Large-scale determination of previously unsolved protein structures using evolutionary information

被引:175
作者
Ovchinnikov, Sergey [1 ]
Kinch, Lisa [2 ]
Park, Hahnbeom [1 ]
Liao, Yuxing [3 ]
Pei, Jimin [2 ]
Kim, David E. [1 ]
Kamisetty, Hetunandan [4 ]
Grishin, Nick V. [2 ,3 ]
Baker, David [1 ,5 ]
机构
[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA
[2] Univ Texas SW Med Ctr Dallas, Howard Hughes Med Inst, Dallas, TX 75390 USA
[3] Univ Texas SW Med Ctr Dallas, Dept Biochem, Dept Biophys, Dallas, TX 75390 USA
[4] Facebook Inc, Seattle, WA USA
[5] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA
来源
ELIFE | 2015年 / 4卷
基金
美国国家卫生研究院;
关键词
UNDECAPRENYL PYROPHOSPHATE PHOSPHATASE; MULTIPLE SEQUENCE ALIGNMENTS; MEMBRANE-ASSOCIATED PROTEINS; ESCHERICHIA-COLI; STRUCTURE PREDICTION; GLUTATHIONE METABOLISM; CRYSTAL-STRUCTURES; IDENTIFICATION; SUPERFAMILY; FAMILIES;
D O I
10.7554/eLife.09248
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder.
引用
收藏
页数:25
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