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259 results on '"Scott A. Lesley"'

151. The Polymerase Incomplete Primer Extension (PIPE) method applied to high-throughput cloning and site-directed mutagenesis

Author

Heath E, Klock and Scott A, Lesley

Subjects
Glycerol, Transformation, Genetic, Cells, Cell Culture Techniques, Mutagenesis, Site-Directed, Cloning, Molecular, Polymerase Chain Reaction, DNA Primers
Abstract

Significant innovations in molecular biology methods have vastly improved the speed and efficiency of traditional restriction site and ligase-based cloning strategies. "Enzyme-free" methods eliminate the need to incorporate constrained sequences or modify Polymerase Chain Reaction (PCR)-generated DNA fragment ends. The Polymerase Incomplete Primer Extension (PIPE) method further condenses cloning and mutagenesis to a very simple two-step protocol with complete design flexibility not possible using related strategies. With this protocol, all major cloning operations are achieved by transforming competent cells with PCR products immediately following amplification. Normal PCRs generate mixtures of incomplete extension products. Using simple primer design rules and PCR, short, overlapping sequences are introduced at the ends of these incomplete extension mixtures which allow complementary strands to anneal and produce hybrid vector/insert combinations. These hybrids are directly transformed into recipient cells without any post-PCR enzymatic manipulations. We have found this method to be very easy and fast as compared to other available methods while retaining high efficiencies. Using this approach, we have cloned thousands of genes in parallel using a minimum of effort. The method is robust and amenable to automation as only a few, simple processing steps are needed.

Published
2008

152. A structural basis for the regulatory inactivation of DnaA

Author

Polat Abdubek, Sanjay Krishna, Daniel McMullan, Tamara Astakhova, Ron Reyes, Amanda Nopakun, Lian Duan, Scott A. Lesley, Debanu Das, Dana Weekes, Henry van den Bedem, Adam Godzik, Piotr Kozbial, Edward Nigoghossian, Marc André Elsliger, Keith O. Hodgson, Linda Okach, Christine B Trame, Mark W. Knuth, John Wooley, David Marciano, Mitchell D. Miller, Dennis Carlton, Hope A. Johnson, Christopher L. Rife, Jessica Paulsen, Thomas Clayton, Hsiu-Ju Chiu, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Ashley M. Deacon, Joanna Hale, Ian A. Wilson, Christina Puckett, Andrew T. Morse, Marc C. Deller, Heath E. Klock, Natasha Sefcovic, Qingping Xu, Lukasz Jaroszewski, Julie Feuerhelm, Kevin K. Jin, and Connie Chen

Subjects
Models, Molecular, Shewanella, ATPase, Dimer, Molecular Sequence Data, Antiparallel (biochemistry), Crystallography, X-Ray, DNA-binding protein, Article, chemistry.chemical_compound, Adenosine Triphosphate, Bacterial Proteins, Structural Biology, ATP hydrolysis, Amino Acid Sequence, Protein Structure, Quaternary, Molecular Biology, Adenosine Triphosphatases, DNA clamp, biology, DnaA, AAA proteins, DNA-Binding Proteins, chemistry, Biochemistry, biology.protein, Biophysics, bacteria, Dimerization, Sequence Alignment
Abstract

Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.

Published
2008

153. Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634

Author

Scott A. Lesley, Andreas Kreusch, Clare J. McCleverty, and Linda Columbus

Subjects
Models, Molecular, Dimer, Molecular Sequence Data, Peptide, Crystal structure, Crystallography, X-Ray, Ligands, Biochemistry, Protein Structure, Secondary, Article, Structural genomics, Polyethylene Glycols, chemistry.chemical_compound, Bacterial Proteins, Thermotoga maritima, Amino Acid Sequence, Binding site, Molecular Biology, Peptide sequence, Nuclear Magnetic Resonance, Biomolecular, Sequence Deletion, chemistry.chemical_classification, Binding Sites, biology, Membrane Proteins, Cobalt, biology.organism_classification, Protein Structure, Tertiary, chemistry, Membrane protein, Solubility, Dimerization
Abstract

As a part of the Joint Center for Structural Genomics (JCSG) biological targets, the structures of soluble domains of membrane proteins from Thermotoga maritima were pursued. Here, we report the crystal structure of the soluble domain of TM1634, a putative membrane protein of 128 residues (15.1 kDa) and unknown function. The soluble domain of TM1634 is an alpha-helical dimer that contains a single tetratrico peptide repeat (TPR) motif in each monomer where each motif is similar to that found in Tom20. The overall fold, however, is unique and a DALI search does not identify similar folds beyond the 38-residue TPR motif. Two different putative ligand binding sites, in which PEG200 and Co(2+) were located, were identified using crystallography and NMR, respectively.

Published
2008

154. Probing the Active and Allosteric Sites of Thermotoga maritima ADPGlucose Pyrophosphorylase: Mutational Analyses of the glgC1 and glgC2 Proteins

Author

Christopher R Meyer, Brent Tennison, Jared Wiig, Scott A. Lesley, Kelly Nguyen, Shannon Lim, David Rafael Abreu Reyes, Michael Susoeff, Onnig Panosian, Rachel N. Lippert, Mikiko Matsui, Herb L Axelrod, Tala Harake, and Janice Gatzke

Subjects
0303 health sciences, biology, Chemistry, Allosteric regulation, biology.organism_classification, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, ADPGlucose Pyrophosphorylase, Thermotoga maritima, Genetics, Molecular Biology, 030217 neurology & neurosurgery, 030304 developmental biology, Biotechnology
Published
2008
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155. Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution

Author

Qingping, Xu, Piotr, Kozbial, Daniel, McMullan, S Sri, Krishna, Scott M, Brittain, Scott B, Ficarro, Michael, DiDonato, Mitchell D, Miller, Polat, Abdubek, Herbert L, Axelrod, Hsiu-Ju, Chiu, Thomas, Clayton, Lian, Duan, Marc-André, Elsliger, Julie, Feuerhelm, Slawomir K, Grzechnik, Joanna, Hale, Gye Won, Han, Lukasz, Jaroszewski, Heath E, Klock, Andrew T, Morse, Edward, Nigoghossian, Jessica, Paulsen, Ron, Reyes, Christopher L, Rife, Henry, van den Bedem, Aprilfawn, White, Keith O, Hodgson, John, Wooley, Ashley M, Deacon, Adam, Godzik, Scott A, Lesley, and Ian A, Wilson

Subjects
Ribosomal Proteins, Protein Folding, Bacterial Proteins, ADP-Ribosylation Factors, Cytidine Deaminase, Molecular Sequence Data, Thermotoga maritima, Amino Acid Sequence, Crystallography, X-Ray, Protein Structure, Tertiary
Published
2008

156. Protein production and purification

Author

Adelinda Yee, R Kim, J.M. Sauder, Youngchang Kim, Thomas Acton, Andrzej Joachimiak, J Weigelt, M. Zhou, J Ming, Kim C-Y., B M Hallberg, Tarun Gheyi, Geoffrey S. Waldo, Gaetano T. Montelione, Udo Oppermann, Konrad Büssow, Shane Atwell, Sirano Dhe-Paganon, Anja Schütz, Yoav Peleg, C K Ho, J.S. Emtage, Stephen K. Burley, Kim S-H., John G. Luz, Mark R. Chance, L Zhao, Jaime Prilusky, Renaud Vincentelli, William H. Eschenfeldt, Lucy Stols, Masayori Inouye, Andrej Sali, Shira Albeck, Raymond C. Stevens, Cheryl H. Arrowsmith, L C Ma, Aled M. Edwards, Christian Cambillau, Udo Heinemann, Pär Nordlund, Hung L-W., Orly Dym, F Zhang, Joel L. Sussman, Ritu Shastry, Park H-W., Ian A. Wilson, Susanne Gräslund, Mark I. Donnelly, Jeffrey B. Bonanno, Scott A. Lesley, Andras Fiser, Kristin C. Gunsalus, James E. Bray, Frank R. Collart, M Jiang, Raymond Hui, Ruiying Wu, D Wang, John F. Hunt, Kellie Cunningham, Rong Xiao, Alexei Savchenko, Raymond J. Owens, Hao Wang, Haleema Janjua, Yunyu Shi, Soumya Swaminathan, Kevin Bain, Stefan Knapp, Zihe Rao, Steven C. Almo, David I. Stuart, S Yokoyama, Irina Dementieva, S Daenke, Thomas C. Terwilliger, Opher Gileadi, D.A. Thompson, Liang Tong, Tamar Unger, Stephen Anderson, and F.W. Studier

Subjects
Genetics, Proteomics, Proteomics methods, Extramural, Management science, Chemistry, Physical, Chemical fractionation, Cell Biology, Biology, Chemical Fractionation, Protein Engineering, Biochemistry, Article, Recombinant Proteins, Molecular Biology, Biotechnology
Abstract

In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.

Published
2008

157. Selecting Folded Proteins from a Library of Secondary Structural Elements

Author

Roshan Perera, Bernhard H. Geierstanger, Scott A. Lesley, Wenshe R. Liu, Peter G. Schultz, and James Graziano

Subjects
Protein Folding, Chemistry, Escherichia coli Proteins, Protein domain, Protein design, Structural gene, Proteins, General Chemistry, Computational biology, Biochemistry, Combinatorial chemistry, Catalysis, Article, Peptide Fragments, Protein Structure, Secondary, Colloid and Surface Chemistry, Protein structure, Solubility, Peptide Library, TIM barrel, Protein folding, Threading (protein sequence), Directed Molecular Evolution, Protein secondary structure
Abstract

Despite the large sequence diversity present in the proteomes of known organisms, most functional proteins characterized to date assume one of relatively few distinct folds1-5, suggesting that nature uses a limited number of stable, soluble folds relative to what is theoretically possible in protein sequence space. These folds likely represent the divergent products of a limited set of ancient protein folds. However, protein sequences that fold into stable, unique topologies but are not encoded by any sequenced genome may also exist. It may be possible to identify other stable folds that simply have not yet been sampled in the course of evolution by means of an artificial selection and molecular evolution process. Methods such as DNA shuffling6 which mimic the combinatorial diversity mechanism of the immune system are among the most efficient methods to modify or enhance protein activity. Unfortunately, the structural diversity generated in a library of shuffled homologues is relatively small7-11, although newer methods for random fragment assembly that overcome sequence homology requirements may lead to libraries with increased structural diversity12,13. Alternatively, natural or in vitro combinatorial assembly of distinct protein subunits (e.g., subdomains, exons, etc.) can create significant structural and functional diversity14-19. For example, the mammalian blood clotting proteins plasminogen, protein C, urokinase and prothrombin are all derived from different combinations of 5 exons14. Sequence and structural studies also suggest that many existing TIM barrel proteins evolved from the combinatorial assembly of subunits from more primitive eightfold βα barrels15,16. Other approaches for creating libraries of novel sequences that fold into native-like protein structures include the use of binary patterned residues designed around an existing known fold and the random assembly of cassettes composed of as few as three amino acid residues17,18. A more recent report details the use of cassettes of binary patterned residues around known protein motifs that are ultimately randomly assembled without fitting any designed folding constraint19. However, these latter methods have not yet yielded stable, novel folds under physiological conditions20. Despite the considerable effort to identify or evolve new folds, only a limited number of distinct protein folds have been identified to date18. Here we describe a system for the synthesis of polypeptides with potentially novel folds in which existing sequence and structural data from bacterial proteins are used to assemble a pool of secondary structural elements (α-helices, β-strands and loops). These secondary structural elements are in turn recombined into a library of de novo sequences that may be screened or selected for folded proteins. Proteins that fold into a native state acquire measurable biophysical characteristics such as solubility, stable secondary structure, well-dispersed 1D NMR spectra indicative of packed side chains, and reversible two-state unfolding behavior. In this work, we chose to initially screen the library for polypeptides that are soluble in aqueous solution using a GFP fusion protein reporter that had been previously reported21. Indeed, several sequences with stable secondary structure are identified.

Published
2007

158. Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution

Author

Irimpan I, Mathews, Daniel, McMullan, Mitchell D, Miller, Jaume M, Canaves, Marc-André, Elsliger, Ross, Floyd, Slawomir K, Grzechnik, Lukasz, Jaroszewski, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Timothy M, McPhillips, Andrew T, Morse, Kevin, Quijano, Christopher L, Rife, Robert, Schwarzenbacher, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Dana, Weekes, Guenter, Wolf, Keith O, Hodgson, John, Wooley, Ashley M, Deacon, Adam, Godzik, Scott A, Lesley, and Ian A, Wilson

Subjects
Phosphotransferases (Alcohol Group Acceptor), Crystallography, Sequence Homology, Amino Acid, Protein Conformation, Molecular Sequence Data, Thermotoga maritima, Amino Acid Sequence
Published
2007

159. Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts

Author

Mark W. Knuth, Scott A. Lesley, Heath E. Klock, and Eric Koesema

Subjects
Genetics, Cloning, biology, Recombinant expression, Quantitative proteomics, Mutagenesis (molecular biology technique), Computational biology, Genomics, Biochemistry, Polymerase Chain Reaction, Primer extension, Protein expression, Structural genomics, Structural Biology, Mutagenesis, biology.protein, Cloning, Molecular, Crystallization, Molecular Biology, Polymerase, DNA Primers
Abstract

Successful protein expression, purification, and crystallization for challenging targets typically requires evaluation of a multitude of expression constructs. Often many iterations of truncations and point mutations are required to identify a suitable derivative for recombinant expression. Making and characterizing these variants is a significant barrier to success. We have developed a rapid and efficient cloning process and combined it with a protein microscreening approach to characterize protein suitability for structural studies. The Polymerase Incomplete Primer Extension (PIPE) cloning method was used to rapidly clone 448 protein targets and then to generate 2143 truncations from 96 targets with minimal effort. Proteins were expressed, purified, and characterized via a microscreening protocol, which incorporates protein quantification, liquid chromatography mass spectrometry and analytical size exclusion chromatography (AnSEC) to evaluate suitability of the protein products for X-ray crystallography. The results suggest that selecting expression constructs for crystal trials based primarily on expression solubility is insufficient. Instead, AnSEC scoring as a measure of protein polydispersity was found to be predictive of ultimate structure determination success and essential for identifying appropriate boundaries for truncation series. Overall structure determination success was increased by at least 38% by applying this combined PIPE cloning and microscreening approach to recalcitrant targets.

Published
2007

160. The challenge of protein structure determination--lessons from structural genomics

Author

Scott A. Lesley, Ian A. Wilson, Lukasz Slabinski, Adam Godzik, Leszek Rychlewski, Lukasz Jaroszewski, and Ana P. C. Rodrigues

Subjects
Proteomics, Magnetic Resonance Spectroscopy, Process (engineering), Protein Conformation, Protein Data Bank (RCSB PDB), Computational biology, Biology, Bioinformatics, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Article, Structural genomics, Protein structure, X ray methods, Sequence Analysis, Protein, Databases, Protein, Molecular Biology, Probability, Computational Biology, Proteins, Genomics, Structural biology, Isoelectric Focusing, Protein crystallization, Crystallization, Protein Structure Initiative
Abstract

The process of experimental determination of protein structure is marred with a high ratio of failures at many stages. With availability of large quantities of data from high-throughput structure determination in structural genomics centers, we can now learn to recognize protein features correlated with failures; thus, we can recognize proteins more likely to succeed and eventually learn how to modify those that are less likely to succeed. Here, we identify several protein features that correlate strongly with successful protein production and crystallization and combine them into a single score that assesses "crystallization feasibility." The formula derived here was tested with a jackknife procedure and validated on independent benchmark sets. The "crystallization feasibility" score described here is being applied to target selection in the Joint Center for Structural Genomics, and is now contributing to increasing the success rate, lowering the costs, and shortening the time for protein structure determination. Analyses of PDB depositions suggest that very similar features also play a role in non-high-throughput structure determination, suggesting that this crystallization feasibility score would also be of significant interest to structural biology, as well as to molecular and biochemistry laboratories.

Published
2007

161. The self-inhibited structure of full-length PCSK9 at 1.9 A reveals structural homology with resistin within the C-terminal domain

Author

Jennifer L. Harris, Jun Li, Eric Hampton, Glen Spraggon, Scott A. Lesley, and Mark W. Knuth

Subjects
Models, Molecular, Saccharomyces cerevisiae Proteins, Structural similarity, Protein Conformation, Molecular Sequence Data, Static Electricity, Biology, Crystallography, X-Ray, Homology (biology), Protein Structure, Secondary, Protein structure, Catalytic Domain, Histidine, Resistin, Amino Acid Sequence, Cysteine, Disulfides, Peptide sequence, Genetics, Furin, Multidisciplinary, Binding Sites, Sequence Homology, Amino Acid, PCSK9, Serine Endopeptidases, Biological Sciences, Proprotein convertase, Protein Structure, Tertiary, Biochemistry, Models, Chemical, Mutation, Kexin, Proprotein Convertases, Proprotein Convertase 9, Baculoviridae, Oligopeptides
Abstract

Mutations in proprotein convertase subtilisin/kexin type 9 (PCSK9) are strongly associated with levels of low-density lipoprotein cholesterol in the blood plasma and, thereby, occurrence or resistance to atherosclerosis and coronary heart disease. Despite this importance, relatively little is known about the biology of PCSK9. Here, the crystal structure of a full-length construct of PCSK9 solved to 1.9-Å resolution is presented. The structure contains a fully folded C-terminal cysteine-rich domain (CRD), showing a distinct structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. This structural relationship between the CRD of PCSK9 and the resistin family is not observed in primary sequence comparisons and strongly suggests a distant evolutionary link between the two molecules. This three-dimensional homology provides insight into the function of PCSK9 at the molecular level and will help to dissect the link between PCSK9 and CHD.

Published
2007

162. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

Author

Ron Reyes, Slawomir K. Grzechnik, Andrew T. Morse, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Mark W. Knuth, Marc-André Elsliger, Edward Nigoghossian, Dennis Carlton, Ian A. Wilson, Qingping Xu, Piotr Kozbial, Eric Hampton, Paul Schimmel, Mitchell D. Miller, Adam Godzik, Herbert L. Axelrod, Chloe Zubieta, John Wooley, Daniel McMullan, Thomas Clayton, Eileen Ambing, Christopher L. Rife, Aprilfawn White, Keith O. Hodgson, Dana Weekes, Scott A. Lesley, Hsiu-Ju Chiu, Kevin K. Jin, Joanna Hale, Henry van den Bedem, Tamara Astakhova, Ashley M. Deacon, Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Mili Kapoor, Heath E. Klock, Linda Okach, Julie Feuerhelm, Marc C. Deller, David Marciano, and Lian Duan

Subjects
Protein Folding, Shewanella, Heme binding, Amino Acid Motifs, Molecular Sequence Data, Heme, Random hexamer, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Multienzyme Complexes, Catalytic Domain, Bacteroides, Amino Acid Sequence, Shewanella oneidensis, Coloring Agents, Molecular Biology, Conserved Sequence, Dye decolorizing peroxidase, biology, Chemistry, Active site, Isothermal titration calorimetry, biology.organism_classification, A-site, Crystallography, Peroxidases, biology.protein, Protein Binding
Abstract

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 Angstroms, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, {alpha}+{beta} ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).

Published
2007

163. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases

Author

Ashley M. Deacon, Ian A. Wilson, Lutz Tautz, Eileen Ambing, Andrew T. Morse, Michael DiDonato, Justin Haugen, Dennis Carlton, Polat Abdubek, Slawomir K. Grzechnik, Thomas Clayton, Tomas Mustelin, Ron Reyes, Eric Koesema, Gye Won Han, Sanjay Krishna, Silvya Oommachen, Joanna Hale, Mark W. Knuth, John Wooley, Mitchell D. Miller, Aprilfawn White, Tamara Astakhova, Christopher L. Rife, Heath E. Klock, Kevin K. Jin, Lukasz Jaroszewski, Daniel McMullan, Scott A. Lesley, Qingping Xu, Dana Weekes, Eric Hampton, Lian Duan, Marc-André Elsliger, Edward Nigoghossian, Hsiu-Ju Chiu, Henry van den Bedem, Adam Godzik, Herbert L. Axelrod, and Keith O. Hodgson

Subjects
Scaffold, Binding Sites, Chemistry, Neisseria meningitidis, Phosphatase, Resolution (electron density), Amino Acid Motifs, Molecular Sequence Data, Crystal structure, medicine.disease_cause, Crystallography, X-Ray, Biochemistry, Phosphoric Monoester Hydrolases, Protein Structure, Secondary, Bacterial Proteins, Structural Biology, Hydrolase, medicine, Amino Acid Sequence, Molecular Biology
Published
2007

164. Integration of inositol phosphate signaling pathways via human ITPK1

Author

Scott A. Lesley, Stephen B. Shears, Elizabeth A. Grabau, Xun Qian, Glen Spraggon, Amanda R. Stiles, Philip P. Chamberlain, David H. Jones, and Jaiesoon Cho

Subjects
PLCB1, Cystic Fibrosis, Inositol Phosphates, PLCB2, Phosphatase, Molecular Sequence Data, Molecular Conformation, Biology, Biochemistry, Article, Substrate Specificity, chemistry.chemical_compound, Humans, Inositol, Amino Acid Sequence, Inositol phosphate, Molecular Biology, chemistry.chemical_classification, Phospholipase C, Sequence Homology, Amino Acid, Cell Membrane, Cell Biology, Inositol trisphosphate receptor, Protein Structure, Tertiary, Enzyme Activation, Phosphotransferases (Alcohol Group Acceptor), chemistry, Type C Phospholipases, biology.protein, Inositol-3-phosphate synthase, Signal Transduction
Abstract

Inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) is a reversible, poly-specific inositol phosphate kinase that has been implicated as a modifier gene in cystic fibrosis. Upon activation of phospholipase C at the plasma membrane, inositol 1,4,5-trisphosphate enters the cytosol and is inter-converted by an array of kinases and phosphatases into other inositol phosphates with diverse and critical cellular activities. In mammals it has been established that inositol 1,3,4-trisphosphate, produced from inositol 1,4,5-trisphosphate, lies in a branch of the metabolic pathway that is separate from inositol 3,4,5,6-tetrakisphosphate, which inhibits plasma membrane chloride channels. We have determined the molecular mechanism for communication between these two pathways, showing that phosphate is transferred between inositol phosphates via ITPK1-bound nucleotide. Intersubstrate phosphate transfer explains how competing substrates are able to stimulate each others' catalysis by ITPK1. We further show that these features occur in the human protein, but not in plant or protozoan homologues. The high resolution structure of human ITPK1 identifies novel secondary structural features able to impart substrate selectivity and enhance nucleotide binding, thereby promoting intersubstrate phosphate transfer. Our work describes a novel mode of substrate regulation and provides insight into the enzyme evolution of a signaling mechanism from a metabolic role.

Published
2007

166. Identification of selective, nonpeptidic nitrile inhibitors of cathepsin s using the substrate activity screening method

Author

Scott A. Lesley, Jonathan A. Ellman, Warren J. L. Wood, Andrew W. Patterson, Michael Hornsby, and Glen Spraggon

Subjects
Models, Molecular, Nitrile, Stereochemistry, Molecular Sequence Data, Triazole, Crystallography, X-Ray, Substrate Specificity, chemistry.chemical_compound, Structure-Activity Relationship, Drug Discovery, Hydrolase, Nitriles, Protease Inhibitors, Amino Acid Sequence, Cathepsin S, Cathepsin, biology, Molecular Structure, Biological activity, Stereoisomerism, Triazoles, Cathepsins, chemistry, Enzyme inhibitor, biology.protein, Molecular Medicine, Pharmacophore
Abstract

The substrate activity screening method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain low nanomolar 1,4-disubstituted-1,2,3-triazole-based aldehyde inhibitors (Wood, W. J. L.; Patterson, A. W.; Tsuruoka, H.; Jain, R. K.; Ellman, J. A. J. Am. Chem. Soc. 2005, 127, 15521-15527). Replacement of the metabolically labile aldehyde pharmacophore with the nitrile pharmacophore provided inhibitors with moderate potency for cathepsin S. The inhibitors showed good selectivity over cathepsins B and L but no selectivity over cathepsin K. X-ray structures of two crystal forms (1.5 and 1.9 A) of a complex between cathepsin S and a triazole inhibitor incorporating a chloromethyl ketone pharmacophore guided the design of triazole substrates with increased cleavage efficiency and selectivity for cathepsin S over cathepsins B, L, and K. Conversion of select substrates to nitrile inhibitors yielded a low molecular weight (414 Da) and potent (15 nM) cathepsin S inhibitor that showed1000-fold selectivity over cathepsins B, L, and K.

Published
2006

167. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution

Author

Daniel McMullan, Inna Levin, Hope A. Johnson, Ian A. Wilson, Scott A. Lesley, Herbert L. Axelrod, Eileen Ambing, Gye Won Han, Marc Fasnacht, Eric Sims, Silvya Oommachen, Tamara Astakhova, Glen Spraggon, Andreas Kreusch, Keith O. Hodgson, Ron Reyes, Rebecca Page, Justin Haugen, Mitchell D. Miller, Thomas Clayton, Sanjay Agarwalla, Mickey Kosloff, Vandana Sridhar, Jaume M. Canaves, Dennis Carlton, Polat Abdubek, Sanjay Krishna, Henry van den Bedem, Heath E. Klock, Raymond C. Stevens, Hsiu-Ju Chiu, Peter Kuhn, Eric Hampton, Slawomir K. Grzechnik, Robert Schwarzenbacher, Guenter Wolf, Christopher L. Rife, Joanna Hale, Carina Grittini, Ashley M. Deacon, Marc-André Elsliger, Edward Nigoghossian, Mark W. Knuth, Kevin Quijano, John Wooley, Eric Koesema, Aprilfawn White, Julie Feuerhelm, Adam Godzik, Qingping Xu, Andrew T. Morse, Lian Duan, Kin Moy, Kevin K. Jin, Michael DiDonato, Jeff Velasquez, Lukasz Jaroszewski, Linda Okach, and Jessica Paulsen

Subjects
Models, Molecular, Molecular Sequence Data, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Structural genomics, Bacterial Proteins, Structural Biology, Phylogenetics, Consensus sequence, Transferase, Amino Acid Sequence, Molecular Biology, Peptide sequence, Phylogeny, Glutathione Transferase, chemistry.chemical_classification, biology, Agrobacterium tumefaciens, Protein engineering, biology.organism_classification, Enzyme, chemistry, Dimerization
Abstract

Glutathione S-transferases (GSTs) comprise a diverse superfamily of enzymes found in organisms from all kingdoms of life. GSTs are involved in diverse processes, notably small-molecule biosynthesis or detoxification, and are frequently also used in protein engineering studies or as biotechnology tools. Here, we report the high-resolution X-ray structure of Atu5508 from the pathogenic soil bacterium Agrobacterium tumefaciens (atGST1). Through use of comparative sequence and structural analysis of the GST superfamily, we identified local sequence and structural signatures, which allowed us to distinguish between different GST classes. This approach enables GST classification based on structure, without requiring additional biochemical or immunological data. Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies.

Published
2006

168. Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p

Author

Andreas Kreusch, Heath E. Klock, Marc-André Elsliger, Jaume M. Canaves, Edward Nigoghossian, Slawomir K. Grzechnik, Henry van den Bedem, Lukasz Jaroszewski, Justin Haugen, Guenter Wolf, Ron Reyes, Andrew T. Morse, Ashley M. Deacon, Hsiu-Ju Chiu, Thomas Clayton, Ian A. Wilson, Mark W. Knuth, Michael DiDonato, Kevin Quijano, John Wooley, Joanna Hale, Peter Kuhn, Kevin K. Jin, Eileen Ambing, Qingping Xu, Lian Duan, Glen Spraggon, Adam Godzik, Christopher L. Rife, Herbert L. Axelrod, Eric Koesema, Tamara Astakhova, Sanjay Agarwalla, Eric Hampton, Julie Feuerhelm, Gye Won Han, Silvya Oommachen, Dennis Carlton, Keith O. Hodgson, Scott A. Lesley, Robert Schwarzenbacher, Polat Abdubek, Sanjay Krishna, Linda Okach, Mitchell D. Miller, Daniel McMullan, Raymond C. Stevens, Aprilfawn White, and Jessica Paulsen

Subjects
Physics, Models, Molecular, Protein Folding, Saccharomyces cerevisiae Proteins, biology, Molecular Sequence Data, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein tertiary structure, Protein Structure, Secondary, ran GTP-Binding Protein, Ran-binding protein, Bacterial Proteins, Structural Biology, Signaling proteins, Thermotoga maritima, Amino Acid Sequence, Molecular Biology
Published
2006

169. Crystal structure of the human TRPV2 channel ankyrin repeat domain

Author

Clare J. McCleverty, Ardem Patapoutian, Scott A. Lesley, Andreas Kreusch, and Eric Koesema

Subjects
Genetics, chemistry.chemical_classification, Models, Molecular, Subfamily, Binding Sites, Sequence Homology, Amino Acid, Chemistry, TRPV2, Molecular Sequence Data, TRPV Cation Channels, Ligand (biochemistry), Biochemistry, TRPV, Protein Structure, Secondary, Ankyrin Repeat, Protein Structure, Tertiary, Protein Structure Report, Biophysics, Ankyrin, Humans, Ankyrin repeat, Amino Acid Sequence, Binding site, Molecular Biology, Peptide sequence
Abstract

TRPV channels are important polymodal integrators of noxious stimuli mediating thermosensation and nociception. An ankyrin repeat domain (ARD), which is a common protein–protein recognition domain, is conserved in the N-terminal intracellular domain of all TRPV channels and predicted to contain three to four ankyrin repeats. Here we report the first structure from the TRPV channel subfamily, a 1.7 A resolution crystal structure of the human TRPV2 ARD. Our crystal structure reveals a six ankyrin repeat stack with multiple insertions in each repeat generating several unique features compared with a canonical ARD. The surface typically used for ligand recognition, the ankyrin groove, contains extended loops with an exposed hydrophobic patch and a prominent kink resulting from a large rotational shift of the last two repeats. The TRPV2 ARD provides the first structural insight into a domain that coordinates nociceptive sensory transduction and is likely to be a prototype for other TRPV channel ARDs.

Published
2006

170. Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site

Author

Lian Duan, Guenter Wolf, Polat Abdubek, Sanjay Krishna, Daniel McMullan, Inna Levin, Keith O. Hodgson, Jessica Paulsen, Jaume M. Canaves, Mark W. Knuth, Kevin Quijano, Joanna Hale, Linda Okach, Michael DiDonato, Andreas Kreusch, Hsiu-Ju Chiu, Sanjay Agarwalla, Marc-André Elsliger, Mitchell D. Miller, Edward Nigoghossian, Scott A. Lesley, Q. Xu, Heath E. Klock, Eric Hampton, Glen Spraggon, Herbert L. Axelrod, Henry van den Bedem, Adam Godzik, Lukasz Jaroszewski, Peter Kuhn, John Wooley, Justin Haugen, Ron Reyes, Robert Schwarzenbacher, Raymond C. Stevens, Eric Koesema, Aprilfawn White, Slawomir K. Grzechnik, Ian A. Wilson, Eileen Ambing, Silvya Oommachen, Scott M. Brittain, Christopher L. Rife, Andrew T. Morse, Ashley M. Deacon, and Kevin K. Jin

Subjects
Models, Molecular, Protein Folding, Binding Sites, Protein Conformation, media_common.quotation_subject, Acid Phosphatase, Molecular Sequence Data, Art, Crystallography, X-Ray, Biochemistry, Structural Biology, 2-phosphosulfolactate phosphatase, Clostridium acetobutylicum, Amino Acid Sequence, Molecular Biology, Humanities, media_common
Abstract

Michael DiDonato, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Sanjay Agarwalla, Scott M. Brittain, Mitchell D. Miller, Polat Abdubek, Eileen Ambing, Herbert L. Axelrod, JaumeM. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Lian Duan, Marc-Andre Elsliger, Adam Godzik, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Inna Levin, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Kevin Quijano, Ron Reyes, Christopher L. Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, AprilfawnWhite, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson* The Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California The University of California, San Diego, La Jolla, California The Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California

Published
2006

171. Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution

Author

Glen Spraggon, Aprilfawn White, Lian Duan, Edward Nigoghossian, Sanjay Agarwalla, Andrew T. Morse, Dennis Carlton, Slawomir K. Grzechnik, Guenter Wolf, Adam Godzik, Marc-André Elsliger, Raymond C. Stevens, Sanjay Krishna, Keith O. Hodgson, Silvya Oommachen, John S. Kovarik, Polat Abdubek, Ian A. Wilson, Ron Reyes, Jaume M. Canaves, Christopher L. Rife, Eileen Ambing, Peter Kuhn, Hsiu-Ju Chiu, John Wooley, Jessica Paulsen, Kevin Quijano, Justin Haugen, Eric Hampton, Linda Okach, Inna Levin, Herbert L. Axelrod, Ashley M. Deacon, Michael Didonato, Henry van den Bedem, Eric Koesema, Scott A. Lesley, Kevin K. Jin, Daniel McMullan, Irimpan I. Mathews, Lukasz Jaroszewski, Robert Schwarzenbacher, Qingping Xu, Heath E. Klock, Andreas Kreusch, Mitchell D. Miller, Thomas Clayton, and Joanna Hale

Subjects
chemistry.chemical_classification, DNA ligase, biology, ATP synthase, Stereochemistry, Chemistry, Protein subunit, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein structure, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Amino Acid Sequence, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor, Crystallization, Protein Structure, Quaternary, Molecular Biology, Peptide sequence
Published
2006

172. Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution

Author

Said Eshaghi, Pär Nordlund, Daniel Martinez Molina, Andreas Kohl, Damian Niegowski, and Scott A. Lesley

Subjects
Models, Molecular, Protein Folding, Protein Conformation, Magnesium transporter, Inorganic chemistry, Molecular Sequence Data, Crystallography, X-Ray, Protein Structure, Secondary, Metal, Protein structure, Bacterial Proteins, Chlorides, Magnesium, Thermotoga maritima, Amino Acid Sequence, Binding site, Protein Structure, Quaternary, Magnesium ion, Cation Transport Proteins, Multidisciplinary, Binding Sites, biology, Chemistry, Water, Periplasmic space, Cobalt, biology.organism_classification, Protein Structure, Tertiary, Crystallography, visual_art, visual_art.visual_art_medium, Protein folding, Hydrophobic and Hydrophilic Interactions, Sequence Alignment
Abstract

CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg 2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone–shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg 2+ and Co 2+ . The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.

Published
2006

173. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution

Author

Justin Haugen, Joanna Hale, John Wooley, Aprilfawn White, Daniel McMullan, Sanjay Agarwalla, Peter Kuhn, Robert Schwarzenbacher, Guenter Wolf, Jessica Paulsen, Ron Reyes, Andreas Kreusch, Mark W. Knuth, Kevin Quijano, Raymond C. Stevens, Kin Moy, Scott A. Lesley, Jaume M. Canaves, Qingping Xu, Slawomir K. Grzechnik, Mitchell D. Miller, Gye Won Han, Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Carina Grittini, Christopher L. Rife, Michael DiDonato, Heath E. Klock, Eric Koesema, Eric Hampton, Michael Hornsby, Henry van den Bedem, Hsiu-Ju Chiu, Keith O. Hodgson, Marc-André Elsliger, Ashley M. Deacon, Edward Nigoghossian, Jeff Velasquez, Glen Spraggon, Herbert L. Axelrod, Tanya Biorac, Adam Godzik, Ian A. Wilson, and Eileen Ambing

Subjects
chemistry.chemical_classification, Models, Molecular, Binding Sites, Molecular Structure, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Biochemistry, Protein Structure, Secondary, Dioxygenases, Protein Structure, Tertiary, Mice, Acireductone dioxygenase, chemistry, Structural Biology, Oxidoreductase, Metals, Animals, Amino Acid Sequence, Crystallization, Databases, Protein, Molecular Biology, Protein Binding
Published
2006

174. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

Author

Raymond C. Stevens, Lukasz Jaroszewski, John Wooley, Carina Grittini, Scott A. Lesley, Qingping Xu, Aprilfawn White, Ron Reyes, Adam Godzik, Ashley M. Deacon, Hsiu-Ju Chiu, Marc-André Elsliger, Edward Nigoghossian, Justin Haugen, Daniel McMullan, Joanna Hale, Eric Hampton, Michael Hornsby, Henry van den Bedem, Peter Kuhn, Polat Abdubek, Christopher L. Rife, Julie Feuerhelm, Sanjay Krishna, Slawomir K. Grzechnik, Heath E. Klock, Jaume M. Canaves, Keith O. Hodgson, Kevin K. Jin, Herbert L. Axelrod, Ian A. Wilson, Robert Schwarzenbacher, Gye Won Han, Silvya Oommachen, Guenter Wolf, Eileen Ambing, Glen Spraggon, Eric Koesema, Mitchell D. Miller, Kin Moy, Jeff Velasquez, Mark W. Knuth, Kevin Quijano, Andreas Kreusch, Michael DiDonato, Sanjay Agarwalla, Jessica Paulsen, and Linda Okach

Subjects
Models, Molecular, Protein Folding, Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Polyethylene Glycols, Cyclophilins, Bacterial Proteins, Structural Biology, Humans, Thermotoga maritima, Amino Acid Sequence, Protein Structure, Quaternary, Molecular Biology, Cyclophilin, Peptidylprolyl isomerase, Binding Sites, biology, Chemistry, Fold (geology), Peptidylprolyl Isomerase, biology.organism_classification, Protein Structure, Tertiary, Crystallography
Published
2006

175. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold

Author

Glen Spraggon, Lukasz Jaroszewski, Robert Schwarzenbacher, Michael DiDonato, Guenter Wolf, Raymond C. Stevens, Christopher L. Rife, Hsiu-Ju Chiu, Carina Grittini, Kin Moy, Marc-André Elsliger, Ashley M. Deacon, Edward Nigoghossian, Andreas Kreusch, Jessica Paulsen, Kevin Quijano, Jaume M. Canaves, Aprilfawn White, Sanjay Agarwalla, Ian A. Wilson, Herbert L. Axelrod, Tanya Biorac, Adam Godzik, Gye Won Han, Scott A. Lesley, Eileen Ambing, Ron Reyes, Keith O. Hodgson, Eric Hampton, Slawomir K. Grzechnik, Jeff Velasquez, John Wooley, Michael Hornsby, Henry van den Bedem, Eric Koesema, Daniel McMullan, Polat Abdubek, Joanna Hale, Mitchell D. Miller, Heath E. Klock, Peter Kuhn, Justin Haugen, and Qingping Xu

Subjects
Physics, Models, Molecular, Protein Folding, biology, Virulence Factors, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Campylobacter jejuni, Virulence factor, Protein Structure, Secondary, Bacterial protein, Bacterial Proteins, Structural Biology, Protein folding, Molecular Biology
Published
2005

176. Structural insights into enzyme regulation for inositol 1,4,5-trisphosphate 3-kinase B

Author

Philip P. Chamberlain, Karsten Sauer, Michael P. Cooke, Scott A. Lesley, Mark L. Sandberg, and Glen Spraggon

Subjects
Models, Molecular, Stereochemistry, Protein Conformation, Molecular Sequence Data, Biology, Antiparallel (biochemistry), Crystallography, X-Ray, Biochemistry, Enzyme activator, Protein structure, Adenosine Triphosphate, Transferase, Animals, Humans, Protein Isoforms, Magnesium, Amino Acid Sequence, Binding site, chemistry.chemical_classification, Binding Sites, Molecular Structure, Kinase, Enzyme Activation, Phosphotransferases (Alcohol Group Acceptor), Enzyme, chemistry, Sequence Alignment, Alpha helix
Abstract

D-Myoinositol 1,4,5-trisphophate 3-kinases (IP(3)-3Ks) play important roles in metazoan cellular signaling. It has been demonstrated that mice without a functional version of IP(3)-3K isoform B are deficient in peripheral T-cells, indicating that IP(3)-3KB is essential to the developing immune system. The recent apo IP(3)-3KA structure exhibited a helix at the catalytic domain N-terminus exhibited a helix at the N-terminus of the catalytic domain, with a tryptophan indole moiety mimicking the binding mode of the substrate ATP purine ring, suggesting a mechanism of autoinhibition. Here we present the structure of the complete catalytic domain of IP(3)-3KB, including the CaM binding domain in complex with Mg(2+) and ATP. The crystal structure reveals a homodimeric arrangement of IP(3)-3KB catalytic domains, mediated via an intermolecular antiparallel beta-sheet formed from part of the CaM binding region. Residues from the putative autoinhibitory helix are rearranged into a loop configuration, with extensive interactions with the bound ATP. Mutagenesis of residues from this region reveals that substitution of the putative autoinhibitory tryptophan generates a hyperactive enzyme which retains Ca(2+)/CaM sensitivity. The IP(3)-3KB structure suggests a mechanism of enzyme activation, and raises the possibility that an interaction between IP(3)-3KB molecules may occur as part of the catalytic or regulatory cycle.

Published
2005

177. Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold

Author

Ian A. Wilson, Eileen Ambing, Ashley M. Deacon, Andreas Kreusch, Jeff Velasquez, Jessica Paulsen, Juli Vincent, Hsiu-Ju Chiu, Herbert L. Axelrod, Polat Abdubek, Michael DiDonato, Gye Won Han, Carina Grittini, Jaume M. Canaves, Raymond C. Stevens, Guenter Wolf, Qingping Xu, Heath E. Klock, Slawomir K. Grzechnik, Michael Hornsby, Christopher L. Rife, Henry van den Bedem, Scott A. Lesley, Kevin Quijano, Marc-André Elsliger, Peter Kuhn, Edward Nigoghossian, Keith O. Hodgson, Aprilfawn White, Joanna Hale, Tanya Biorac, Adam Godzik, Eric Hampton, Mitchell D. Miller, Eric Koesema, Justin Haugen, Eric Sims, John Wooley, Ron Reyes, Daniel McMullan, Robert Schwarzenbacher, Kin Moy, Lukasz Jaroszewski, and Glen Spraggon

Subjects
Models, Molecular, Protein Folding, Chemistry, Hypothetical protein, Proteins, Fold (geology), Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Molecular Weight, Crystallography, Mice, Open Reading Frames, Structural Biology, Transferase, Animals, Databases, Protein, Molecular Biology, Conserved Sequence
Published
2005

178. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold

Author

Peter Kuhn, Kevin Quijano, Slawomir K. Grzechnik, Marc-André Elsliger, Ian A. Wilson, Justin Haugen, Polat Abdubek, Edward Nigoghossian, Aprilfawn White, Eileen Ambing, John Wooley, Glen Spraggon, Kin Moy, Carina Grittini, Robert Schwarzenbacher, Daniel McMullan, Heath E. Klock, Hsiu-Ju Chiu, Raymond C. Stevens, Ashley M. Deacon, Guenter Wolf, Mitchell D. Miller, Ron Reyes, Joanna Hale, Jessica Paulsen, Eric Koesema, Gye Won Han, Scott A. Lesley, Andreas Kreusch, Lukasz Jaroszewski, Tanya Biorac, Adam Godzik, Juli Vincent, Qingping Xu, Keith O. Hodgson, Michael Hornsby, Henry van den Bedem, Eric Sims, Herbert L. Axelrod, Michael DiDonato, Jeff Velasquez, Christopher L. Rife, Eric Hampton, and Jaume M. Canaves

Subjects
Regulation of gene expression, Models, Molecular, Protein Folding, biology, Chemistry, Stereochemistry, Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, DNA gyrase, Bacterial Proteins, Structural Biology, DNA Gyrase, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Dimerization
Published
2005

179. Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution

Author

John Wooley, Justin Haugen, Peter Kuhn, Heath E. Klock, Scott A. Lesley, Joanna Hale, Hsiu-Ju Chiu, Guenter Wolf, Tanya Biorac, Adam Godzik, Qingping Xu, Xiaoping Dai, Polat Abdubek, Slawomir K. Grzechnik, Ron Reyes, Glen Spraggon, Michael DiDonato, Eric Koesema, Carina Grittini, Gye Won Han, Raymond C. Stevens, Marc-André Elsliger, Jeff Velasquez, Edward Nigoghossian, Daniel McMullan, Mitchell D. Miller, Kevin Quijano, Keith O. Hodgson, Aprilfawn White, Robert Schwarzenbacher, Eric Hampton, Juli Vincent, Kin Moy, Lukasz Jaroszewski, Ian A. Wilson, Herbert L. Axelrod, Michael Hornsby, Henry van den Bedem, Eileen Ambing, Ashley M. Deacon, Jessica Paulsen, Jaume M. Canaves, Andreas Kreusch, and Timothy M. McPhillips

Subjects
Models, Molecular, Messenger RNA, Chemistry, Resolution (electron density), DCPS, Molecular Sequence Data, RNA-binding protein, Crystal structure, Crystallography, X-Ray, Biochemistry, Sensitivity and Specificity, Protein Structure, Secondary, Mice, Apoenzymes, Structural Biology, Endoribonucleases, Animals, Amino Acid Sequence, RNA, Messenger, Molecular Biology, Decapping enzyme
Published
2005

180. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold

Author

Jaume M. Canaves, Slawomir K. Grzechnik, Peter Kuhn, Heath E. Klock, Lukasz Jaroszewski, Jie Ouyang, Ron Reyes, Raymond C. Stevens, John Wooley, Keith O. Hodgson, Olga Zagnitko, Kin Moy, Polat Abdubek, Guenter Wolf, Andreas Kreusch, Rebecca Page, Jeff Velasquez, Glen Spraggon, Michael DiDonato, Joanna Hale, Xianhong Wang, Scott A. Lesley, Qingping Xu, Mitchell D. Miller, Cathy Karlak, Michael Hornsby, Henry van den Bedem, Daniel McMullan, Inna Levin, Alyssa Robb, Kevin Quijano, Bill West, Eric Sims, Eric Hampton, Andrew T. Morse, Juli Vincent, Jamison Cambell, Eric Koesema, Justin Haugen, Robert Schwarzenbacher, Ashley M. Deacon, Carina Grittini, Ian A. Wilson, Hsiu-Ju Chiu, Eileen Ambing, Marc-André Elsliger, Edward Nigoghossian, Tanya Biorac, Adam Godzik, and Gye Won Han

Subjects
Models, Molecular, Protein Folding, biology, ATP synthase, Chemistry, Stereochemistry, Protein Conformation, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Molecular Biology, Indigoidine, Piperidones
Published
2005

181. Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

Author

Guenter Wolf, Gye Won Han, Kin Moy, Kevin Quijano, Slawomir K. Grzechnik, Michael Hornsby, Henry van den Bedem, Andreas Kreusch, Jessica Paulsen, Heath E. Klock, Polat Abdubek, Hsiu-Ju Chiu, Rebecca Page, Qingping Xu, Ron Reyes, Marc-André Elsliger, Peter Kuhn, Edward Nigoghossian, Eric Hampton, Andrew T. Morse, Jeff Velasquez, Frank von Delft, Juli Vincent, Lukasz Jaroszewski, Tanya Biorac, Adam Godzik, Olga Zagnitko, Michael DiDonato, Daniel McMullan, Inna Levin, Carina Grittini, Bill West, Keith O. Hodgson, Joanna Hale, Xiaoping Dai, Eric Koesema, Mitchell D. Miller, Justin Haugen, John Wooley, Xianhong Wang, Scott A. Lesley, Timothy M. McPhillips, Ashley M. Deacon, Glen Spraggon, Eric Sims, Robert Schwarzenbacher, Ian A. Wilson, Eileen Ambing, Jie Ouyang, Raymond C. Stevens, Jaume M. Canaves, and Aprilfawn White

Subjects
Models, Molecular, Protein Conformation, Stereochemistry, Molecular Sequence Data, Anabaena sp, Alanine glyoxylate aminotransferase, Electrons, Crystal structure, Crystallography, X-Ray, Biochemistry, Cofactor, Structural Biology, Humans, Transferase, Amino Acid Sequence, Molecular Biology, Transaminases, Sequence Homology, Amino Acid, biology, Chemistry, Resolution (electron density), Proteins, Stereoisomerism, Anabaena, Protein Structure, Tertiary, biology.protein
Published
2005

182. Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

Author

Timothy M. McPhillips, Eric Sims, Eric Hampton, Xiaoping Dai, Jaume M. Canaves, John Wooley, Aprilfawn White, Carina Grittini, Slawomir K. Grzechnik, Daniel McMullan, Inna Levin, Joanna Hale, Heath E. Klock, Lukasz Jaroszewski, Peter Kuhn, Keith O. Hodgson, Justin Haugen, Olga Zagnitko, Guenter Wolf, Kevin Quijano, Kin Moy, Hsiu-Ju Chiu, W. Peti, Joseph W. Arndt, Qingping Xu, Polat Abdubek, Mitchell D. Miller, Andrew T. Morse, Jeff Velasquez, Juli Vincent, Bill West, Jie Ouyang, Marc-André Elsliger, Gye Won Han, Edward Nigoghossian, Andreas Kreusch, Michael Hornsby, Henry van den Bedem, Rebecca Page, Robert Schwarzenbacher, Michael Didonato, Eric Koesema, Frank von Delft, Xianhong Wang, Scott A. Lesley, Ashley M. Deacon, Glen Spraggon, Raymond C. Stevens, Ian A. Wilson, Eileen Ambing, Ron Reyes, Tanya Biorac, and Adam Godzik

Subjects
Models, Molecular, Saccharomyces cerevisiae Proteins, Hydrolases, Protein Conformation, Molecular Sequence Data, Saccharomyces cerevisiae, Molecular Conformation, Alpha (ethology), Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Structural Biology, Hydrolase, Serine, Amino Acid Sequence, Beta (finance), Molecular Biology, Binding Sites, biology, Chemistry, Resolution (electron density), Computational Biology, Serine hydrolase, biology.organism_classification, Protein Structure, Tertiary, Software
Published
2005

184. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold

Author

Keith O. Hodgson, Kin Moy, Jie Ouyang, Polat Abdubek, Guenter Wolf, Heath E. Klock, Hsiu-Ju Chiu, Xiaoping Dai, Mitchell D. Miller, Marc-André Elsliger, Frank von Delft, Robert Schwarzenbacher, Michael Hornsby, Henry van den Bedem, Carina Grittini, Jeff Velasquez, Tanya Biorac, Adam Godzik, Lukasz Jaroszewski, Olga Zagnitko, Eric Sims, Raymond C. Stevens, Qingping Xu, Eric Koesema, Andreas Kreusch, Michael DiDonato, Rebecca Page, Bill West, Jaume M. Canaves, Peter Kuhn, Aprilfawn White, Daniel McMullan, Inna Levin, Alyssa Robb, Andrew T. Morse, Juli Vincent, Eric Hampton, Ian A. Wilson, Slawomir K. Grzechnik, Xianhong Wang, Scott A. Lesley, Eileen Ambing, Ashley M. Deacon, Glen Spraggon, John Wooley, Kevin Quijano, and Ron Reyes

Subjects
Models, Molecular, Ammonia-Lyases, Stereochemistry, Protein Conformation, Molecular Sequence Data, Molecular Conformation, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Formiminotetrahydrofolate cyclodeaminase, Structural Biology, Enzyme Stability, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Binding Sites, biology, Chemistry, Fold (geology), Lyase, biology.organism_classification, Protein Structure, Tertiary, Models, Chemical, Crystallization
Published
2005

185. Crystal structures of human HSP90alpha-complexed with dihydroxyphenylpyrazoles

Author

Achim Brinker, Yun He, Vicki Zhou, Jeremy S. Caldwell, Shulin Han, Andreas Kreusch, Scott A. Lesley, Xiang-ju Gu, and Ha-Soon Choi

Subjects
Models, Molecular, Time Factors, Molecular model, Stereochemistry, Clinical Biochemistry, Drug Evaluation, Preclinical, Pharmaceutical Science, Crystal structure, Pyrazole, Crystallography, X-Ray, Biochemistry, Cell Line, chemistry.chemical_compound, Structure-Activity Relationship, Cell Line, Tumor, Drug Discovery, Side chain, Molecule, Humans, HSP90 Heat-Shock Proteins, Molecular Biology, Adenine binding, Molecular Structure, Hydrogen bond, Chemistry, Organic Chemistry, Hydrogen Bonding, Protein Structure, Tertiary, Molecular Medicine, Pyrazoles, Binding domain
Abstract

A series of dihydroxyphenylpyrazole compounds were identified as a unique class of reversible Hsp90 inhibitors. The crystal structures for two of the identified compounds complexed with the N-terminal ATP binding domain of human Hsp90α were determined. The dihydroxyphenyl ring of the compounds fits deeply into the adenine binding pocket with the C2 hydroxyl group forming a direct hydrogen bond with the side chain of Asp93. The pyrazole ring forms hydrogen bonds to the backbone carbonyl of Gly97, the hydroxyl group of Thr184 and to a water molecule, which is present in all of the published HSP90 structures. One of the identified compounds (G3130) demonstrated cellular activities (in Her-2 degradation and activation of Hsp70 promoter) consistent with the inhibition of cellular Hsp90 functions.

Published
2004

186. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

Author

Jaume M. Canaves, Timothy M. McPhillips, Kevin Quijano, Linda S. Brinen, Mitchell D. Miller, Peter Kuhn, Polat Abdubek, Ross Floyd, Mike DiDonato, John Wooley, Guenter Wolf, Jamison Cambell, Eric Koesema, Marc-André Elsliger, Raymond C. Stevens, Carina Grittini, Daniel McMullan, Inna Levin, Xiaoping Dai, Henry van den Bedem, Said Eshagi, Cathy Karlak, Alyssa Robb, Andrew T. Morse, Juli Vincent, Kin Moy, Jie Ouyang, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Bill West, Frank von Delft, Keith O. Hodgson, Heath E. Klock, Hsiu-Ju Chiu, Robert Schwarzenbacher, Xianhong Wang, Scott A. Lesley, John S. Kovarik, Jeff Velasquez, Lukasz Jaroszewski, Qingping Xu, Eric Hampton, Tanya Biorac, Adam Godzik, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, and Glen Spraggon

Subjects
Models, Molecular, Crystallography, biology, Tandem, Resolution (electron density), Molecular Sequence Data, CBS domain, Cystathionine beta-Synthase, Crystal structure, biology.organism_classification, Biochemistry, Cystathionine beta synthase, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Transferase, Amino Acid Sequence, Molecular Biology
Published
2004

187. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

Author

Lukasz Jaroszewski, Alyssa Robb, Glen Spraggon, John Wooley, Andrew T. Morse, Jie Ouyang, Juli Vincent, Qingping Xu, Jaume M. Canaves, John S. Kovarik, Slawomir K. Grzechnik, Jamison Cambell, Eric Koesema, Mitchell D. Miller, Guenter Wolf, Linda S. Brinen, Daniel McMullan, Bill West, Xianhong Wang, Scott A. Lesley, Eric Hampton, Fred Rezezadeh, Raymond C. Stevens, Inna Levin, Timothy M. McPhillips, Heath E. Klock, Ian A. Wilson, Eric Sims, Mike DiDonato, Jeff Velasquez, Carina Grittini, Peter Kuhn, Eileen Ambing, Henry van den Bedem, Andreas Kreusch, Rebecca Page, Cathy Karlak, Ross Floyd, Robert Schwarzenbacher, Keith O. Hodgson, Ashley M. Deacon, Xiaoping Dai, Kevin Quijano, Kin Moy, Polat Abdubek, Ron Reyes, Tanya Biorac, Adam Godzik, Marc-André Elsliger, Frank von Delft, and Hsiu-Ju Chiu

Subjects
Models, Molecular, biology, Chemistry, Molecular Sequence Data, Resolution (electron density), Saccharomyces cerevisiae, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Ureohydrolases, Protein Structure, Tertiary, Multienzyme Complexes, Structural Homology, Protein, Structural Biology, Hydrolase, Allantoicase, Amino Acid Sequence, Molecular Biology, Conserved Sequence
Published
2004

188. A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome

Author

Daniel McMullan, Scott A. Lesley, Michael DiDonato, Heath E. Klock, and Ashley M. Deacon

Subjects
Models, Molecular, Proteomics, Protein Folding, Proteome, Genomic data, Computational biology, Biology, Biochemistry, Structural genomics, Bacterial Proteins, Structural Biology, Genetics, Thermotoga maritima, Cloning, Molecular, General Medicine, Robotics, biology.organism_classification, Pipeline (software), Recombinant Proteins, Crystallography, Solubility, Fermentation, bacteria, Crystallization, Genome, Bacterial, Protein Structure Initiative
Abstract

The wealth of genomic data available for many organisms has set the stage for the next phase of structure—function analysis. High-throughput structural genomics is currently the method of choice for rapid analysis of protein structure—function relationships on a proteome-wide basis. The Joint Center for Structural Genomics (JCSG), established in 2000 under the NIH/NIGMS Protein Structure Initiative, has developed and implemented an integrated high-throughput structure pipeline and applied it in a 2-tiered approach to mining the proteome of the thermophilic bacterium Thermotoga maritima. In the first tier, the successful application of this integrated pipeline has resulted in the cloning and expression of 73% of the T. maritima proteome (1376 out of 1877 predicted genes), and has identified 465 proteins which produced crystal hits. These 465 proteins were compared with existing structural information and a subset of 269 targets were selected to process towards structure determination in a second tier effort. To date, the JCSG pipeline applied to the Thermotoga maritima proteome has resulted in 55 new structures and has identified 6 novel folds and continues to identify structures with novel features.

Published
2004

189. NMR for structural proteomics of Thermotoga maritima: screening and structure determination

Author

Kurt Wüthrich, T. Herrmann, Wolfgang Peti, Scott A. Lesley, Touraj Etezady-Esfarjani, and Heath E. Klock

Subjects
Proteomics, biology, General Medicine, biology.organism_classification, Biochemistry, Ribosome, Recombinant Proteins, Protein Structure, Tertiary, Folding (chemistry), Turn (biochemistry), Bacterial Proteins, Structural Biology, Ribosomal protein, Thermotoga maritima, Genetics, Proton NMR, Isoleucine, Nuclear Magnetic Resonance, Biomolecular
Abstract

This paper describes the NMR screening of 141 small (

Published
2004

190. Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold

Author

Lukasz Jaroszewski, Ian A. Wilson, Alyssa Robb, Bill West, Carina Grittini, Glen Spraggon, Andrew T. Morse, Juli Vincent, Said Eshagi, Marc-André Elsliger, Timothy M. McPhillips, Raymond C. Stevens, Kevin Quijano, Keith O. Hodgson, Ashley M. Deacon, Frank von Delft, Guenter Wolf, Jaume M. Canaves, Mitchell D. Miller, Kin Moy, Adam Godzik, Xianhong Wang, Scott A. Lesley, Jie Ouyang, Eric Koesema, Henry van den Bedem, Linda S. Brinen, Robert Schwarzenbacher, Xiaoping Dai, Constantina Bakolitsa, Daniel McMullan, Andreas Kreusch, Rebecca Page, Peter Kuhn, H. Klock, Ross Floyd, Cathy Karlak, Slawomir K. Grzechnik, John Wooley, Jeff Velasquez, and John S. Kovarik

Subjects
Models, Molecular, Molecular Sequence Data, Sequence Homology, Fold (geology), Crystal structure, Biology, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Crystallography, Bacterial Proteins, Structural Biology, Structural Homology, Protein, Thermotoga maritima, Multiprotein Complexes, Amino Acid Sequence, Molecular Biology
Published
2004

191. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution

Author

Andreas Kreusch, Rebecca Page, Qingping Xu, Henry van den Bedem, Carina Grittini, Xiaoping Dai, Raymond C. Stevens, Slawomir K. Grzechnik, Hsiu-Ju Chiu, Jie Ouyang, Guenter Wolf, Bill West, Kevin Quijano, Heath E. Klock, Xianhong Wang, Scott A. Lesley, Michael Didonato, Jamison Cambell, Polat Abdubek, Marc-André Elsliger, Jaume M. Canaves, Eric Koesema, Kin Moy, Lukasz Jaroszewski, Frank von Delft, Alyssa Robb, Keith O. Hodgson, Andrew T. Morse, Juli Vincent, Inna Levin, Jeff Velasquez, John Wooley, Cathy Karlak, Mitchell D. Miller, Glen Spraggon, Peter Kuhn, Eric Hampton, Robert Schwarzenbacher, Tanya Biorac, Adam Godzik, Daniel McMullan, Ron Reyes, Timothy M. McPhillips, Eric Sims, Ian A. Wilson, Eileen Ambing, and Ashley M. Deacon

Subjects
chemistry.chemical_classification, Models, Molecular, Binding Sites, Chemistry, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, Mice, Structural Biology, Oxidoreductase, Structural Homology, Protein, Animals, Amino Acid Sequence, Quinone Reductases, Oxidoreductases, Molecular Biology, NADP
Published
2004

192. Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution

Author

Xianhong Wang, Scott A. Lesley, Jie Ouyang, Timothy M. McPhillips, Marc-André Elsliger, Kevin Quijano, John S. Kovarik, Linda S. Brinen, Guenter Wolf, Ashley M. Deacon, Robert Schwarzenbacher, Kin Moy, Henry van den Bedem, Frank von Delft, John Wooley, Raymond C. Stevens, Glen Spraggon, Peter Kuhn, Alyssa Robb, Jeff Velasquez, Ross Floyd, Andrew T. Morse, Mitchell D. Miller, Juli Vincent, Jaume M. Canaves, Andreas Kreusch, Keith O. Hodgson, Rebecca Page, Xiaoping Dai, Slawomir K. Grzechnik, Bill West, Said Eshagi, Cathy Karlak, Ian A. Wilson, Carina Grittini, Eric Koesema, Adam Godzik, Daniel McMullan, Inna Levin, Lukasz Jaroszewski, Qingping Xu, and Heath E. Klock

Subjects
Models, Molecular, biology, Chemistry, Stereochemistry, Resolution (electron density), Reproducibility of Results, Isomerase, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Ribose-5-phosphate isomerase, Structural Biology, Thermotoga maritima, Crystallization, Molecular Biology, Aldose-Ketose Isomerases
Published
2004

193. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

Author

Jie Ouyang, Andreas Kreusch, Rebecca Page, John Wooley, Heath E. Klock, Ashley M. Deacon, Mitchell D. Miller, Hsiu-Ju Chiu, Jaume M. Canaves, Glen Spraggon, Mike DiDonato, Jamison Campbell, Henry van den Bedem, Linda S. Brinen, Guenter Wolf, Kin Moy, Eric Hampton, Marc-André Elsliger, Keith O. Hodgson, Tanya Biorac, Adam Godzik, Ian A. Wilson, Peter Kuhn, Jeff Velasquez, Fred Rezezadeh, Ross Floyd, Bill West, Eileen Ambing, Ron Reyes, Raymond C. Stevens, Timothy M. McPhillips, Frank von Delft, Xiaoping Dai, Eric Sims, John S. Kovarik, Eric Koesema, Robert Schwarzenbacher, Alyssa Robb, Andrew T. Morse, Juli Vincent, Xianhong Wang, Scott A. Lesley, Kevin Quijano, Carina Grittini, Slawomir K. Grzechnik, Polat Abdubek, Daniel McMullan, Inna Levin, Cathy Karlak, Qingping Xu, and Lukasz Jaroszewski

Subjects
Exonucleases, Models, Molecular, Protein Folding, Protein Conformation, Archaeal Proteins, Molecular Sequence Data, Crystal structure, Siphoviridae, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Viral Proteins, Protein structure, Structural Biology, Amino Acid Sequence, Molecular Biology, Peptide sequence, Binding Sites, Sequence Homology, Amino Acid, Resolution (electron density), Archaeoglobus fulgidus, Protein Structure, Tertiary, N-terminus, Crystallography, Protein folding, PIN domain
Published
2004

194. NMR structure determination of the hypothetical protein TM1290 from Thermotoga maritima using automated NOESY analysis

Author

Touraj, Etezady-Esfarjani, Torsten, Herrmann, Wolfgang, Peti, Heath E, Klock, Scott A, Lesley, and Kurt, Wüthrich

Subjects
Models, Molecular, Proteomics, Magnetic Resonance Spectroscopy, Bacterial Proteins, Protein Conformation, Amino Acid Motifs, Proteins, Thermotoga maritima, Algorithms, Protein Structure, Secondary, Software, Plasmids, Protein Structure, Tertiary
Published
2004

195. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

Author

Glen Spraggon, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Kevin Quijano, Polat Abdubek, Jie Ouyang, Marc-André Elsliger, H.-J. Chiu, Cathy Karlak, Adam Godzik, Raymond C. Stevens, Alyssa Robb, Said Eshagi, Frank von Delft, Kin Moy, Tanja Biorac, Guenter Wolf, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Heath E. Klock, Jaume M. Canaves, Carina Grittini, Robert Schwarzenbacher, John Wooley, Ashley M. Deacon, Daniel McMullan, Inna Levin, Peter Kuhn, Xiaoping Dai, Jamison Cambell, Ian A. Wilson, Ross Floyd, Eric Koesema, Mitchell D. Miller, Jeff Velasquez, Eileen Ambing, Xianhong Wang, Scott A. Lesley, Keith O. Hodgson, John S. Kovarik, Lukasz Jaroszewski, Mike DiDonato, Henry van den Bedem, Qingping Xu, Eric Hampton, Bill West, and Timothy M. McPhillips

Subjects
Models, Molecular, biology, Chemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Crystallography, Bacterial Proteins, Structural Biology, Thermotoga maritima, Transferase, Amino Acid Sequence, Aspartate Aminotransferases, Molecular Biology, Peptide sequence
Published
2004

196. Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution

Author

Heidi, Erlandsen, Jaume M, Canaves, Marc-André, Elsliger, Frank, von Delft, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Lukasz, Jaroszewski, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Scott A, Lesley, Daniel, McMullan, Timothy M, McPhillips, Mitchell D, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Rebecca, Page, Alyssa, Robb, Kevin, Quijano, Robert, Schwarzenbacher, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, Keith O, Hodgson, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Bacterial Proteins, Genes, Bacterial, Molecular Sequence Data, Reproducibility of Results, Thermotoga maritima, Amino Acid Sequence, Crystallography, X-Ray, Protein Structure, Tertiary
Published
2004

197. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

Author

John Wooley, Xiaoping Dai, Glen Spraggon, Said Eshaghi, Keith O. Hodgson, Slawomir K. Grzechnik, Jaume M. Canaves, Mitchell D. Miller, Lukasz Jaroszewski, John S. Kovarik, Jie Ouyang, Eric Koesema, Timothy M. McPhillips, Adam Godzik, Frank von Delft, Kin Moy, Alyssa Robb, Andrew T. Morse, Juli Vincent, Jeff Velasquez, Raymond C. Stevens, Guenter Wolf, Ian A. Wilson, Andreas Kreusch, Peter Kuhn, Rebecca Page, Ross Floyd, Robert Schwarzenbacher, Marc A. Elsliger, Xianhong Wang, Scott A. Lesley, Ashley M. Deacon, Linda S. Brinen, Henry van den Bedem, Kevin Rodrigues, Bill West, Thomas L. Selby, Daniel McMullan, Carina Grittini, Mark A. Miller, Cathy Karlak, Chittibabu Guda, and Heath E. Klock

Subjects
Models, Molecular, Stereochemistry, Molecular Sequence Data, Alcohol oxidoreductase, Dehydrogenase, Crystal structure, Crystallography, X-Ray, Biochemistry, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Oxidoreductase, Iron-Binding Proteins, Thermotoga maritima, 1,3-Propanediol, Amino Acid Sequence, Molecular Biology, Alcohol dehydrogenase, chemistry.chemical_classification, biology, Resolution (electron density), Alcohol Dehydrogenase, biology.organism_classification, Alcohol Oxidoreductases, chemistry, biology.protein
Published
2004

198. Preparation and Use of E. coli S-30 Extracts

Author

Scott A. Lesley

Subjects
biology, Chemistry, medicine.disease_cause, Galactokinase, Cell-free system, Biochemistry, Genetic marker, Genotype, biology.protein, medicine, Protein biosynthesis, Beta-galactosidase, Ultracentrifuge, Escherichia coli
Published
2003
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200. Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution

Author

Robert, Schwarzenbacher, Jaume M, Canaves, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Marc A, Elsliger, Said, Eshaghi, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Chittibabu, Guda, Lukasz, Jaroszewski, Cathy, Karlak, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Scott A, Lesley, Daniel, McMullan, Timothy M, McPhillips, Mark A, Miller, Mitchell D, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Alyssa, Robb, Kevin, Rodrigues, Thomas L, Selby, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, Keith O, Hodgson, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Molecular Structure, Thermotoga maritima, Crystallography, X-Ray, Aldose-Ketose Isomerases, Protein Structure, Tertiary
Published
2003

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