Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

June 2008

Volume 71, Issue 4

Pages 1597–2113

  1. Prediction Report

    1. Top of page
    2. Prediction Report
    3. Short Communications
    4. Research Articles
    5. Research Commentary
    6. Structure Notes
    1. Calcineurin B-like domains in the large regulatory α/β subunits of phosphorylase kinase (pages 1597–1606)

      Cathelène Carrière, Jean-Paul Mornon, Catherine Venien-Bryan, Nicolas Boisset and Isabelle Callebaut

      Version of Record online: 4 MAR 2008 | DOI: 10.1002/prot.22006

  2. Short Communications

    1. Top of page
    2. Prediction Report
    3. Short Communications
    4. Research Articles
    5. Research Commentary
    6. Structure Notes
  3. Research Articles

    1. Top of page
    2. Prediction Report
    3. Short Communications
    4. Research Articles
    5. Research Commentary
    6. Structure Notes
    1. Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses (pages 1617–1636)

      Kanako Kuwasako, Naoshi Dohmae, Mio Inoue, Mikako Shirouzu, Seiichi Taguchi, Peter Güntert, Bertrand Séraphin, Yutaka Muto and Shigeyuki Yokoyama

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21839

    2. Using quantum mechanics to improve estimates of amino acid side chain rotamer energies (pages 1637–1646)

      P. Douglas Renfrew, Glenn L. Butterfoss and Brian Kuhlman

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21845

    3. Exploring the protein G helix free-energy surface by solute tempering metadynamics (pages 1647–1654)

      Carlo Camilloni, Davide Provasi, Guido Tiana and Ricardo A. Broglia

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21852

    4. Computational prediction of the binding site of proteinase 3 to the plasma membrane (pages 1655–1669)

      Eric Hajjar, Maja Mihajlovic, Véronique Witko-Sarsat, Themis Lazaridis and Nathalie Reuter

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21853

    5. Solvent-exposed residues located in the β-sheet modulate the stability of the tetramerization domain of p53—A structural and combinatorial approach (pages 1670–1685)

      Puig Mora, Rodrigo J. Carbajo, Antonio Pineda-Lucena, Manuel M. Sánchez del Pino and Enrique Pérez-Payá

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21854

    6. Huntingtin interacting protein HYPK is intrinsically unstructured (pages 1686–1698)

      Swasti Raychaudhuri, Pritha Majumder, Somosree Sarkar, Kalyan Giri, Debashis Mukhopadhyay and Nitai P. Bhattacharyya

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21856

    7. Overexpression, physicochemical characterization, and modeling of a hyperthermophilic pyrococcus furiosus type 2 IPP isomerase (pages 1699–1707)

      Raphaël Dutoit, Jérôme de Ruyck, Virginie Durisotti, Christianne Legrain, Eric Jacobs and Johan Wouters

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21863

    8. Tandem use of X-ray crystallography and mass spectrometry to obtain ab initio the complete and exact amino acids sequence of HPBP, a human 38-kDa apolipoprotein (pages 1708–1720)

      Hélène Diemer, Mikael Elias, Frédérique Renault, Daniel Rochu, Carlos Contreras-Martel, Christine Schaeffer, Alain Van Dorsselaer and Eric Chabriere

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21866

    9. Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius (pages 1721–1731)

      Luigi Mandrich, Valeria Menchise, Vincenzo Alterio, Giuseppina De Simone, Carlo Pedone, Mosè Rossi and Giuseppe Manco

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21877

    10. Analyzing and modeling the inhibitory effect of phosphatidic acid on the GTP-γ-S binding activity of Goα (pages 1732–1743)

      Liang Qu, Jia Wan, Yu Cao, Yinghao Zhang, Runsheng Chen and Youguo Huang

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21826

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      The protein fluorescence and structural toolkit: Database and programs for the analysis of protein fluorescence and structural data (pages 1744–1754)

      Chi Shen, Rajiv Menon, Dipanwita Das, Nidhi Bansal, Neha Nahar, Neelima Guduru, Stephen Jaegle, Joan Peckham and Yana K. Reshetnyak

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21857

    12. A simple and fuzzy method to align and compare druggable ligand-binding sites (pages 1755–1778)

      Claire Schalon, Jean-Sébastien Surgand, Esther Kellenberger and Didier Rognan

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21858

    13. Functional and computational studies of the ligand-associated metal binding site of β3 integrins (pages 1779–1791)

      Marta Murcia, Marketa Jirouskova, Jihong Li, Barry S. Coller and Marta Filizola

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21859

    14. Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and II (pages 1792–1812)

      Rhonda A. Newman, Wendy S. Van Scyoc, Brenda R. Sorensen, Olav R. Jaren and Madeline A. Shea

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21861

    15. pH sensitivity of type III secretion system tip proteins (pages 1830–1842)

      Aaron P. Markham, Susan E. Birket, William D. Picking, Wendy L. Picking and C. Russell Middaugh

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21864

    16. A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase (pages 1843–1852)

      Silvia Sommaruga, Antonella De Palma, Pier Luigi Mauri, Manuela Trisciani, Fabrizio Basilico, Pier Luigi Martelli, Rita Casadio, Paolo Tortora and Emanuela Occhipinti

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21868

    17. Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein (pages 1889–1898)

      Ivano Eberini, Alessandro Guerini Rocco, Anna Rita Ientile, António M. Baptista, Elisabetta Gianazza, Simona Tomaselli, Henriette Molinari and Laura Ragona

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21875

    18. Understanding of known drug-target interactions in the catalytic pocket of neuraminidase subtype N1 (pages 1908–1918)

      Maturos Malaisree, Thanyada Rungrotmongkol, Panita Decha, Pathumwadee Intharathep, Ornjira Aruksakunwong and Supot Hannongbua

      Version of Record online: 3 JAN 2008 | DOI: 10.1002/prot.21897

    19. Protein–protein docking by simulating the process of association subject to biochemical constraints (pages 1955–1969)

      Domantas Motiejunas, Razif Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn and Rebecca C. Wade

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21867

    20. Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment (pages 1970–1983)

      Tsutomu Yamane, Hideyasu Okamura, Mitsunori Ikeguchi, Yoshifumi Nishimura and Akinori Kidera

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21874

    21. The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation (pages 1984–1994)

      Bing Xiong, David L. Burk, Jianhua Shen, Xiaomin Luo, Hong Liu, Jingkang Shen and Albert M. Berghuis

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21876

    22. Hydrophobic clusters in protein structures (pages 2012–2025)

      J. Arunachalam and N. Gautham

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21881

    23. A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor (pages 2038–2050)

      Thierry Doan, Laetitia Martin, Silvia Zorrilla, Denis Chaix, Stéphane Aymerich, Gilles Labesse and Nathalie Declerck

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21883

    24. The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein–protein interaction (pages 2051–2064)

      Marina Marques Teixeira Vanini, Alberto Spisni, Maurício Luis Sforça, Thelma Aguiar Pertinhez and Celso Eduardo Benedetti

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21886

    25. The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity (pages 2065–2075)

      Andrea Ilari, Alessandra Bonamore, Stefano Franceschini, Annarita Fiorillo, Alberto Boffi and Gianni Colotti

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21898

    26. Sequence–structure–function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA (pages 2076–2085)

      Martine Roovers, Yamina Oudjama, Katarzyna H. Kaminska, Elzbieta Purta, Joël Caillet, Louis Droogmans and Janusz M. Bujnicki

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21918

  4. Research Commentary

    1. Top of page
    2. Prediction Report
    3. Short Communications
    4. Research Articles
    5. Research Commentary
    6. Structure Notes
    1. Response to András Szilágyi's Commentary (pages 2089–2090)

      Joseph P. Zbilut, Alessandro Giuliani and Charles L. Webber Jr

      Version of Record online: 12 MAR 2008 | DOI: 10.1002/prot.22031

  5. Structure Notes

    1. Top of page
    2. Prediction Report
    3. Short Communications
    4. Research Articles
    5. Research Commentary
    6. Structure Notes
    1. You have free access to this content
    2. You have free access to this content
      Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins (pages 2097–2101)

      Akio Ebihara, Miho Manzoku, Hitoshi Iino, Mayumi Kanagawa, Akeo Shinkai, Shigeyuki Yokoyama and Seiki Kuramitsu

      Version of Record online: 12 MAR 2008 | DOI: 10.1002/prot.22018

    3. You have free access to this content
      Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12 (pages 2102–2108)

      Sankar Manicka, Yoav Peleg, Tamar Unger, Shira Albeck, Orly Dym, Harry M. Greenblatt, Gleb Bourenkov, Victor Lamzin, Sankaran Krishnaswamy and Joel L. Sussman

      Version of Record online: 24 MAR 2008 | DOI: 10.1002/prot.22023

    4. You have free access to this content
      Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source (pages 2109–2113)

      Yang Li, Pazilat Bahti, Neil Shaw, Gaojie Song, Shunmei Chen, Xuejun Zhang, Min Zhang, Chongyun Cheng, Jie Yin, Jin-Yi Zhu, Hua Zhang, Dongsheng Che, Hao Xu, Abdulla Abbas, Bi-Cheng Wang and Zhi-Jie Liu

      Version of Record online: 24 MAR 2008 | DOI: 10.1002/prot.22025

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