Proteins: Structure, Function, and Bioinformatics

Cover image for Proteins: Structure, Function, and Bioinformatics

15 February 2008

Volume 70, Issue 3

Pages 611–1123

  1. Review Article

    1. Top of page
    2. Review Article
    3. Research Articles
    4. Research Commentaries
    5. Structure Notes
    1. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre (pages 611–625)

      Riccardo M. Bennett-Lovsey, Alex D. Herbert, Michael J. E. Sternberg and Lawrence A. Kelley

      Version of Record online: 17 SEP 2007 | DOI: 10.1002/prot.21688

  2. Research Articles

    1. Top of page
    2. Review Article
    3. Research Articles
    4. Research Commentaries
    5. Structure Notes
    1. A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding (pages 626–638)

      Eng-Hui Yap, Nicolas Lux Fawzi and Teresa Head-Gordon

      Version of Record online: 24 AUG 2007 | DOI: 10.1002/prot.21515

    2. Molecular determinants of sarco/endoplasmic reticulum calcium ATPase inhibition by hydroquinone-based compounds (pages 639–649)

      Michael Lape, Christopher Elam, Maria Versluis, Robert Kempton and Stefan Paula

      Version of Record online: 24 AUG 2007 | DOI: 10.1002/prot.21542

    3. Electrospray ionization mass spectrometry of soybean lipoxygenases: N-terminal acetylation, chemical modification, and solution conformation (pages 650–658)

      Amber M. Peariso, Kellie M. Nicholson, R. Benjamin Jones, Kari B. Green-Church and Max O. Funk Jr.

      Version of Record online: 24 AUG 2007 | DOI: 10.1002/prot.21543

    4. MAAP: Malarial adhesins and adhesin-like proteins predictor (pages 659–666)

      Faraz Alam Ansari, Naveen Kumar, Mekapati Bala Subramanyam, Muthiah Gnanamani and Srinivasan Ramachandran

      Version of Record online: 24 AUG 2007 | DOI: 10.1002/prot.21568

    5. A chirality index for investigating protein secondary structures and their time evolution (pages 667–677)

      Adriana Pietropaolo, Luca Muccioli, Roberto Berardi and Claudio Zannoni

      Version of Record online: 24 AUG 2007 | DOI: 10.1002/prot.21578

    6. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease (pages 678–694)

      Michael D. Altman, Ellen A. Nalivaika, Moses Prabu-Jeyabalan, Celia A. Schiffer and Bruce Tidor

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21514

    7. Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding (pages 695–706)

      Chao-Sheng Cheng, Ming-Nan Chen, Yen-Ting Lai, Ting Chen, Ku-Feng Lin, Yaw-Jen Liu and Ping-Chiang Lyu

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21520

    8. Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods (pages 707–717)

      Michal Otyepka, Pavel Banáš, Alessandra Magistrato, Paolo Carloni and Jiří Damborský

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21523

    9. Molecular dynamics simulations of HIV-1 protease monomer: Assembly of N-terminus and C-terminus into β-sheet in water solution (pages 731–738)

      Mao-Cai Yan, Yu Sha, Jian Wang, Xu-Qiong Xiong, Jin-Hong Ren and Mao-Sheng Cheng

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21539

    10. Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain (pages 748–760)

      Pompea Del Vecchio, Paola Carullo, Guido Barone, Bruno Pagano, Giuseppe Graziano, Alessio Iannetti, Renato Acquaviva, Antonio Leonardi and Silvestro Formisano

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21552

    11. Membrane-bound structure and energetics of α-synuclein (pages 761–778)

      Maja Mihajlovic and Themis Lazaridis

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21558

    12. The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge (pages 779–785)

      Gabriele Petraglio, Manuela Bartolini, Davide Branduardi, Vincenza Andrisano, Maurizio Recanatini, Francesco Luigi Gervasio, Andrea Cavalli and Michele Parrinello

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21560

    13. Surface recognition elements of membrane protein oligomerization (pages 786–793)

      Arianna Rath and Charles M. Deber

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21569

    14. Residual structure in disordered peptides and unfolded proteins from multivariate analysis and ab initio simulation of Raman optical activity data (pages 823–833)

      Fujiang Zhu, Josef Kapitan, George E. Tranter, Paul D. A. Pudney, Neil W. Isaacs, Lutz Hecht and Laurence D. Barron

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21593

    15. You have full text access to this OnlineOpen article
      Loop modeling: Sampling, filtering, and scoring (pages 834–843)

      Cinque S. Soto, Marc Fasnacht, Jiang Zhu, Lucy Forrest and Barry Honig

      Version of Record online: 29 AUG 2007 | DOI: 10.1002/prot.21612

    16. Lipoprotein lipase: A bioinformatics criterion for assessment of mutations as a risk factor for cardiovascular disease (pages 855–862)

      Sanja Glisic, Patrizio Arrigo, Dragan Alavantic, Vladimir Perovic, Jelena Prljic and Nevena Veljkovic

      Version of Record online: 5 SEP 2007 | DOI: 10.1002/prot.21581

    17. An evolutionary and structure-based docking model for glucocerebrosidase–saposin C and glucocerebrosidase–substrate interactions—Relevance for Gaucher disease (pages 882–891)

      Sílvia Atrian, Eduardo López-Viñas, Paulino Gómez-Puertas, Amparo Chabás, Lluïsa Vilageliu and Daniel Grinberg

      Version of Record online: 5 SEP 2007 | DOI: 10.1002/prot.21554

    18. GRID-MD—A tool for massive simulation of protein channels (pages 892–899)

      Oliver Carrillo and Modesto Orozco

      Version of Record online: 5 SEP 2007 | DOI: 10.1002/prot.21592

    19. New insight into long-range nonadditivity within protein double-mutant cycles (pages 915–924)

      Andrei Y. Istomin, M. Michael Gromiha, Oleg K. Vorov, Donald J. Jacobs and Dennis R. Livesay

      Version of Record online: 5 SEP 2007 | DOI: 10.1002/prot.21620

    20. Epitope mapping and structural analysis of an anti-ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism (pages 938–949)

      Siyi Hu, Zhiqiang Zhu, Liangwei Li, Liang Chang, Weifang Li, Liansheng Cheng, Maikun Teng and Jing Liu

      Version of Record online: 10 SEP 2007 | DOI: 10.1002/prot.21551

    21. Distance dependent centroid to centroid force fields using high resolution decoys (pages 950–970)

      R. Rajgaria, S. R. McAllister and C. A. Floudas

      Version of Record online: 10 SEP 2007 | DOI: 10.1002/prot.21561

    22. Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans (pages 1000–1009)

      Dong Hae Shin, Michael Proudfoot, Hyo Jin Lim, In-Kyu Choi, Hisao Yokota, Alexander F. Yakunin, Rosalind Kim and Sung-Hou Kim

      Version of Record online: 10 SEP 2007 | DOI: 10.1002/prot.21584

    23. Proton pathways in a [NiFe]-hydrogenase: A theoretical study (pages 1010–1022)

      Vitor H. Teixeira, Cláudio M. Soares and António M. Baptista

      Version of Record online: 10 SEP 2007 | DOI: 10.1002/prot.21588

    24. Context shapes: Efficient complementary shape matching for protein–protein docking (pages 1056–1073)

      Zujun Shentu, Mohammad Al Hasan, Christopher Bystroff and Mohammed J. Zaki

      Version of Record online: 10 SEP 2007 | DOI: 10.1002/prot.21600

  3. Research Commentaries

    1. Top of page
    2. Review Article
    3. Research Articles
    4. Research Commentaries
    5. Structure Notes
    1. Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study (pages 1084–1098)

      Maria Carola Colombo, Joost VandeVondele, Sabine Van Doorslaer, Alessandro Laio, Leonardo Guidoni and Ursula Rothlisberger

      Version of Record online: 17 SEP 2007 | DOI: 10.1002/prot.21604

  4. Structure Notes

    1. Top of page
    2. Review Article
    3. Research Articles
    4. Research Commentaries
    5. Structure Notes
    1. You have free access to this content
      Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 Å (pages 1103–1107)

      Koji Nagata, Jun Ohtsuka, Mihoko Takahashi, Atsuko Asano, Hitoshi Iino, Akio Ebihara and Masaru Tanokura

      Version of Record online: 14 NOV 2007 | DOI: 10.1002/prot.21765

    2. You have free access to this content
      X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7 (pages 1108–1111)

      Yoshihiro Agari, Shinya Sato, Taisuke Wakamatsu, Yoshitaka Bessho, Akio Ebihara, Shigeyuki Yokoyama, Seiki Kuramitsu and Akeo Shinkai

      Version of Record online: 14 NOV 2007 | DOI: 10.1002/prot.21794

    3. You have free access to this content
    4. You have free access to this content
      Solution structure and neutralizing antibody binding studies of domain III of the dengue-2 virus envelope protein (pages 1116–1119)

      Kuo-Chun Huang, Ming-Che Lee, Chih-Wei Wu, Kao-Jean Huang, Huan-Yao Lei and Jya-Wei Cheng

      Version of Record online: 14 NOV 2007 | DOI: 10.1002/prot.21806

    5. Structure and biochemical analysis of Kokobera virus helicase (pages 1120–1123)

      Silvia Speroni, Luigi De Colibus, Eloise Mastrangelo, Ernest Gould, Bruno Coutard, Naomi L. Forrester, Séverine Blanc, Bruno Canard and Andrea Mattevi

      Version of Record online: 14 NOV 2007 | DOI: 10.1002/prot.21812

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