Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library
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 syst...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2020-10-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/60924 |
| _version_ | 1811181450976821248 |
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| author | Thuy-Lan V Lite Robert A Grant Isabel Nocedal Megan L Littlehale Monica S Guo Michael T Laub |
| author_facet | Thuy-Lan V Lite Robert A Grant Isabel Nocedal Megan L Littlehale Monica S Guo Michael T Laub |
| author_sort | Thuy-Lan V Lite |
| collection | DOAJ |
| description | 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 | 2024-04-11T09:17:56Z |
| format | Article |
| id | doaj.art-44387ca2d4864218b45b55e20d7105f2 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:17:56Z |
| publishDate | 2020-10-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-44387ca2d4864218b45b55e20d7105f22022-12-22T04:32:16ZengeLife Sciences Publications LtdeLife2050-084X2020-10-01910.7554/eLife.60924Uncovering the basis of protein-protein interaction specificity with a combinatorially complete libraryThuy-Lan V Lite0https://orcid.org/0000-0003-2743-4231Robert A Grant1Isabel Nocedal2https://orcid.org/0000-0002-4706-1113Megan L Littlehale3Monica S Guo4Michael T Laub5https://orcid.org/0000-0002-8288-7607Department of Biology Massachusetts Institute of Technology, Cambridge, United StatesDepartment of Biology Massachusetts Institute of Technology, Cambridge, United StatesDepartment of Biology Massachusetts Institute of Technology, Cambridge, United StatesDepartment of Biology Massachusetts Institute of Technology, Cambridge, United StatesDepartment of Biology Massachusetts Institute of Technology, Cambridge, United StatesDepartment of Biology Massachusetts Institute of Technology, Cambridge, United States; Howard Hughes Medical Institute Massachusetts Institute of Technology, Cambridge, United StatesProtein-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.https://elifesciences.org/articles/60924protein-protein interactionspecificitydeep mutational scanning |
| spellingShingle | Thuy-Lan V Lite Robert A Grant Isabel Nocedal Megan L Littlehale Monica S Guo Michael T Laub Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library eLife protein-protein interaction specificity deep mutational scanning |
| 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 |
| topic | protein-protein interaction specificity deep mutational scanning |
| url | https://elifesciences.org/articles/60924 |
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