Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

1 June 2006

Volume 63, Issue 4

Pages 719–1137

  1. Short Communications

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    5. Erratum
    1. Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses (pages 719–726)

      Catherine H. Schein, David E. Volk, Numan Oezguen and Aniko Paul

      Version of Record online: 23 FEB 2006 | DOI: 10.1002/prot.20891

    2. Crystal structure of VC0702 at 2.0 Å: Conserved hypothetical protein from Vibrio cholerae (pages 733–741)

      Shuisong Ni, Farhad Forouhar, Dirksen E. Bussiere, Howard Robinson and Michael A. Kennedy

      Version of Record online: 23 FEB 2006 | DOI: 10.1002/prot.20919

  2. Research Articles

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    5. Erratum
    1. Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: Thermodynamic and crystallographic studies (pages 742–753)

      Evangelia G. Kapetaniou, Angelos Thanassoulas, Anatoly P. Dubnovitsky, George Nounesis and Anastassios C. Papageorgiou

      Version of Record online: 10 MAR 2006 | DOI: 10.1002/prot.20935

    2. D-Trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis: The binding of trehalose and maltose results in different protein conformational states (pages 754–767)

      Petr Herman, Maria Staiano, Anna Marabotti, Antonio Varriale, Andrea Scirè, Fabio Tanfani, Jaroslav Vecer, Mose' Rossi and Sabato D'Auria

      Version of Record online: 10 MAR 2006 | DOI: 10.1002/prot.20952

    3. Structures of intact glycoproteins from vibrational circular dichroism (pages 768–776)

      Ganesh Shanmugam and Prasad L. Polavarapu

      Version of Record online: 23 FEB 2006 | DOI: 10.1002/prot.20884

    4. Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids (pages 777–786)

      Yaw-Jen Liu, Chao-Sheng Cheng, Szu-Ming Lai, Ming-Pin Hsu, Ching-San Chen and Ping-Chiang Lyu

      Version of Record online: 16 MAR 2006 | DOI: 10.1002/prot.20962

    5. Interdomain mobility in di-ubiquitin revealed by NMR (pages 787–796)

      Yaroslav Ryabov and David Fushman

      Version of Record online: 14 FEB 2006 | DOI: 10.1002/prot.20917

    6. Detailed microscopic study of the full zipA:FtsZ interface (pages 811–821)

      I.S. Moreira, P.A. Fernandes and M.J. Ramos

      Version of Record online: 14 MAR 2006 | DOI: 10.1002/prot.20944

    7. Codep: Maximizing co-evolutionary interdependencies to discover interacting proteins (pages 822–831)

      Elisabeth R. M. Tillier, Laurence Biro, Ginny Li and Desiree Tillo

      Version of Record online: 21 APR 2006 | DOI: 10.1002/prot.20948

    8. Effective handling of induced-fit motion in flexible docking (pages 878–891)

      Miho Yamada Mizutani, Yoshihiro Takamatsu, Tazuko Ichinose, Kensuke Nakamura and Akiko Itai

      Version of Record online: 10 MAR 2006 | DOI: 10.1002/prot.20931

    9. Chemical compound navigator: A web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds (pages 907–917)

      M.D. Prasanna, Jiri Vondrasek, Alexander Wlodawer, H. Rodriguez and T. N. Bhat

      Version of Record online: 28 FEB 2006 | DOI: 10.1002/prot.20914

    10. Polyglutamine repeats and β-helix structure: Molecular dynamics study (pages 918–927)

      Antonello Merlino, Luciana Esposito and Luigi Vitagliano

      Version of Record online: 2 MAR 2006 | DOI: 10.1002/prot.20941

    11. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules (pages 928–938)

      Jonathan Myers, Greg Grothaus, Shivaram Narayanan and Alexey Onufriev

      Version of Record online: 21 FEB 2006 | DOI: 10.1002/prot.20922

    12. ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes (pages 967–975)

      Mi-Ran Yun, R. Lavery, N. Mousseau, K. Zakrzewska and P. Derreumaux

      Version of Record online: 7 MAR 2006 | DOI: 10.1002/prot.20938

    13. Fold recognition and accurate sequence–structure alignment of sequences directing β-sheet proteins (pages 976–985)

      Andrew V. McDonnell, Matthew Menke, Nathan Palmer, Jonathan King, Lenore Cowen and Bonnie Berger

      Version of Record online: 17 MAR 2006 | DOI: 10.1002/prot.20942

    14. Terminal ion pairs stabilize the second β-hairpin of the B1 domain of protein G (pages 1005–1017)

      Beatrice M. P. Huyghues-Despointes, Xiaotoa Qu, Jerry Tsai and J. Martin Scholtz

      Version of Record online: 8 FEB 2006 | DOI: 10.1002/prot.20916

    15. Modeling and functional analysis of AEBP1, a transcriptional repressor (pages 1069–1083)

      Peter J. Lyons, Neil R. Mattatall and Hyo-Sung Ro

      Version of Record online: 14 MAR 2006 | DOI: 10.1002/prot.20946

  3. Structure Notes

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    5. Erratum
    1. You have free access to this content
      Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3 (pages 1084–1086)

      Ui Okada, Naoki Sakai, Min Yao, Nobuhisa Watanabe and Isao Tanaka

      Version of Record online: 27 FEB 2006 | DOI: 10.1002/prot.20913

    2. You have free access to this content
      Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis (pages 1087–1091)

      Jayaraman Seetharaman, Desigan Kumaran, Jeffrey B. Bonanno, Stephen K. Burley and Subramanyam Swaminathan

      Version of Record online: 10 FEB 2006 | DOI: 10.1002/prot.20924

    3. You have free access to this content
      Crystal structures of two putative phosphoheptose isomerases (pages 1092–1096)

      Jayaraman Seetharaman, Kanagalaghatta R. Rajashankar, Veronica Solorzano, Ryan Kniewel, Christopher D. Lima, Jeffrey B. Bonanno, Stephen K. Burley and Subramanyam Swaminathan

      Version of Record online: 13 FEB 2006 | DOI: 10.1002/prot.20908

    4. You have free access to this content
      Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 Å resolution (pages 1097–1101)

      Youngchang Kim, Natalia Maltseva, Irina Dementieva, Frank Collart, Denise Holzle and Andrzej Joachimiak

      Version of Record online: 23 FEB 2006 | DOI: 10.1002/prot.20589

    5. You have free access to this content
      1.6 Å Crystal structure of a PA2721 protein from pseudomonas aeruginosa—A potential drug-resistance protein (pages 1102–1105)

      B. Nocek, M. Cuff, E. Evdokimova, A. Edwards, A. Joachimiak and A. Savchenko

      Version of Record online: 21 FEB 2006 | DOI: 10.1002/prot.20659

    6. You have free access to this content
      Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution (pages 1106–1111)

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

      Version of Record online: 16 MAR 2006 | DOI: 10.1002/prot.20650

    7. You have free access to this content
      Crystal structure of TM1367 from Thermotoga maritima at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold (pages 1112–1118)

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

      Version of Record online: 16 MAR 2006 | DOI: 10.1002/prot.20894

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    9. You have free access to this content
      The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: An intermediate conformation with T-state and R-state features (pages 1123–1126)

      Christine M. Lukacs, Nikos G. Oikonomakos, Robert L. Crowther, Li-Na Hong, R. Ursula Kammlott, Wayne Levin, Shirley Li, Chao-Min Liu, Debra Lucas-McGady, Sherrie Pietranico and Linda Reik

      Version of Record online: 7 MAR 2006 | DOI: 10.1002/prot.20939

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    11. You have free access to this content
      Crystal structure of human protein tyrosine phosphatase 14 (PTPN14) at 1.65-Å resolution (pages 1132–1136)

      Alastair J. Barr, Judit É. Debreczeni, Jeyanthy Eswaran and Stefan Knapp

      Version of Record online: 13 MAR 2006 | DOI: 10.1002/prot.20958

  4. Erratum

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    5. Erratum
    1. You have free access to this content
      Structural characterization of an iron–sulfur cluster assembly protein IscU in a zinc-bound form (page 1137)

      Jinyu Liu, Natalia Oganesyan, Dong-Hae Shin, Jarmila Jancarik, Hisao Yokota, Rosalind Kim and Sung-Hou Kim

      Version of Record online: 21 FEB 2006 | DOI: 10.1002/prot.20856

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