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Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell 2024; 187:999-1010.e15. [PMID: 38325366 DOI: 10.1016/j.cell.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
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Affiliation(s)
- Hugo Schweke
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Prasun Kumar
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Yoan Duhoo
- Protein Production and Structure Characterization Core Facility (PTPSP), School of Life Sciences, École polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin Dubreuil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, India.
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LÁ, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin A, Savojardo C, Martelli PL, Casadio R, Tubiana J, Wolfson H, Oliva R, Barradas-Bautista D, Ricciardelli T, Cavallo L, Venclovas Č, Olechnovič K, Guerois R, Andreani J, Martin J, Wang X, Kihara D, Marchand A, Correia B, Zou X, Dey S, Dunbrack R, Levy E, Wodak S. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics 2023; 23:e2200323. [PMID: 37365936 PMCID: PMC10937251 DOI: 10.1002/pmic.202200323] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/28/2023]
Abstract
Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Julia K. Varga
- Hebrew University of Jerusalem Institute for Medical Research Israel-Canada
| | | | | | | | | | | | | | - Jérôme Tubiana
- Tel Aviv University Blavatnik School of Computer Science
| | - Haim Wolfson
- Tel Aviv University Blavatnik School of Computer Science
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Institute for Data Science and Informatics, University of Missouri
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Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes J, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes A. Meet-U: Educating through research immersion. PLoS Comput Biol 2018; 14:e1005992. [PMID: 29543809 PMCID: PMC5854232 DOI: 10.1371/journal.pcbi.1005992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.
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Affiliation(s)
- Nika Abdollahi
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Alexandre Albani
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Eric Anthony
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Agnes Baud
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Mélissa Cardon
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Robert Clerc
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Dariusz Czernecki
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Romain Conte
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Laurent David
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Agathe Delaune
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Samia Djerroud
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Pauline Fourgoux
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Nadège Guiglielmoni
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Jeanne Laurentie
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Nathalie Lehmann
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Camille Lochard
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Rémi Montagne
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Vasiliki Myrodia
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Vaitea Opuu
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Elise Parey
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Lélia Polit
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Sylvain Privé
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Chloé Quignot
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Maria Ruiz-Cuevas
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Mariam Sissoko
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Nicolas Sompairac
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Audrey Vallerix
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Violaine Verrecchia
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, CNRS, Institut Pasteur, Paris, France
| | - Raphael Guérois
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Yann Ponty
- AMIBio team, Laboratoire d’informatique de l’École polytechnique (LIX, UMR 7161) / Inria Saclay, UPSay, Palaiseau, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, Paris, France
| | - Alessandra Carbone
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
- Institut Universitaire de France
| | | | - Stéphane Le Crom
- Sorbonne Université / UPMC, Univ. Antilles, Univ. Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Martin Weigt
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Samer Abboud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Juliana Bernardes
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Guillaume Bouvier
- Department of Structural Biology and CheImistry (CNRS UMR3528) - Center of Bioinformatics, Biostatistics and Integrative Biology (CNRS USR3756) - Structural Bioinformatics Unit, Institut Pasteur, Paris, France
| | - Chloé Dequeker
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Arnaud Ferré
- MaIAGE, INRA, UPSay, Jouy-en-Josas, France and LIMSI, CNRS, UPSay, Orsay, France
| | - Patrick Fuchs
- Sorbonne Université / UPMC, Ecole Normale Supérieure - PLS Research University, Département de Chimie, CNRS, Laboratoire des Biomolécules, UMR 7203 - Univ. Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Pierre Poulain
- Mitochondria, Metals and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Univ. Paris Diderot, CNRS, Sorbonne Paris Cité, Paris, France
| | - Hugues Richard
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Hugo Schweke
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Elodie Laine
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
- * E-mail: (EL); (AL)
| | - Anne Lopes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
- * E-mail: (EL); (AL)
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