Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

April 2008

Volume 71, Issue 1

Pages 1–523

  1. Short Communications

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    1. You have full text access to this OnlineOpen article
      Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer (pages 1–7)

      Cedric R. Clapier, Srinivas Chakravarthy, Carlo Petosa, Carlos Fernández-Tornero, Karolin Luger and Christoph W. Müller

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21720

    2. Atomic resolution (1.1 Å) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves (pages 8–15)

      Alessia Ruggiero, Angela Chambery, Antimo Di Maro, Augusto Parente and Rita Berisio

      Version of Record online: 26 OCT 2007 | DOI: 10.1002/prot.21712

    3. In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin (pages 24–34)

      Vadim Cherezov, Wei Liu, Jeremy P. Derrick, Binquan Luan, Aleksei Aksimentiev, Vsevolod Katritch and Martin Caffrey

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/prot.21841

  2. Research Articles

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    1. Hydrophobic interactions and ionic networks play an important role in thermal stability and denaturation mechanism of the porcine odorant-binding protein (pages 35–44)

      Olesya V. Stepanenko, Anna Marabotti, Irina M. Kuznetsova, Konstantin K. Turoverov, Carlo Fini, Antonio Varriale, Maria Staiano, Mose' Rossi and Sabato D'Auria

      Version of Record online: 5 OCT 2007 | DOI: 10.1002/prot.21658

    2. Predicting the order in which contacts are broken during single molecule protein stretching experiments (pages 45–60)

      Joanna I. Sułkowska, Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak and Robert L. Jernigan

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21652

    3. Common occurrence of internal repeat symmetry in membrane proteins (pages 68–80)

      Sungwon Choi, Jouhyun Jeon, Jae-Seong Yang and Sanguk Kim

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21656

    4. In silico local structure approach: A case study on Outer Membrane Proteins (pages 92–109)

      Juliette Martin, Alexandre G. de Brevern and Anne-Claude Camproux

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21659

    5. Osmolyte effect on the stability and folding of a hyperthermophilic protein (pages 110–118)

      Atsushi Mukaiyama, Yuichi Koga, Kazufumi Takano and Shigenori Kanaya

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21660

    6. Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures (pages 119–130)

      David P. Simmons, Victor A. Streltsov, Olan Dolezal, Peter J. Hudson, Andrew M. Coley, Michael Foley, David F. Proll and Stewart D. Nuttall

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21663

    7. Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution (pages 131–143)

      Chen Hu, Jianwen Fang, Ronald T. Borchardt, Richard L. Schowen and Krzysztof Kuczera

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21664

    8. Engineering proteins with tunable thermodynamic and kinetic stabilities (pages 165–174)

      Angel L. Pey, David Rodriguez-Larrea, Susanne Bomke, Susanne Dammers, Raquel Godoy-Ruiz, Maria M. Garcia-Mira and Jose M. Sanchez-Ruiz

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21670

    9. An efficient conformational sampling method for homology modeling (pages 175–188)

      Rongsheng Han, Alejandra Leo-Macias, Daniel Zerbino, Ugo Bastolla, Bruno Contreras-Moreira and Angel R. Ortiz

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21672

    10. Prediction of RNA binding sites in a protein using SVM and PSSM profile (pages 189–194)

      Manish Kumar, M. Michael Gromiha and G. P. S. Raghava

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21677

    11. The peculiar structural features of kiwi fruit pectin methylesterase: Amino acid sequence, oligosaccharides structure, and modeling of the interaction with its natural proteinaceous inhibitor (pages 195–206)

      M. Antonietta Ciardiello, Rossana D'Avino, Angela Amoresano, Lisa Tuppo, Andrea Carpentieri, Vito Carratore, Maurizio Tamburrini, Alfonso Giovane, Piero Pucci and Laura Camardella

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21681

    12. Improved model building and assessment of the Calcium-sensing receptor transmembrane domain (pages 215–226)

      Lintao Bu, Mayako Michino, Romain M. Wolf and Charles L. Brooks III

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21685

    13. Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation (pages 227–240)

      Clare-Louise Evans, Jed E. Long, Thomas R. A. Gallagher, Jonathan D. Hirst and Mark S. Searle

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21692

    14. Altering the laccase functionality by in vivo assembly of mutant libraries with different mutational spectra (pages 250–260)

      Miren Zumárraga, Susana Camarero, Sergey Shleev, Arturo Martínez-Arias, Antonio Ballesteros, Francisco J. Plou and Miguel Alcalde

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21699

    15. QMEAN: A comprehensive scoring function for model quality assessment (pages 261–277)

      Pascal Benkert, Silvio C. E. Tosatto and Dietmar Schomburg

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21715

    16. Local interactions in protein folding determined through an inverse folding model (pages 278–299)

      Ugo Bastolla, Markus Porto and Angel R. Ortíz

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21730

    17. Methylene substitution at the α–β bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site (pages 308–319)

      Júlia Kovári, Orsolya Barabás, Balázs Varga, Angéla Békési, Ferenc Tölgyesi, Judit Fidy, József Nagy and Beáta G. Vértessy

      Version of Record online: 11 OCT 2007 | DOI: 10.1002/prot.21757

    18. Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3 (pages 336–352)

      Eva Stjernschantz, Barbara M. A. van Vugt-Lussenburg, Alois Bonifacio, Stephanie B. A. de Beer, Gert van der Zwan, Cees Gooijer, Jan N. M. Commandeur, Nico P. E. Vermeulen and Chris Oostenbrink

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21697

    19. Comparison of vertebrate and invertebrate CLIC proteins: The crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC (pages 364–378)

      Dene R. Littler, Stephen J. Harrop, Louise J. Brown, Greg J. Pankhurst, Andrew V. Mynott, Paolo Luciani, Ramya A. Mandyam, Michele Mazzanti, Soichi Tanda, Mark A. Berryman, Samuel N. Breit and Paul M. G. Curmi

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21704

    20. YesT: A new rhamnogalacturonan acetyl esterase from Bacillus subtilis (pages 379–388)

      Irene Martínez-Martínez, José Navarro-Fernández, José Daniel Lozada-Ramírez, Francisco García-Carmona and Álvaro Sánchez-Ferrer

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21705

    21. Free-energy landscape of kinesin by a realistic lattice model (pages 389–395)

      Hiroo Kenzaki and Macoto Kikuchi

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21707

    22. Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori (pages 396–406)

      Chen-Hsi Chu, Yi-Ju Lai, Haimei Huang and Yuh-Ju Sun

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21709

    23. Residue conservation in viral capsid assembly (pages 407–414)

      Ranjit P. Bahadur and Joël Janin

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21710

    24. N-linked glycans of the human insulin receptor and their distribution over the crystal structure (pages 426–439)

      Lindsay G. Sparrow, Michael C. Lawrence, Jeffrey J. Gorman, Phillip M. Strike, Christine P. Robinson, Neil M. McKern and Colin W. Ward

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21768

    25. Flexible protein–flexible ligand docking with disrupted velocity simulated annealing (pages 440–454)

      Zunnan Huang, Chung F. Wong and Ralph A. Wheeler

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21781

    26. Contact rearrangements form coupled networks from local motions in allosteric proteins (pages 455–466)

      Michael D. Daily, Tarak J. Upadhyaya and Jeffrey J. Gray

      Version of Record online: 23 OCT 2007 | DOI: 10.1002/prot.21800

    27. Structural basis for the cold adaptation of psychrophilic M37 lipase from Photobacterium lipolyticum (pages 476–484)

      Suk-Kyeong Jung, Dae Gwin Jeong, Mi Sook Lee, Jung-Kee Lee, Hyung-Kwoun Kim, Seong Eon Ryu, Byoung Chul Park, Jae Hoon Kim and Seung Jun Kim

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21884

    28. A covalent S-F heterodimer of leucotoxin reveals molecular plasticity of β-barrel pore-forming toxins (pages 485–496)

      Pierre Roblin, Valérie Guillet, Olivier Joubert, Daniel Keller, Monique Erard, Laurent Maveyraud, Gilles Prévost and Lionel Mourey

      Version of Record online: 23 JAN 2008 | DOI: 10.1002/prot.21900

  3. Structure Notes

    1. Top of page
    2. Short Communications
    3. Research Articles
    4. Structure Notes
    1. You have free access to this content
      First crystallographic models of human TBC domains in the context of a family-wide structural analysis (pages 497–502)

      Wolfram Tempel, Yufeng Tong, Svetoslav Dimov, Alexey Bochkarev and Heewon Park

      Version of Record online: 10 JAN 2008 | DOI: 10.1002/prot.21885

    2. You have free access to this content
    3. You have free access to this content
    4. Solution structure of human DESR1, a CSL zinc-binding protein (pages 514–518)

      Fangming Wu, Jiahai Zhang, Jianping Sun, Hongda Huang, Peng Ji, Wangsheng Chu, Meijuan Yu, Feifei Yang, Ziyu Wu, Jihui Wu and Yunyu Shi

      Version of Record online: 23 JAN 2008 | DOI: 10.1002/prot.21915

    5. You have free access to this content
      Crystal structure of N-acylamino acid racemase from Thermus thermophilus HB8 (pages 519–523)

      Minoru Hayashida, Seong-Hoon Kim, Kazuki Takeda, Tamao Hisano and Kunio Miki

      Version of Record online: 23 JAN 2008 | DOI: 10.1002/prot.21926

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