Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library
© 2020, eLife Sciences Publications Ltd. All rights reserved. Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence d...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications, Ltd
2021
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| Online Access: | https://hdl.handle.net/1721.1/134624 |
| _version_ | 1826190444988465152 |
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| author | Lite, Thuy-Lan V Grant, Robert A Nocedal, Isabel Littlehale, Megan L Guo, Monica S Laub, Michael T |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Lite, Thuy-Lan V Grant, Robert A Nocedal, Isabel Littlehale, Megan L Guo, Monica S Laub, Michael T |
| author_sort | Lite, Thuy-Lan V |
| collection | MIT |
| description | © 2020, eLife Sciences Publications Ltd. All rights reserved. Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition. |
| first_indexed | 2024-09-23T08:40:21Z |
| format | Article |
| id | mit-1721.1/134624 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T08:40:21Z |
| publishDate | 2021 |
| publisher | eLife Sciences Publications, Ltd |
| record_format | dspace |
| spelling | mit-1721.1/1346242023-12-08T21:05:00Z Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library Lite, Thuy-Lan V Grant, Robert A Nocedal, Isabel Littlehale, Megan L Guo, Monica S Laub, Michael T Massachusetts Institute of Technology. Department of Biology Howard Hughes Medical Institute © 2020, eLife Sciences Publications Ltd. All rights reserved. Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition. 2021-10-27T20:05:50Z 2021-10-27T20:05:50Z 2020 2021-07-21T14:18:29Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/134624 en 10.7554/ELIFE.60924 eLife Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf eLife Sciences Publications, Ltd eLife |
| spellingShingle | Lite, Thuy-Lan V Grant, Robert A Nocedal, Isabel Littlehale, Megan L Guo, Monica S Laub, Michael T Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library |
| title | Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library |
| title_full | Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library |
| title_fullStr | Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library |
| title_full_unstemmed | Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library |
| title_short | Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library |
| title_sort | uncovering the basis of protein protein interaction specificity with a combinatorially complete library |
| url | https://hdl.handle.net/1721.1/134624 |
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