期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 105, 期 12, 页码 4685-4690出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0800256105
关键词
molecular fragment replacement; protein structure prediction; ROSETTA; structural genomics
资金
- Howard Hughes Medical Institute Funding Source: Medline
- Intramural NIH HHS Funding Source: Medline
- NIGMS NIH HHS [U54-GM074958, U54 GM074958] Funding Source: Medline
Protein NMR chemical shifts are highly sensitive,to local structure. A robust protocol is described that exploits this relation for de novo protein structure generation, using as input experimental parameters the C-13(alpha), C-13(beta), C-13', N-15, H-1(alpha) and H-1(N) NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7-1.8 angstrom root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination.
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