Protein structure determination using metagenome sequence data

Journal Article · 19 January 2017 · Science

DOI: https://doi.org/10.1126/science.aah4043 · OSTI ID:1436529

Ovchinnikov, Sergey ^[1]; Park, Hahnbeom ^[2]; Varghese, Neha ^[3]; Huang, Po-Ssu ^[2]; Pavlopoulos, Georgios A. ^[3]; Kim, David E. ^[4]; Kamisetty, Hetunandan ^[5]; Kyrpides, Nikos C. ^[6]; Baker, David ^[7]

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1. Department of Biochemistry, University of Washington, Seattle, WA 98105, USA., Institute for Protein Design, University of Washington, Seattle, WA 98105, USA., Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.
2. Department of Biochemistry, University of Washington, Seattle, WA 98105, USA., Institute for Protein Design, University of Washington, Seattle, WA 98105, USA.
3. Joint Genome Institute, Walnut Creek, CA 94598, USA.
4. Department of Biochemistry, University of Washington, Seattle, WA 98105, USA., Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98105, USA.
5. Facebook Inc., Seattle, WA 98109, USA.
6. Joint Genome Institute, Walnut Creek, CA 94598, USA., Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
7. Department of Biochemistry, University of Washington, Seattle, WA 98105, USA., Institute for Protein Design, University of Washington, Seattle, WA 98105, USA., Howard Hughes Medical Institute, University of Washington, Box 357370, Seattle, WA 98105, USA.

Filling in the protein fold picture Fewer than a third of the 14,849 known protein families have at least one member with an experimentally determined structure. This leaves more than 5000 protein families with no structural information. Protein modeling using residue-residue contacts inferred from evolutionary data has been successful in modeling unknown structures, but it requires large numbers of aligned sequences. Ovchinnikov et al. augmented such sequence alignments with metagenome sequence data (see the Perspective by Söding). They determined the number of sequences required to allow modeling, developed criteria for model quality, and, where possible, improved modeling by matching predicted contacts to known structures. Their method predicted quality structural models for 614 protein families, of which about 140 represent newly discovered protein folds. Science , this issue p. 294 ; see also p. 248

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: National Institutes of Health (NIH); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1436529
• Journal Information: Science, Journal Name: Science Journal Issue: 6322 Vol. 355; ISSN 0036-8075
• Publisher: American Association for the Advancement of Science (AAAS)Copyright Statement
• Country of Publication: United States
• Language: English