{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T04:11:15Z","timestamp":1775016675897,"version":"3.50.1"},"reference-count":110,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T00:00:00Z","timestamp":1658793600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100019481","name":"Southwestern Medical Foundation","doi-asserted-by":"publisher","award":["RP210041"],"award-info":[{"award-number":["RP210041"]}],"id":[{"id":"10.13039\/100019481","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["I-2095-20220331"],"award-info":[{"award-number":["I-2095-20220331"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein\u2013protein interactions (PPIs) and modeling protein complexes at the proteome level.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We applied RoseTTAFold and AlphaFold, two of the latest deep-learning methods for structure predictions, to analyze coevolution of human proteins residing in mitochondria, an organelle of vital importance in many cellular processes including energy production, metabolism, cell death and antiviral response. Variations in mitochondrial proteins have been linked to a plethora of human diseases and genetic conditions. RoseTTAFold, with high computational speed, was used to predict the coevolution of about 95% of mitochondrial protein pairs. Top-ranked pairs were further subject to modeling of the complex structures by AlphaFold, which also produced contact probability with high precision and in many cases consistent with RoseTTAFold. Most top-ranked pairs with high contact probability were supported by known PPIs and\/or similarities to experimental structural complexes. For high-scoring pairs without experimental complex structures, our coevolution analyses and structural models shed light on the details of their interfaces, including CHCHD4\u2013AIFM1, MTERF3\u2013TRUB2, FMC1\u2013ATPAF2 and ECSIT\u2013NDUFAF1. We also identified novel PPIs (PYURF\u2013NDUFAF5, LYRM1\u2013MTRF1L and COA8\u2013COX10) for several proteins without experimentally characterized interaction partners, leading to predictions of their molecular functions and the biological processes they are involved in.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Data of mitochondrial proteins and their interactions are available at: http:\/\/conglab.swmed.edu\/mitochondria.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac527","type":"journal-article","created":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T13:59:38Z","timestamp":1658843978000},"page":"4301-4311","source":"Crossref","is-referenced-by-count":33,"title":["Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3505-9665","authenticated-orcid":false,"given":"Jimin","family":"Pei","sequence":"first","affiliation":[{"name":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4190-3065","authenticated-orcid":false,"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"}]},{"given":"Qian","family":"Cong","sequence":"additional","affiliation":[{"name":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,7,26]]},"reference":[{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.ajhg.2019.12.001","article-title":"Pathogenic bi-allelic mutations in NDUFAF8 cause Leigh syndrome with an isolated complex I deficiency","volume":"106","author":"Alston","year":"2020","journal-title":"Am. J. Hum. Genet"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1126\/science.aaa1193","article-title":"Ribosome. 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Commun"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1126\/science.1099320","article-title":"The pathophysiology of mitochondrial cell death","volume":"305","author":"Green","year":"2004","journal-title":"Science"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1006\/jmbi.1998.1668","article-title":"Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice","volume":"277","author":"Grigorieff","year":"1998","journal-title":"J. Mol. 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Natl. Acad. Sci. USA"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"eabc4209","DOI":"10.1126\/science.abc4209","article-title":"The coupling mechanism of mammalian respiratory complex I","volume":"370","author":"Kampjut","year":"2020","journal-title":"Science"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. 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Commun"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/jb\/mvz090","article-title":"Mass spectrometry-based methods for analysing the mitochondrial interactome in mammalian cells","volume":"167","author":"Koshiba","year":"2020","journal-title":"J. Biochem"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"D807","DOI":"10.1093\/nar\/gky1053","article-title":"OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs","volume":"47","author":"Kriventseva","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"D835","DOI":"10.1093\/nar\/gkz972","article-title":"ClinVar: improvements to accessing data","volume":"48","author":"Landrum","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023041408373437500_","doi-asserted-by":"crossref","first-page":"e1005653","DOI":"10.1371\/journal.pcbi.1005653","article-title":"CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets","volume":"13","author":"Li","year":"2017","journal-title":"PLoS Comput. 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