@article {1412, title = {Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase from Pyrococcus sp. ST04.}, journal = {Acta Crystallogr D Biol Crystallogr}, volume = {70}, year = {2014}, month = {2014 Jun}, pages = {1659-68}, abstract = {

A novel maltose-forming \α-amylase (PSMA) was recently found in the hyperthermophilic archaeon Pyrococcus sp. ST04. This enzyme shows \<13\% amino-acid sequence identity to other known \α-amylases and displays a unique enzymatic property in that it hydrolyzes both \α-1,4-glucosidic and \α-1,6-glucosidic linkages of substrates, recognizing only maltose units, in an exo-type manner. Here, the crystal structure of PSMA at a resolution of 1.8 \Å is reported, showing a tight ring-shaped tetramer with monomers composed of two domains: an N-domain (amino acids 1-341) with a typical GH57 family (\β/\α)7-barrel fold and a C-domain (amino acids 342-597) composed of \α-helical bundles. A small closed cavity observed in proximity to the catalytic residues Glu153 and Asp253 at the domain interface has the appropriate volume and geometry to bind a maltose unit, accounting for the selective exo-type maltose hydrolysis of the enzyme. A narrow gate at the putative subsite +1 formed by residue Phe218 and Phe452 is essential for specific cleavage of glucosidic bonds. The closed cavity at the active site is connected to a short substrate-binding channel that extends to the central hole of the tetramer, exhibiting a geometry that is significantly different from classical maltogenic amylases or \β-amylases. The structural features of this novel exo-type maltose-forming \α-amylase provide a molecular basis for its unique enzymatic characteristics and for its potential use in industrial applications and protein engineering.

}, keywords = {Amylases, Catalytic Domain, Maltose, Models, Molecular, Mutagenesis, Site-Directed, Protein Conformation, Proteolysis, Pyrococcus, Substrate Specificity}, issn = {1399-0047}, doi = {10.1107/S1399004714006567}, author = {Park, Kwang-Hyun and Jung, Jong-Hyun and Park, Sung-Goo and Lee, Myeong-Eun and Holden, James F and Park, Cheon-Seok and Woo, Eui-Jeon} } @article {676, title = {Proteopedia: a status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules.}, journal = {J Struct Biol}, volume = {175}, year = {2011}, month = {2011 Aug}, pages = {244-52}, abstract = {Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other biomolecule structures. Created as a means for communicating biomolecule structures to a diverse scientific audience, Proteopedia (http://www.proteopedia.org) presents structural annotation in an intuitive, interactive format and allows members of the scientific community to easily contribute their own annotations. Here, we provide a status report on Proteopedia by describing advances in the web resource since its inception three and a half years ago, focusing on features of potential direct use to the scientific community. We discuss its progress as a collaborative 3D-encyclopedia of structures as well as its use as a complement to scientific publications and PowerPoint presentations. We also describe Proteopedia{\textquoteright}s use for 3D visualization in structure-related pedagogy.}, keywords = {Encyclopedias as Topic, Information Dissemination, Information Management, Information Services, Models, Molecular, Molecular Biology, Online Systems, Protein Conformation, Proteins, User-Computer Interface}, issn = {1095-8657}, doi = {10.1016/j.jsb.2011.04.011}, author = {Prilusky, Jaime and Hodis, Eran and Canner, David and Decatur, Wayne A and Oberholser, Karl and Martz, Eric and Berchanski, Alexander and Harel, Michal and Sussman, Joel L} } @article {677, title = {ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.}, journal = {Nucleic Acids Res}, volume = {38}, year = {2010}, month = {2010 Jul}, pages = {W529-33}, abstract = {It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.}, keywords = {Amino Acid Sequence, Base Sequence, Conserved Sequence, Evolution, Molecular, Internet, Nucleic Acid Conformation, Protein Conformation, Sequence Analysis, Sequence Homology, Amino Acid, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkq399}, author = {Ashkenazy, Haim and Erez, Elana and Martz, Eric and Pupko, Tal and Ben-Tal, Nir} } @article {680, title = {Proteopedia - a scientific {\textquoteright}wiki{\textquoteright} bridging the rift between three-dimensional structure and function of biomacromolecules.}, journal = {Genome Biol}, volume = {9}, year = {2008}, month = {2008}, pages = {R121}, abstract = {Many scientists lack the background to fully utilize the wealth of solved three-dimensional biomacromolecule structures. Thus, a resource is needed to present structure/function information in a user-friendly manner to a broad scientific audience. Proteopedia http://www.proteopedia.org is an interactive, wiki web-resource whose pages have embedded three-dimensional structures surrounded by descriptive text containing hyperlinks that change the appearance (view, representations, colors, labels) of the adjacent three-dimensional structure to reflect the concept explained in the text.}, keywords = {Databases, Protein, Internet, Models, Molecular, Protein Conformation, Protein Structure, Tertiary, Proteins, Software}, issn = {1465-6914}, doi = {10.1186/gb-2008-9-8-r121}, author = {Hodis, Eran and Prilusky, Jaime and Martz, Eric and Silman, Israel and Moult, John and Sussman, Joel L} } @article {1212, title = {Characterization of malate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum.}, journal = {Extremophiles}, volume = {11}, year = {2007}, month = {2007 Sep}, pages = {741-6}, abstract = {

Native and recombinant malate dehydrogenase (MDH) was characterized from the hyperthermophilic, facultatively autotrophic archaeon Pyrobaculum islandicum. The enzyme is a homotetramer with a subunit mass of 33 kDa. The activity kinetics of the native and recombinant proteins are the same. The apparent K ( m ) values of the recombinant protein for oxaloacetate (OAA) and NADH (at 80 degrees C and pH 8.0) were 15 and 86 microM, respectively, with specific activity as high as 470 U mg(-1). Activity decreased more than 90\% when NADPH was used. The catalytic efficiency of OAA reduction by P. islandicum MDH using NADH was significantly higher than that reported for any other archaeal MDH. Unlike other archaeal MDHs, specific activity of the P. islandicum MDH back-reaction also decreased more than 90\% when malate and NAD(+) were used as substrates and was not detected with NADP(+). A phylogenetic tree of 31 archaeal MDHs shows that they fall into 5 distinct groups separated largely along taxonomic lines suggesting minimal lateral mdh transfer between Archaea.

}, keywords = {Citric Acid Cycle, Hydrogen-Ion Concentration, Kinetics, Malate Dehydrogenase, Malates, Molecular Weight, NAD, NADP, Oxaloacetic Acid, Phylogeny, Protein Conformation, Protein Subunits, Pyrobaculum, Recombinant Proteins, Sequence Analysis, Protein, Substrate Specificity, Temperature}, issn = {1431-0651}, doi = {10.1007/s00792-007-0081-2}, author = {Yennaco, Lynda J and Hu, Yajing and Holden, James F} } @article {683, title = {ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.}, journal = {Nucleic Acids Res}, volume = {33}, year = {2005}, month = {2005 Jul 1}, pages = {W299-302}, abstract = {Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf (http://consurf.tau.ac.il/) is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.}, keywords = {Amino Acid Substitution, Amino Acids, Bacterial Proteins, Bayes Theorem, Evolution, Molecular, Internet, Models, Molecular, Potassium Channels, Protein Conformation, Software}, issn = {1362-4962}, doi = {10.1093/nar/gki370}, author = {Landau, Meytal and Mayrose, Itay and Rosenberg, Yossi and Glaser, Fabian and Martz, Eric and Pupko, Tal and Ben-Tal, Nir} } @article {750, title = {Simple oligomers as antimicrobial peptide mimics.}, journal = {J Ind Microbiol Biotechnol}, volume = {32}, year = {2005}, month = {2005 Jul}, pages = {296-300}, abstract = {New approaches to antibiotic design are desperately needed. The design of simple oligomers that capture the shape and biological function of natural antimicrobial peptides could prove to be versatile and highly successful. We discuss the use of aromatic backbones to design facially amphiphilic (FA) beta-sheet like structures which are potently antimicrobial. These oligomers capture the physiochemical properties of peptides like the Magainins and Defensins, which fold into specific conformations that are amphiphilic resulting in antimicrobial activity. However, natural peptides are expensive to prepare and difficult to produce on large scale. The design of polymers and oligomers that mimic the complex structures and remarkable biological properties of proteins is an important endeavor and provides attractive alternatives to the difficult synthesis of natural peptides. We therefore have designed a series of FA oligomers that are easy to prepare from inexpensive monomers. They adopt structures very reminiscent of amphiphilic beta-sheets and have significant activity with minimal inhibitory concentrations at 6 h in the low microgram per ml range (muM to nM). They are active against a broad spectrum of bacteria including gram-positive and gram-negative as well as antibiotic resistant strains.}, keywords = {Amides, Anti-Bacterial Agents, Antimicrobial Cationic Peptides, Drug Resistance, Bacterial, Gram-Negative Bacteria, Gram-Positive Bacteria, Inhibitory Concentration 50, Peptides, Protein Conformation}, issn = {1367-5435}, doi = {10.1007/s10295-005-0219-0}, author = {Rennie, Jason and Arnt, Lachelle and Tang, Haizhong and N{\"u}sslein, Klaus and Tew, Gregory N} } @article {684, title = {ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.}, journal = {Bioinformatics}, volume = {19}, year = {2003}, month = {2003 Jan}, pages = {163-4}, abstract = {We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues. Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally highly variable) residues that are often of important biological function. We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins. AVAILABILITY: The ConSurf web server is available at:http://consurf.tau.ac.il. SUPPLEMENTARY INFORMATION: A set of examples is available at http://consurf.tau.ac.il under {\textquoteright}GALLERY{\textquoteright}.}, keywords = {Amino Acids, bcl-X Protein, Conserved Sequence, Databases, Protein, Evolution, Molecular, Internet, Phylogeny, Protein Conformation, Proteins, Proto-Oncogene Proteins c-bcl-2, Sequence Alignment, Sequence Analysis, Protein, User-Computer Interface}, issn = {1367-4803}, author = {Glaser, Fabian and Pupko, Tal and Paz, Inbal and Bell, Rachel E and Bechor-Shental, Dalit and Martz, Eric and Ben-Tal, Nir} } @article {1739, title = {Bacterial metabolism of resorcinylic compounds: purification and properties of orcinol hydroxylase and resorcinol hydroxylase from Pseudomonas putida ORC.}, journal = {Eur J Biochem}, volume = {61}, year = {1976}, month = {1976 Jan 2}, pages = {259-69}, abstract = {

The hydroxylase activities observed in extracts of Pseudomonas putida ORC after growth on orcinol and resorcinol as sole source of carbon have been purified to homogeneity. Both enzymes were shown to be flavoproteins and to contain approximately 1 mol of FAD for each polypeptide chain, S20,W values for each enzyme are 4.1 +/- 0.1 and are independent of the presence of their aromatic substrates. Molecular weight determinations under native (approximately 68000) and denaturing (approximately 70000) conditions indicated that they are monomeric. The visible absorption spectra identical but the circular dichroic spectra of the two proteins can be distinguished. Although each protein catalyzes the NAD(P)H and O2-dependent hydroxylation of both orcinol and resorcinol, the efficiency of the transformations of the substrates by the two enzymes is radically different; furthermore resorcinol hydroxylase is much more versatile in the aromatic compounds it can utilize as substrates and effectors. Other properties of the enzymes which clearly establish their own identity include their serological characteristics and amino acid composition; the latter property is particularly evident when the quantities of valine and alanine residues are compared. The synthesis of each enzyme is also under different regulatory constraints, being controlled by the substrate used for growth.

}, keywords = {Amino Acids, Circular Dichroism, Flavin-Adenine Dinucleotide, Mixed Function Oxygenases, Molecular Weight, NAD, NADP, Oxidation-Reduction, Protein Conformation, Pseudomonas, Resorcinols, Spectrophotometry, Spectrophotometry, Ultraviolet}, issn = {0014-2956}, author = {Ohta, Y and Ribbons, D W} } @article {1735, title = {[Spectral properties of porcine plasminogen: study of the acidic transition (author{\textquoteright}s transl)].}, journal = {Eur J Biochem}, volume = {63}, year = {1976}, month = {1976 Apr 1}, pages = {553-62}, abstract = {

The acidic transition of porcine plasminogen, prepared by affinity chromatography, was studied by non-destructive methods. These methods are based on the analysis of the behaviour of the tryptophyls under various conditions. The perturbation of the absorption and emission spectra by pH or temperature and the dynamic quenching of the intrinsic fluorescence are used to obtain information on structural changes which affect the environment of these residues. It is shown that by decreasing pH the fluorescence emission spectra are shifted toward the long wavelengths, with a broadening of the fluorescence band. The same effect can be obtained at constant pH by heating the protein solution. In order to analyze these phenomena, it is assumed that the fluorescence intensities at 355 nm and 328 nm reflect the proportion of the tryptophans which are exposed to the solvent, and buried, respectively. The plot of the ratio of the fluorescence intensities at these wavelengths versus pH or temperature leads to a titration curve showing an unmasking of tryptophans. The proportion of exposed tryptophans is measured by the dynamic fluorescence quenching technique and the data analyzed according to Lehrer. The plot of the fraction of exposed tryptophyls versus pH also shows the unmasking of these chromophores. Thermal perturbation of a solution of plaminogen at neutral pH induces a difference absorption spectrum whose amplitudes at the maxima are proportional to the number of exposed aromatic residues. The comparison with a solution of fully denatured plasminogen in 6 M guanidium chloride, where all the tryptophyls are exposed, shows that the percentage of exposure is equal to 59\%. This number is significantly higher than the percentage found by the fluorescence quenching technique (20\%), indicating that some tryptophyls are located in crevices, exposed to the solvent but not to the iodide. At acidic pH the absorption difference spectra induced by thermal perturbation are not classical, since they show an inversion and a new band between 300 nm and 305 nm. This band is mentioned in the literature as a minor band of tryptophan which appears when this chromophore is located in an asymmetric environment. On plotting the maximum amplitude of these spectra obtained at acidic pH versus temperature, we obtain a curve indicating that two types of antagonistic interactions are involved in the perturbation of the chromophores spectra. The spectrophotometric titration of plasminogen gives classical absorption difference spectra. By plotting the maximum amplitude at 292 nm versus pH, we obtain a titration curve with an apparent pK of 2.9 units. This pK is acidic which respect to the pK value of a normal carboxyl. This low value can be due to a positively charged group in the neighbourhood of a carboxyl, which interacts with one or more chromophores. When the carboxyl becomes protonated, this positively charged group is free and available to perturb the environment of some chromophores...

}, keywords = {Animals, Binding Sites, Guanidines, Hydrogen-Ion Concentration, Plasminogen, Protein Binding, Protein Conformation, Spectrometry, Fluorescence, Spectrophotometry, Spectrophotometry, Ultraviolet, Swine, Temperature}, issn = {0014-2956}, author = {Rodier, F} } @article {1736, title = {Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin.}, journal = {Biochem Biophys Res Commun}, volume = {66}, year = {1975}, month = {1975 Oct 27}, pages = {1349-56}, keywords = {Animals, Cnidaria, Computers, Hemerythrin, Metalloproteins, Models, Molecular, Muscle Proteins, Protein Conformation, Species Specificity}, issn = {0006-291X}, author = {Hendrickson, W A and Ward, K B} } @article {1719, title = {Metal substitutions incarbonic anhydrase: a halide ion probe study.}, journal = {Biochem Biophys Res Commun}, volume = {66}, year = {1975}, month = {1975 Oct 27}, pages = {1281-6}, keywords = {Animals, Binding Sites, Cadmium, Carbonic Anhydrases, Cattle, Humans, Hydrogen-Ion Concentration, Magnetic Resonance Spectroscopy, Mercury, Protein Binding, Protein Conformation, Zinc}, issn = {0006-291X}, author = {Smith, R J and Bryant, R G} }