Ten thousand interactions for the molecular biologist

被引:143
作者
Aloy, P
Russell, RB
机构
[1] EMBL, D-69117 Heidelberg, Germany
[2] EMBL, European Bioinformat Inst, Cambridge CB10 1SD, England
关键词
D O I
10.1038/nbt1018
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Previous studies have suggested that nature is restricted to about 1,000 protein folds to perform a great diversity of functions. Here, we use protein interaction data from different sources and three-dimensional structures to suggest that the total number of interaction types is also limited, and estimate that most interactions in nature will conform to one of about 10,000 types. We currently know fewer than 2,000, and at the present rate of structure determination, it will be more than 20 years before we know a full representative set.
引用
收藏
页码:1317 / 1321
页数:5
相关论文
共 28 条
[11]   Functional organization of the yeast proteome by systematic analysis of protein complexes [J].
Gavin, AC ;
Bösche, M ;
Krause, R ;
Grandi, P ;
Marzioch, M ;
Bauer, A ;
Schultz, J ;
Rick, JM ;
Michon, AM ;
Cruciat, CM ;
Remor, M ;
Höfert, C ;
Schelder, M ;
Brajenovic, M ;
Ruffner, H ;
Merino, A ;
Klein, K ;
Hudak, M ;
Dickson, D ;
Rudi, T ;
Gnau, V ;
Bauch, A ;
Bastuck, S ;
Huhse, B ;
Leutwein, C ;
Heurtier, MA ;
Copley, RR ;
Edelmann, A ;
Querfurth, E ;
Rybin, V ;
Drewes, G ;
Raida, M ;
Bouwmeester, T ;
Bork, P ;
Seraphin, B ;
Kuster, B ;
Neubauer, G ;
Superti-Furga, G .
NATURE, 2002, 415 (6868) :141-147
[12]   A protein interaction map of Drosophila melanogaster [J].
Giot, L ;
Bader, JS ;
Brouwer, C ;
Chaudhuri, A ;
Kuang, B ;
Li, Y ;
Hao, YL ;
Ooi, CE ;
Godwin, B ;
Vitols, E ;
Vijayadamodar, G ;
Pochart, P ;
Machineni, H ;
Welsh, M ;
Kong, Y ;
Zerhusen, B ;
Malcolm, R ;
Varrone, Z ;
Collis, A ;
Minto, M ;
Burgess, S ;
McDaniel, L ;
Stimpson, E ;
Spriggs, F ;
Williams, J ;
Neurath, K ;
Ioime, N ;
Agee, M ;
Voss, E ;
Furtak, K ;
Renzulli, R ;
Aanensen, N ;
Carrolla, S ;
Bickelhaupt, E ;
Lazovatsky, Y ;
DaSilva, A ;
Zhong, J ;
Stanyon, CA ;
Finley, RL ;
White, KP ;
Braverman, M ;
Jarvie, T ;
Gold, S ;
Leach, M ;
Knight, J ;
Shimkets, RA ;
McKenna, MP ;
Chant, J ;
Rothberg, JM .
SCIENCE, 2003, 302 (5651) :1727-1736
[13]   PQS: a protein quaternary structure file server [J].
Henrick, K ;
Thornton, JM .
TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (09) :358-361
[14]   Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry [J].
Ho, Y ;
Gruhler, A ;
Heilbut, A ;
Bader, GD ;
Moore, L ;
Adams, SL ;
Millar, A ;
Taylor, P ;
Bennett, K ;
Boutilier, K ;
Yang, LY ;
Wolting, C ;
Donaldson, I ;
Schandorff, S ;
Shewnarane, J ;
Vo, M ;
Taggart, J ;
Goudreault, M ;
Muskat, B ;
Alfarano, C ;
Dewar, D ;
Lin, Z ;
Michalickova, K ;
Willems, AR ;
Sassi, H ;
Nielsen, PA ;
Rasmussen, KJ ;
Andersen, JR ;
Johansen, LE ;
Hansen, LH ;
Jespersen, H ;
Podtelejnikov, A ;
Nielsen, E ;
Crawford, J ;
Poulsen, V ;
Sorensen, BD ;
Matthiesen, J ;
Hendrickson, RC ;
Gleeson, F ;
Pawson, T ;
Moran, MF ;
Durocher, D ;
Mann, M ;
Hogue, CWV ;
Figeys, D ;
Tyers, M .
NATURE, 2002, 415 (6868) :180-183
[15]   A comprehensive two-hybrid analysis to explore the yeast protein interactome [J].
Ito, T ;
Chiba, T ;
Ozawa, R ;
Yoshida, M ;
Hattori, M ;
Sakaki, Y .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (08) :4569-4574
[16]   MOLSCRIPT - A PROGRAM TO PRODUCE BOTH DETAILED AND SCHEMATIC PLOTS OF PROTEIN STRUCTURES [J].
KRAULIS, PJ .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1991, 24 :946-950
[17]   Design of a novel globular protein fold with atomic-level accuracy [J].
Kuhlman, B ;
Dantas, G ;
Ireton, GC ;
Varani, G ;
Stoddard, BL ;
Baker, D .
SCIENCE, 2003, 302 (5649) :1364-1368
[18]   A map of the interactome network of the metazoan C-elegans [J].
Li, SM ;
Armstrong, CM ;
Bertin, N ;
Ge, H ;
Milstein, S ;
Boxem, M ;
Vidalain, PO ;
Han, JDJ ;
Chesneau, A ;
Hao, T ;
Goldberg, DS ;
Li, N ;
Martinez, M ;
Rual, JF ;
Lamesch, P ;
Xu, L ;
Tewari, M ;
Wong, SL ;
Zhang, LV ;
Berriz, GF ;
Jacotot, L ;
Vaglio, P ;
Reboul, J ;
Hirozane-Kishikawa, T ;
Li, QR ;
Gabel, HW ;
Elewa, A ;
Baumgartner, B ;
Rose, DJ ;
Yu, HY ;
Bosak, S ;
Sequerra, R ;
Fraser, A ;
Mango, SE ;
Saxton, WM ;
Strome, S ;
van den Heuvel, S ;
Piano, F ;
Vandenhaute, J ;
Sardet, C ;
Gerstein, M ;
Doucette-Stamm, L ;
Gunsalus, KC ;
Harper, JW ;
Cusick, ME ;
Roth, FP ;
Hill, DE ;
Vidal, M .
SCIENCE, 2004, 303 (5657) :540-543
[19]   MIPS:: a database for genomes and protein sequences [J].
Mewes, HW ;
Frishman, D ;
Güldener, U ;
Mannhaupt, G ;
Mayer, K ;
Mokrejs, M ;
Morgenstern, B ;
Münsterkötter, M ;
Rudd, S ;
Weil, B .
NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :31-34
[20]   The CATH database: an extended protein family resource for structural and functional genomics [J].
Pearl, FMG ;
Bennett, CF ;
Bray, JE ;
Harrison, AP ;
Martin, N ;
Shepherd, A ;
Sillitoe, I ;
Thornton, J ;
Orengo, CA .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :452-455