Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likeliho...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2014-05-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/02030 |
| _version_ | 1811237001292152832 |
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| author | Sergey Ovchinnikov Hetunandan Kamisetty David Baker |
| author_facet | Sergey Ovchinnikov Hetunandan Kamisetty David Baker |
| author_sort | Sergey Ovchinnikov |
| collection | DOAJ |
| description | Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein–protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter. |
| first_indexed | 2024-04-12T12:17:26Z |
| format | Article |
| id | doaj.art-140dcf77db30497d994cde9768982e03 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T12:17:26Z |
| publishDate | 2014-05-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-140dcf77db30497d994cde9768982e032022-12-22T03:33:22ZengeLife Sciences Publications LtdeLife2050-084X2014-05-01310.7554/eLife.02030Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary informationSergey Ovchinnikov0Hetunandan Kamisetty1David Baker2Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States; Molecular and Cellular Biology Program, University of Washington, Seattle, United StatesDepartment of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United States; Facebook Inc., Seattle, United StatesDepartment of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, United StatesDo the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein–protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.https://elifesciences.org/articles/02030protein coevolutionprotein complexpseudo-likelihood |
| spellingShingle | Sergey Ovchinnikov Hetunandan Kamisetty David Baker Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information eLife protein coevolution protein complex pseudo-likelihood |
| title | Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information |
| title_full | Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information |
| title_fullStr | Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information |
| title_full_unstemmed | Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information |
| title_short | Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information |
| title_sort | robust and accurate prediction of residue residue interactions across protein interfaces using evolutionary information |
| topic | protein coevolution protein complex pseudo-likelihood |
| url | https://elifesciences.org/articles/02030 |
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