Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.
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.
Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
Andriy
A
Kryshtafovych
John
J
Moult
Sergio G
SG
Bartual
J Fernando
JF
Bazan
Helen
H
Berman
Darren E
DE
Casteel
Evangelos
E
Christodoulou
John K
JK
Everett
Jens
J
Hausmann
Tatjana
T
Heidebrecht
Tanya
T
Hills
Raymond
R
Hui
John F
JF
Hunt
Jayaraman
J
Seetharaman
Andrzej
A
Joachimiak
Michael A
MA
Kennedy
Choel
C
Kim
Andreas
A
Lingel
Karolina
K
Michalska
Gaetano T
GT
Montelione
José M
JM
Otero
Anastassis
A
Perrakis
Juan C
JC
Pizarro
Mark J
MJ
van Raaij
Theresa A
TA
Ramelot
Francois
F
Rousseau
Liang
L
Tong
Amy K
AK
Wernimont
Jasmine
J
Young
Torsten
T
Schwede
D000595:Amino Acid Sequence; D000818:Animals; D017122:Bacteriophage T4 / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D017869:Cyclic GMP-Dependent Protein Kinases / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D006801:Humans; D007711:Klebsiella pneumoniae / Q000737:chemistry / Q000201:enzymology; D007891:Leishmania / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000737:chemistry; D010963:Plasmodium falciparum / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015800:Protozoan Proteins / Q000737:chemistry; D014345:Trypanosoma / Q000737:chemistry; D014764:Viral Proteins / Q000737:chemistry; D000099189:Lysophospholipase D
D017869:Cyclic GMP-Dependent Protein Kinases; D004268:DNA-Binding Proteins; D010727:Phosphoric Diester Hydrolases; D017853:Phosphotransferases (Alcohol Group Acceptor); D011506:Proteins; D015800:Protozoan Proteins; D014764:Viral Proteins; D000099189:Lysophospholipase D; C402790:J-specific DNA-binding protein, protozoa