Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction

Andriy Kryshtafovych; John Moult; Sergio G Bartual; J. Fernando Bazan; Helen Berman; Darren E Casteel; Evangelos Christodoulou; John K Everett; Jens Hausmann; Tatjana Heidebrecht; Tanya Hills; Raymond Hui; John F Hunt; Seetharaman Jayaraman; Andrzej Joachimiak; Michael A Kennedy; Choel Kim; Andreas Lingel; Karolina Michalska; Gaetano T Montelione; José M Otero; Anastassis Perrakis; Juan C Pizarro; Mark J van Raaij; Theresa A Ramelot; Francois Rousseau; Liang Tong; Amy K Wernimont; Jasmine Young; Torsten Schwede

doi:10.1002/prot.23196

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Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction

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Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction

Andriy Kryshtafovych, John Moult, Sergio G Bartual, J. Fernando Bazan, Helen Berman, Darren E Casteel, Evangelos Christodoulou, John K Everett, Jens Hausmann, Tatjana Heidebrecht, …

Proteins, structure, function, and bioinformatics, Vol.79(10), pp.6-20

2011

DOI: https://doi.org/10.1002/prot.23196

PMCID: PMC3692002

PMID: 22020785

Abstract

CASP

NMR

protein structure

structure prediction

X-ray crystallography

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, i.e. 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 manuscript, 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 fibre protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ (PKGIβ) dimerization/docking domain, the ectodomain of the JTB (Jumping Translocation Breakpoint) transmembrane receptor, Autotaxin (ATX) in complex with an inhibitor, the DNA-Binding J-Binding Protein 1 (JBP1) 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 (PBS) core-membrane linker (LCM) phycobiliprotein ApcE from Synechocystis , the Heat shock protein 90 (Hsp90) activators PFC0360w and PFC0270w from Plasmodium falciparum , and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae .

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Title: Target Highlights in CASP9: Experimental Target Structures for the Critical Assessment of Techniques for Protein Structure Prediction
Creators: Andriy Kryshtafovych - Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
John Moult - Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Sergio G Bartual - Departamento de Cristalografia y Biologia Estructural, Instituto de Quimica-Fisica Rocasolano, Consejo Superior de Investigaciones Cientificas, calle Serrano 119, E-28006 Madrid, Spain
J. Fernando Bazan - Genentech, Departments of Protein Engineering and Structural Biology, 1 DNA Way, South San Francisco, CA 94080, USA
Helen Berman - Rutgers, the State University of New Jersey, RCSB PDB, 610 Taylor Road Piscataway, NJ, USA 08854-8087
Darren E Casteel - University of California San Diego, Department of Medicine, 9500 Gilman Dr., La Jolla, CA 92093-0652, USA
Evangelos Christodoulou - Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
John K Everett - 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, NJ, 08854, USA
Jens Hausmann - Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
Tatjana Heidebrecht - Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
Tanya Hills - Structural Genomics Consortium (SGC), MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
Raymond Hui - Structural Genomics Consortium (SGC), MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
John F Hunt - Department of Biological Sciences, Northeast Structural Genomics Consortium (NESG), Columbia University, New York, NY 10027, USA
Seetharaman Jayaraman - Department of Biological Sciences, Northeast Structural Genomics Consortium (NESG), Columbia University, New York, NY 10027, USA
Andrzej Joachimiak - Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, USA
Michael A Kennedy - Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, OH 45056, USA
Choel Kim - Department of Pharmacology, The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
Andreas Lingel - Genentech, Departments of Protein Engineering and Structural Biology, 1 DNA Way, South San Francisco, CA 94080, USA
Karolina Michalska - Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA; on the leave from Adam Mickiewicz University, Poznan, Poland
Gaetano T Montelione - 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 NJ 08854, USA
José M Otero - Departamento de Bioquimica y Biologia Molecular, Facultad de Farmacia, Campus Vida, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
Anastassis Perrakis - Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
Juan C Pizarro - Structural Genomics Consortium, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
Mark J van Raaij - Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología - CSIC, c/Darwin 3, E-28049 Madrid, Spain
Theresa A Ramelot - Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (NESG), Miami University, Oxford, Ohio 45056
Francois Rousseau - Genentech, Departments of Protein Engineering and Structural Biology, 1 DNA Way South San Francisco, CA, USA 94080
Liang Tong - Department of Biological Sciences and Northeast Structural Genomics Consortium (NESG), Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
Amy K Wernimont - Structural Genomics Consortium (SGC), MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
Jasmine Young - RCSB PDB, Rutgers, the State University of New Jersey, Piscataway, NJ 08854-8087, USA
Torsten Schwede - Biozentrum University of Basel and SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
Publication Details: Proteins, structure, function, and bioinformatics, Vol.79(10), pp.6-20
Date published: 2011
Grant note: U54 GM074942-01 || GM / National Institute of General Medical Sciences : NIGMS U54 GM094585-01 || GM / National Institute of General Medical Sciences : NIGMS P41 LM007085-01 || LM / National Library of Medicine : NLM K22 CA124517-03 || CA / National Cancer Institute : NCI
Academic Unit: Center for Advanced Biotechnology and Medicine; Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine
Language: English
Resource Type: Journal article
Identifiers: 991031665189004646