Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

1 November 2007

Volume 69, Issue 2

Pages 215–447

  1. Prediction Reports

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

    1. Top of page
    2. Prediction Reports
    3. Short Communications
    4. Research Articles
    5. Structure Notes
    1. Crystal structures of two novel dye-decolorizing peroxidases reveal a β-barrel fold with a conserved heme-binding motif (pages 223–233)

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

      Version of Record online: 24 JUL 2007 | DOI: 10.1002/prot.21550

    2. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA (pages 234–243)

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

      Version of Record online: 24 JUL 2007 | DOI: 10.1002/prot.21673

  3. Research Articles

    1. Top of page
    2. Prediction Reports
    3. Short Communications
    4. Research Articles
    5. Structure Notes
    1. You have full text access to this OnlineOpen article
    2. Annexin A2/P11 interaction: New insights into annexin A2 tetramer structure by chemical crosslinking, high-resolution mass spectrometry, and computational modeling (pages 254–269)

      Daniela M. Schulz, Stefan Kalkhof, Andreas Schmidt, Christian Ihling, Christoph Stingl, Karl Mechtler, Olaf Zschörnig and Andrea Sinz

      Version of Record online: 2 JUL 2007 | DOI: 10.1002/prot.21445

    3. Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity (pages 270–284)

      Jared R. Auclair, Karin M. Green, Shivender Shandilya, James E. Evans, Mohan Somasundaran and Celia A. Schiffer

      Version of Record online: 27 JUN 2007 | DOI: 10.1002/prot.21471

    4. NMR study and molecular dynamics simulations of optimized β-hairpin fragments of protein G (pages 285–296)

      Yun Wei, Beatrice M. P. Huyghues-Despointes, Jerry Tsai and J. Martin Scholtz

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/prot.21494

    5. Monte carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane (pages 297–308)

      Jakob P. Ulmschneider, Martin B. Ulmschneider and Alfredo Di Nola

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/prot.21519

    6. Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: A molecular modeling study (pages 309–325)

      Yana A. Vereshaga, Pavel E. Volynsky, Julia E. Pustovalova, Dmitry E. Nolde, Alexander S. Arseniev and Roman G. Efremov

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/prot.21555

    7. A novel approach to local similarity of protein binding sites substantially improves computational drug design results (pages 349–357)

      Vasily Ramensky, Alexandr Sobol, Natalia Zaitseva, Anatoly Rubinov and Victor Zosimov

      Version of Record online: 10 JUL 2007 | DOI: 10.1002/prot.21487

    8. Hallmarks of mycolic acid biosynthesis: A comparative genomics study (pages 358–368)

      Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/prot.21591

    9. Protein–thiol substitution or protein dethiolation by thiol/disulfide exchange reactions: The albumin model (pages 369–378)

      Domenico Summa, Ottavia Spiga, Andrea Bernini, Vincenzo Venditti, Raffaella Priora, Simona Frosali, Antonios Margaritis, Danila Di Giuseppe, Neri Niccolai and Paolo Di Simplicio

      Version of Record online: 2 JUL 2007 | DOI: 10.1002/prot.21532

    10. Ideal amino acid exchange forms for approximating substitution matrices (pages 379–393)

      Piotr Pokarowski, Andrzej Kloczkowski, Szymon Nowakowski, Maria Pokarowska, Robert L. Jernigan and Andrzej Kolinski

      Version of Record online: 10 JUL 2007 | DOI: 10.1002/prot.21509

    11. A coarse-grained protein force field for folding and structure prediction (pages 394–408)

      Julien Maupetit, P. Tuffery and Philippe Derreumaux

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/prot.21505

  4. Structure Notes

    1. Top of page
    2. Prediction Reports
    3. Short Communications
    4. Research Articles
    5. Structure Notes
    1. Crystal structure of a transcriptional activator of comK gene from Bacillus halodurans (pages 409–414)

      Qian Steven Xu, Irina Ankoudinova, Yun Lou, Hisao Yokota, Rosalind Kim and Sung-Hou Kim

      Version of Record online: 16 JUL 2007 | DOI: 10.1002/prot.21292

    2. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 Å resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases (pages 415–421)

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

      Version of Record online: 16 JUL 2007 | DOI: 10.1002/prot.21314

    3. Crystal structure of an acetyltransferase protein from Vibrio cholerae strain N16961 (pages 422–427)

      M.E. Cuff, H. Li, S. Moy, J. Watson, A. Cipriani and A. Joachimiak

      Version of Record online: 10 JUL 2007 | DOI: 10.1002/prot.21417

    4. Crystal structure of Dim2p: A preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 Å (pages 428–432)

      Min Ze Jia, Jun Ohtsuka, Woo Cheol Lee, Koji Nagata and Masaru Tanokura

      Version of Record online: 24 JUL 2007 | DOI: 10.1002/prot.21381

    5. Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 Å resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (pages 433–439)

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

      Version of Record online: 25 JUL 2007 | DOI: 10.1002/prot.21602

    6. The crystal structure of CagS from the Helicobacter pylori pathogenicity island (pages 440–443)

      Laura Cendron, Elisabetta Tasca, Tommaso Seraglio, Anke Seydel, Alessandro Angelini, Roberto Battistutta, Cesare Montecucco and Giuseppe Zanotti

      Version of Record online: 10 JUL 2007 | DOI: 10.1002/prot.21576

    7. Solution structure of the hypothetical novel-fold protein TA0956 from Thermoplasma acidophilum (pages 444–447)

      Bon-Kyung Koo, Jinwon Jung, Hyunseob Jung, Hyung Wook Nam, Yu Sam Kim, Adelinda Yee and Weontae Lee

      Version of Record online: 16 JUL 2007 | DOI: 10.1002/prot.21490

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