. In contrast to the class A and class D β‐lactamases, which contain a glutamate residue and a carbamylated lysine in their respective active sites that are thought to serve as general base catalysts for β‐lactam hydrolysis, the mechanism of activation of the serine and water nucleophiles in the class C enzymes is...

Abstract A strong similarity between the major aspects of protein folding and protein recognition is one of the emerging fundamental principles in protein science. A crucial importance of steric complementarity in protein recognition is a well‐established fact. The goal of this study was to assess the importance of the steric complementarity in protein folding, namely, in the packing of the secondary structure elements. Although the...

Abstract A method to predict lipoprotein signal peptides in Gram‐negative Eubacteria, LipoP, has been developed. The hidden Markov model (HMM) was able to distinguish between lipoproteins (SPaseII‐cleaved proteins), SPaseI‐cleaved proteins, cytoplasmic proteins, and transmembrane proteins. This predictor was able to predict 96.8% of the lipoproteins correctly with only 0.3% false positives in a set of SPaseI‐cleaved, cytoplasmic,...

Abstract The stability of Rhodobacter capsulatus bacterioferritin, a 24‐meric homopolymer, toward denaturation on variation in pH and temperature, and increasing concentrations of urea and guanidine. HCl was investigated with native PAGE, and CD and fluorescence spectroscopies. With temperature and urea, the wild‐type protein denatured without discernible intermediates in the equilibrium experiments, but with guanidine.HCl (Gnd.HCl)...

Abstract We demonstrated that amyloid‐forming peptides could be selected from phage‐displayed library via proteolysis‐based selection protocol. The library of 28‐residue peptides based on a sequence of the second zinc finger domain of Zif268, and computationally designed ββα peptide, FSD‐1, was presented monovalently on the surface of M13 phage. The library coupled the infectivity of phage particles to proteolytic stability of a...

  • Library analysis of SCHEMA‐guided protein recombination

  • Michelle M. Meyer, Jonathan J. Silberg, Christopher A. Voigt, Jeffrey B. Endelman, Stephen L. Mayo, Zhen‐Gang Wang, Frances H. Arnold
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.0306603 (p 1686-1693)

Abstract The computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in the three‐dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well SCHEMA predicts disruption, we have shuffled the distantly‐related β‐lactamases PSE‐4 and TEM‐1 at 13 sites to create a library of 214 (16,384) chimeras and examined which ones...

Abstract Adenylosuccinate lyase is a homotetramer that catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide (SAICAR). Several point mutations in the gene encoding the enzyme have been implicated in human disease. Bacillus subtilis adenylosuccinate lyase was used as a model system in which mutations were constructed corresponding to those mutations...

Abstract Mutations in HIV‐1 drug targets lead to resistance and consequent therapeutic failure of antiretroviral drugs. Phenotypic resistance assays are time‐consuming and costly, and genotypic rules‐based interpretations may fail to predict the effects of multiple mutations. We have developed a computational procedure that rapidly evaluates changes in the binding energy of inhibitors to mutant HIV‐1 PR variants. Models of WT...

Abstract Native‐state hydrogen exchange (HX) studies, used in conjunction with NMR spectroscopy, have been carried out on Escherichia coli thioredoxin (Trx) for characterizing two folding subdomains of the protein. The backbone amide protons of only the slowest‐exchanging 24 amino acid residues, of a total of 108 amino acid residues, could be followed at pH 7. The free energy of the opening event that results in an amide hydrogen exchanging...

Abstract Although progress has been made in understanding the thermodynamic stability of water‐soluble proteins, our understanding of the folding of membrane proteins is at a relatively primitive level. A major obstacle to understanding the folding of membrane proteins is the discovery of systems in which the folding is in thermodynamic equilibrium, and the development of methods to quantitatively assess this equilibrium in micelles...

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