Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

Article Article scientifique Article Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study eng 2023-06-27 2023-06-27 author Schweke Hugo Charles Jean Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot Israel 419247 Département de biologie moléculaire et cellulaire (MOCEL) author Xu Qifang Institute for Cancer Research Fox Chase Cancer Center Philadelphia Pennsylvania USA author Tauriello Gerardo 0000-0002-5921-7007 Biozentrum University of Basel & SIB Swiss Institute of Bioinformatics Basel Switzerland author Pantolini Lorenzo Biozentrum University of Basel & SIB Swiss Institute of Bioinformatics Basel Switzerland author Schwede Torsten 0000-0003-2715-335X Biozentrum University of Basel & SIB Swiss Institute of Bioinformatics Basel Switzerland author Cazals Frédéric Centre Inria d'Université Côte d'Azur Sophia‐Antipolis France author Lhéritier Alix Amadeus SAS Sophia‐Antipolis France author Fernandez‐Recio Juan Instituto de Ciencias de la Vid y del Vino (ICVV) CSIC‐UR‐Gobierno de La Rioja Logroño Spain author Rodríguez‐Lumbreras Luis Angel Instituto de Ciencias de la Vid y del Vino (ICVV) CSIC‐UR‐Gobierno de La Rioja Logroño Spain author Schueler‐Furman Ora Department of Microbiology and Molecular Genetics The Institute for Medical Research Israel‐Canada Hebrew University‐Hadassah Medical School Jerusalem Israel author Varga Julia K. Department of Microbiology and Molecular Genetics The Institute for Medical Research Israel‐Canada Hebrew University‐Hadassah Medical School Jerusalem Israel author Jiménez‐García Brian Computational Structural Biology Group Department of Chemistry Bijvoet Centre Faculty of Science Utrecht University Utrecht The Netherlands author Réau Manon F. Computational Structural Biology Group Department of Chemistry Bijvoet Centre Faculty of Science Utrecht University Utrecht The Netherlands author Bonvin Alexandre M. J. J. Computational Structural Biology Group Department of Chemistry Bijvoet Centre Faculty of Science Utrecht University Utrecht The Netherlands author Savojardo Castrense Biocomputing Group Department of Pharmacy and Biotechnology University of Bologna Bologna Italy author Martelli Pier‐Luigi Biocomputing Group Department of Pharmacy and Biotechnology University of Bologna Bologna Italy author Casadio Rita Biocomputing Group Department of Pharmacy and Biotechnology University of Bologna Bologna Italy author Tubiana Jérôme Blavatnik School of Computer Science Tel Aviv University Tel Aviv Israel author Wolfson Haim J. Blavatnik School of Computer Science Tel Aviv University Tel Aviv Israel author Oliva Romina 0000-0002-6156-6249 Department of Sciences and Technologies University of Naples “Parthenope” Naples Italy author Barradas‐Bautista Didier Kaust Visualization Lab Core lab Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia author Ricciardelli Tiziana 0000-0001-9114-4250 Physical Sciences and Engineering Division Kaust Catalysis Center King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia author Cavallo Luigi Physical Sciences and Engineering Division Kaust Catalysis Center King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia author Venclovas Česlovas Institute of Biotechnology Life Sciences Center Vilnius University Vilnius Lithuania author Olechnovič Kliment Institute of Biotechnology Life Sciences Center Vilnius University Vilnius Lithuania author Guerois Raphael Institute for Integrative Biology of the Cell (I2BC) Commissariat à l'Energie Atomique CNRS Université Paris‐Sud Université Paris‐Saclay Gif‐sur‐Yvette France author Andreani Jessica Institute for Integrative Biology of the Cell (I2BC) Commissariat à l'Energie Atomique CNRS Université Paris‐Sud Université Paris‐Saclay Gif‐sur‐Yvette France author Martin Juliette Univ Lyon Université Claude Bernard Lyon 1 CNRS, UMR 5086 MMSB Lyon France author Wang Xiao 0000-0003-4435-7098 Department of Computer Science Purdue University West Lafayette Indiana USA author Terashi Genki Department of Biological Sciences Purdue University West Lafayette Indiana USA author Sarkar Daipayan 0000-0002-4167-2108 Department of Biological Sciences Purdue University West Lafayette Indiana USA author Christoffer Charles 0000-0002-6163-6323 Department of Computer Science Purdue University West Lafayette Indiana USA author Aderinwale Tunde 0000-0003-3592-3844 Department of Computer Science Purdue University West Lafayette Indiana USA author Verburgt Jacob 0000-0002-8524-1342 Department of Biological Sciences Purdue University West Lafayette Indiana USA author Kihara Daisuke 0000-0003-4091-6614 Department of Computer Science Purdue University West Lafayette Indiana USA author Marchand Anthony Laboratory of Protein Design and Immunoengineering Ecole polytechnique fédérale de Lausanne (EPFL) Lausanne Switzerland author Santos Correia Bruno Luiz Laboratory of Protein Design and Immunoengineering Ecole polytechnique fédérale de Lausanne (EPFL) Lausanne Switzerland 805232 author Duan Rui 0000-0003-1646-4013 Department of Physics and Astronomy Department of Biochemistry Dalton Cardiovascular Research Center Institute for Data Science and Informatics University of Missouri Columbia Missouri USA author Qiu Liming Department of Physics and Astronomy Department of Biochemistry Dalton Cardiovascular Research Center Institute for Data Science and Informatics University of Missouri Columbia Missouri USA author Xu Xianjin Department of Physics and Astronomy Department of Biochemistry Dalton Cardiovascular Research Center Institute for Data Science and Informatics University of Missouri Columbia Missouri USA author Zhang Shuang Department of Physics and Astronomy Department of Biochemistry Dalton Cardiovascular Research Center Institute for Data Science and Informatics University of Missouri Columbia Missouri USA author Zou Xiaoqin Department of Physics and Astronomy Department of Biochemistry Dalton Cardiovascular Research Center Institute for Data Science and Informatics University of Missouri Columbia Missouri USA author Dey Sucharita Department of Bioscience and Bioengineering Indian Institute of Technology Jodhpur Karwar Rajasthan India author Dunbrack Roland L. Institute for Cancer Research Fox Chase Cancer Center Philadelphia Pennsylvania USA author Levy Emmanuel 0000-0001-8959-7365 Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot Israel 417450 Département de biologie moléculaire et cellulaire (MOCEL) author Wodak Shoshana J. 0000-0002-0701-6545 VIB‐VUB Center for Structural Biology Brussels Belgium 2200323 10.1002/pmic.202200323 37365936 1615-9853 PMC10937251 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200323 <p>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.</p> Crystal contacts Homodimers Potential energy Protein interactions Protein structure European Commission ACCIÓ programme to foster mobility of researchers with a focus in applied research and technology transfer 801342 TECNIOspringINDUSTRY EU H2020 European Commission BioExcel Centre of Excellence for ComputationalBiomolecular Research 823830 BioExcel-2 EU H2020 European Commission Infinite Protein Self-Assembly in Health and Disease 819318 Agglomerates EU H2020 Netherlands Organisation for Scientific Research (NWO) Caught in the act: a combined magnetic resonance -modelling approach to capture cellular machines at work 718.015.001 NL TOP PUNT subsidies 2014 CW true Proteomics 23 17 3ad9cdd0-433a-4a25-b112-1352ce41ee55 Article (Published version) Restricted LEVY04.pdf 4179866 application/pdf 35d6a3cc35b81848d78fc3247d44b2161ed30f6621e7abae5b1af8c653a9d4f7 restrictedAccess

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