Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction§††

Authors

  • Andriy Kryshtafovych,

    1. Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616
    Search for more papers by this author
  • John Moult,

    1. Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850
    Search for more papers by this author
  • Sergio G. Bartual,

    1. Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Cientificas, calle Serrano 119, E-28006 Madrid, Spain
    2. Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
    Search for more papers by this author
  • J. Fernando Bazan,

    1. Genentech, Departments of Protein Engineering and Structural Biology, 1 DNA Way, South San Francisco, California 94080
    Search for more papers by this author
  • Helen Berman,

    1. Rutgers, the State University of New Jersey, RCSB PDB, 610 Taylor Road, Piscataway, New Jersey 08854-8087
    Search for more papers by this author
  • Darren E. Casteel,

    1. University of California San Diego, Department of Medicine, 9500 Gilman Dr., La Jolla, California 92093-0652
    Search for more papers by this author
  • Evangelos Christodoulou,

    1. Department of Biochemistry, NKI, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
    Search for more papers by this author
  • John K. Everett,

    1. Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
    Search for more papers by this author
  • Jens Hausmann,

    1. Department of Biochemistry, NKI, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
    Search for more papers by this author
  • Tatjana Heidebrecht,

    1. Department of Biochemistry, NKI, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
    Search for more papers by this author
  • Tanya Hills,

    1. Structural Genomics Consortium (SGC), MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
    Search for more papers by this author
  • Raymond Hui,

    1. Structural Genomics Consortium (SGC), MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
    Search for more papers by this author
  • John F. Hunt,

    1. Department of Biological Sciences, Northeast Structural Genomics Consortium (NESG), Columbia University, New York, New York 10027
    Search for more papers by this author
  • Jayaraman Seetharaman,

    1. Department of Biological Sciences, Northeast Structural Genomics Consortium (NESG), Columbia University, New York, New York 10027
    Search for more papers by this author
  • Andrzej Joachimiak,

    1. Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory
    2. Structural Biology Center, Biosciences Division, Argonne National Laboratory
    3. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
    Search for more papers by this author
  • Michael A. Kennedy,

    1. Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
    Search for more papers by this author
  • Choel Kim,

    1. Department of Pharmacology, The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
    Search for more papers by this author
  • Andreas Lingel,

    1. Genentech, Departments of Protein Engineering and Structural Biology, 1 DNA Way, South San Francisco, California 94080
    Search for more papers by this author
  • Karolina Michalska,

    1. Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory
    Search for more papers by this author
  • Gaetano T. Montelione,

    1. Rutgers, The State University of New Jersey, Robert Wood Johnson Medical School, and Northeast Structural Genomics Consortium (NESG), Center for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry. CABM 679 Hoes Lane, Piscataway, New Jersey 08854
    Search for more papers by this author
  • José M. Otero,

    1. Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
    Search for more papers by this author
  • Anastassis Perrakis,

    1. Department of Biochemistry, NKI, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
    Search for more papers by this author
  • Juan C. Pizarro,

    1. Structural Genomics Consortium (SGC), MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
    Search for more papers by this author
  • Mark J. van Raaij,

    1. Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
    2. Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología - CSIC, c/Darwin 3, E-28049 Madrid, Spain
    Search for more papers by this author
  • Theresa A. Ramelot,

    1. Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
    Search for more papers by this author
  • Francois Rousseau,

    1. Genentech, Departments of Protein Engineering and Structural Biology, 1 DNA Way, South San Francisco, California 94080
    Search for more papers by this author
  • Liang Tong,

    1. Department of Biological Sciences, Northeast Structural Genomics Consortium (NESG), Columbia University, New York, New York 10027
    Search for more papers by this author
  • Amy K. Wernimont,

    1. Structural Genomics Consortium (SGC), MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
    Search for more papers by this author
  • Jasmine Young,

    1. Rutgers, the State University of New Jersey, RCSB PDB, 610 Taylor Road, Piscataway, New Jersey 08854-8087
    Search for more papers by this author
  • Torsten Schwede

    Corresponding author
    1. Biozentrum University of Basel and SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
    • Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
    Search for more papers by this author

  • The parts of the article on target T0629 were contributed by M.v.R., S.B., and J.O.; target T0605 by D.C. and C.K.; target T0531 by F.R., A.L., and J.B.; target T0543 by J.H., E.C., and A.P.; target T0561 by T.H. and A.P.; targets T0624 and T0555 by T.R., S.J., J.H., M.K., L.T., J.E., and G.M.; targets T0594 and T0566 by T.H., A.W., J.P., and R.H.; and target T0628 by K.M. and A.J. Editing, introduction, discussion, and coordination by A.K., J.M., and T.S..

  • Evangelos Christodoulou's current address is MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom

  • §

    Andreas Lingel's current address is Novartis, Novartis Institutes for Biomedical Research, 4560 Horton Street, Emeryville, California 94608

  • Francois Rousseau's current address is NovImmune, SA, 14 ch. des Aulx, Plan-les-Ouates, CH 1228, Switzerland

  • J. Fernando Bazan's current address is NeuroScience, Inc., 373 280th St. Osceola, Wisconsin 54020

  • ††

    The authors state that AL was employed by Genentech.

Abstract

One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA-binding J-binding protein 1 domain essential for biosynthesis and maintenance of DNA base-J (β-D-glucosyl-hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae. Proteins 2011; © 2011 Wiley-Liss, Inc.

Ancillary