absorption spectroscopy Characterization of metalloproteins by high-throughput X-ray Material

Material Supplemental http://genome.cshlp.org/content/suppl/2011/04/05/gr.115097.110.DC1.html References http://genome.cshlp.org/content/21/6/898.full.html#ref-list-1 This article cites 44 articles, 16 of which can be accessed free at: License Commons Creative http://creativecommons.org/licenses/by-nc/3.0/. described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as ). After six months, it is available under http://genome.cshlp.org/site/misc/terms.xhtml first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the

[1]  Aleksandar Cvetkovic,et al.  Microbial metalloproteomes are largely uncharacterized , 2010, Nature.

[2]  J. Bartel,et al.  Metalloproteome of the prostate: carcinoma cell line DU-145 in comparison to healthy rat tissue. , 2010, Cancer genomics & proteomics.

[3]  Antonio Rosato,et al.  Metalloproteomes: a bioinformatic approach. , 2009, Accounts of chemical research.

[4]  S. Costantini,et al.  Structure of the human RECQ1 helicase reveals a putative strand-separation pin , 2009, Proceedings of the National Academy of Sciences.

[5]  Torsten Schwede,et al.  The SWISS-MODEL Repository and associated resources , 2008, Nucleic Acids Res..

[6]  Stephen K. Burley,et al.  Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies , 2009, Journal of Structural and Functional Genomics.

[7]  Y. Ishino,et al.  Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm , 2009, BMC Structural Biology.

[8]  Burkhard Rost,et al.  MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence , 2008, Bioinform..

[9]  M. R. Chance,et al.  Metallomics and metalloproteomics , 2008, Cellular and Molecular Life Sciences.

[10]  Nanjiang Shu,et al.  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm618 Sequence analysis Prediction of zinc-binding sites in proteins from sequence , 2008 .

[11]  K. Gunsalus,et al.  Protein production and purification , 2008, Nature Methods.

[12]  Stephen K Burley,et al.  High throughput protein production and crystallization at NYSGXRC. , 2008, Methods in molecular biology.

[13]  A. Lyon,et al.  Simultaneous Cu-, Fe-, and Zn-specific detection of metalloproteins contained in rabbit plasma by size-exclusion chromatography–inductively coupled plasma atomic emission spectroscopy , 2008, JBIC Journal of Biological Inorganic Chemistry.

[14]  I. Bertini,et al.  Metals in the “omics” world: copper homeostasis and cytochrome c oxidase assembly in a new light , 2007, JBIC Journal of Biological Inorganic Chemistry.

[15]  I. Bertini,et al.  A structural characterization of human SCO2. , 2007, Structure.

[16]  András Fiser,et al.  A high-throughput approach to protein structure analysis. , 2007, Genetic engineering.

[17]  M. Kenward,et al.  An Introduction to the Bootstrap , 2007 .

[18]  J. Gerlt,et al.  Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum. , 2006, Biochemistry.

[19]  B. Rost,et al.  Identifying cysteines and histidines in transition‐metal‐binding sites using support vector machines and neural networks , 2006, Proteins.

[20]  Antonio Rosato,et al.  Zinc through the three domains of life. , 2006, Journal of proteome research.

[21]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[22]  Y. She,et al.  Proteomics of Metal Transport and Metal-Associated Diseases , 2006 .

[23]  Michael Sullivan,et al.  Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics. , 2005, Structure.

[24]  J Bettmer,et al.  Metalloproteomics: a challenge for analytical chemists , 2005, Analytical and bioanalytical chemistry.

[25]  M Newville,et al.  ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT. , 2005, Journal of synchrotron radiation.

[26]  Joanna Szpunar,et al.  Advances in analytical methodology for bioinorganic speciation analysis: metallomics, metalloproteomics and heteroatom-tagged proteomics and metabolomics. , 2005, The Analyst.

[27]  P. A. Lay,et al.  Three-dimensional structure determination using multiple-scattering analysis of XAFS: applications to metalloproteins and coordination chemistry , 2005 .

[28]  M. Adams,et al.  Bottlenecks and roadblocks in high-throughput XAS for structural genomics. , 2005, Journal of synchrotron radiation.

[29]  Stephen K. Burley,et al.  New York-Structural GenomiX Research Consortium (NYSGXRC): A Large Scale Center for the Protein Structure Initiative , 2005, Journal of Structural and Functional Genomics.

[30]  G. Bunker,et al.  XAFS Debye-Waller factors for Zn metalloproteins , 2004 .

[31]  Narayanan Eswar,et al.  High-throughput computational and experimental techniques in structural genomics. , 2004, Genome research.

[32]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[33]  J. Keck,et al.  High‐resolution structure of the E.coli RecQ helicase catalytic core , 2003, The EMBO journal.

[34]  Burkhard Rost,et al.  UniqueProt: creating representative protein sequence sets , 2003, Nucleic Acids Res..

[35]  Gary L Gilliland,et al.  Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site , 2003, Proteins.

[36]  R. Sternglanz,et al.  Crystal Structure of a SIR2 Homolog–NAD Complex , 2001, Cell.

[37]  M Newville,et al.  EXAFS analysis using FEFF and FEFFIT. , 2001, Journal of synchrotron radiation.

[38]  Kirill Degtyarenko,et al.  Bioinorganic motifs: towards functional classification of metalloproteins , 2000, Bioinform..

[39]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[40]  A. Kletzin Tungsten-containing aldehyde ferredoxin oxidoreductases , 1997 .

[41]  G. H. Reed,et al.  The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. , 1996, Biochemistry.

[42]  D. Rees,et al.  Crystal Structure of DMSO Reductase: Redox-Linked Changes in Molybdopterin Coordination , 1996, Science.

[43]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[44]  Robert Huber,et al.  Crystal Structure of the Xanthine Oxidase-Related Aldehyde Oxido-Reductase from D. gigas , 1995, Science.

[45]  L. Ljungdahl,et al.  Formate Dehydrogenase of Clostridium thermoaceticum: Incorporation of Selenium-75, and the Effects of Selenite, Molybdate, and Tungstate on the Enzyme , 1973, Journal of bacteriology.