{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T12:33:17Z","timestamp":1786365197874,"version":"build-2736575974"},"reference-count":47,"publisher":"American Chemical Society (ACS)","issue":"15","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100004731","name":"Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","award":["LQ21c060004"],"award-info":[{"award-number":["LQ21c060004"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32300482"],"award-info":[{"award-number":["32300482"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U25A20134"],"award-info":[{"award-number":["U25A20134"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The mitochondrial ADP\/ATP carrier (AAC) is essential for cellular energy metabolism and responsible for exchanging ADP for ATP across the inner mitochondrial membrane. However, the precise molecular determinants of substrate binding and the mechanisms underlying the phenotypic heterogeneity of AAC-related diseases remain poorly understood. Here, we combined AlphaFold3 predictions, molecular dynamics simulations, and experimental validation to identify and characterize a previously unrecognized ADP-binding site in AAC (site S2), which is distinct from the canonical bottom site (site S1). AlphaFold3 predictions on AAC variants with disrupted site S1 consistently placed ADP at site S2, interacting with residues R188, K92, and K96, a finding that was independently corroborated by our prior MD simulations. Systematic mutagenesis and functional analysis revealed distinct roles for site S2 residues: R188 serves as the primary phosphate-specific anchor; K92 and K96 facilitate initial recruitment and stabilization; and the aromatic ladder (Y187\/Y191\/F192\/Y195) assists the conformational transition of ADP from anti to syn, a critical step enabling downward translocation. Functional characterization demonstrated that mutations in site S2 significantly impaired ADP transport and oxidative phosphorylation. Notably, the spatial distribution of AAC disease mutations correlates with this bipartite architecture: mild PEOA2-associated mutations cluster near site S2 and perturb the local conformation without abolishing binding, whereas lethal mutations cluster near site S1 and disrupt both ADP binding and structural integrity of the m-gate. Our findings provide new mechanistic insights into stepwise substrate transport and potential therapeutic targets for AAC-related diseases.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c01006","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T18:13:26Z","timestamp":1781720006000},"page":"9328-9343","source":"Crossref","is-referenced-by-count":0,"title":["Structural Basis\nfor Stepwise Substrate Transport\nand Disease Phenotypic Heterogeneity of the Mitochondrial ADP\/ATP\nCarrier"],"prefix":"10.1021","volume":"66","author":[{"given":"Shihao","family":"Yao","sequence":"first","affiliation":[{"name":"Zhejiang University School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International Institute of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"He","sequence":"additional","affiliation":[{"name":"Zhejiang University School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International Institute of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiuzi","family":"Yi","sequence":"additional","affiliation":[{"name":"Zhejiang University International School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang University School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International Institute of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5067-6736","authenticated-orcid":true,"given":"Min-Xin","family":"Guan","sequence":"additional","affiliation":[{"name":"Zhejiang University School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International School of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University International Institute of Medicine , , , ,","place":["Yiwu, Zhejiang, China, 322000"]},{"name":"Zhejiang University and University of Toronto, Zhejiang University , , ,","place":["Hangzhou, China, 310058"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,6,17]]},"reference":[{"key":"2026081008105599500_cit1","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/nature02056","article-title":"Structure of mitochondrial ADP\/ATP\ncarrier in complex with carboxyatractyloside","volume":"426","author":"Pebay-Peyroula","year":"2003","journal-title":"Nature"},{"key":"2026081008105599500_cit2","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1016\/j.cell.2018.11.025","article-title":"The\nMolecular Mechanism of Transport by the Mitochondrial ADP\/ATP Carrier","volume":"176","author":"Ruprecht","year":"2019","journal-title":"Cell"},{"key":"2026081008105599500_cit3","doi-asserted-by":"publisher","first-page":"1978","DOI":"10.1016\/j.bbamem.2008.04.011","article-title":"The ADP and\nATP transport in mitochondria and its carrier","volume":"1778","author":"Klingenberg","year":"2008","journal-title":"Bba-Biomembranes"},{"key":"2026081008105599500_cit4","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1007\/BF01875961","article-title":"The ADP-ATP\ntranslocation in mitochondria, a membrane potential controlled transport","volume":"56","author":"Klingenberg","year":"1980","journal-title":"J. Membr. Biol."},{"key":"2026081008105599500_cit5","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.nmd.2004.12.004","article-title":"A novel ANT1 gene mutation\nwith probable germline mosaicism in autosomal\ndominant progressive external ophthalmoplegia","volume":"15","author":"Deschauer","year":"2005","journal-title":"Neuromuscul Disord"},{"key":"2026081008105599500_cit6","doi-asserted-by":"publisher","first-page":"2295","DOI":"10.1212\/WNL.57.12.2295","article-title":"A novel\nmissense adenine nucleotide translocator-1 gene mutation in a Greek\nadPEO family","volume":"57","author":"Napoli","year":"2001","journal-title":"Neurology"},{"key":"2026081008105599500_cit7","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1002\/ana.10172","article-title":"A novel D104G mutation in the adenine nucleotide translocator 1 gene\nin autosomal dominant progressive external ophthalmoplegia patients\nwith mitochondrial DNA with multiple deletions","volume":"51","author":"Komaki","year":"2002","journal-title":"Ann. 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Genet."},{"key":"2026081008105599500_cit10","doi-asserted-by":"publisher","first-page":"3079","DOI":"10.1093\/hmg\/ddi341","article-title":"Complete loss-of-function\nof the heart\/muscle-specific adenine nucleotide translocator is associated\nwith mitochondrial myopathy and cardiomyopathy","volume":"14","author":"Palmieri","year":"2005","journal-title":"Hum. Mol. Genet."},{"key":"2026081008105599500_cit11","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1136\/jmedgenet-2011-100504","article-title":"Complete loss of expression of the ANT1 gene causing\ncardiomyopathy and myopathy","volume":"49","author":"Echaniz-Laguna","year":"2012","journal-title":"J. Med. 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Biotechnol.\nJ."},{"key":"2026081008105599500_cit15","doi-asserted-by":"publisher","first-page":"2617","DOI":"10.1073\/pnas.0509994103","article-title":"Mitochondrial carriers\nin the cytoplasmic state have\na common substrate binding site","volume":"103","author":"Robinson","year":"2006","journal-title":"Proc. Natl.\nAcad. Sci. U. S. A."},{"key":"2026081008105599500_cit16","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1016\/j.bbabio.2006.03.021","article-title":"The conserved substrate\nbinding site of mitochondrial\ncarriers","volume":"1757","author":"Kunji","year":"2006","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"2026081008105599500_cit17","doi-asserted-by":"publisher","first-page":"10877","DOI":"10.3390\/ijms231810877","article-title":"Function-Related\nAsymmetry of the Interactions between Matrix Loops and Conserved Sequence\nMotifs in the Mitochondrial ADP\/ATP Carrier","volume":"23","author":"Yi","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"2026081008105599500_cit18","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure\nprediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026081008105599500_cit19","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"the Universal Protein Knowledgebase\nin 2025","volume":"53","author":"UniProt.","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"2026081008105599500_cit20","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: protein structure and function prediction","volume":"12","author":"Yang","year":"2015","journal-title":"Nat. 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Chem."},{"key":"2026081008105599500_cit28","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: Validation\nbased on comparison to NMR data","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput.\nChem."},{"key":"2026081008105599500_cit29","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nmeth.4067","article-title":"CHARMM36m:\nan improved force field for folded and intrinsically disordered proteins","volume":"14","author":"Huang","year":"2017","journal-title":"Nat. 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Chem.\nPhys."},{"key":"2026081008105599500_cit33","doi-asserted-by":"publisher","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","article-title":"gmx_MMPBSA:\nA New Tool to Perform End-State Free Energy Calculations with GROMACS","volume":"17","author":"Valde\u0301s-Tresanco","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"2026081008105599500_cit34","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/0076-6879(83)01015-0","article-title":"One-Step\nGene Disruption in Yeast","volume":"101","author":"Rothstein","year":"1983","journal-title":"Method Enzymol"},{"key":"2026081008105599500_cit35","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1002\/yea.320070307","article-title":"Applications of\nHigh-Efficiency Lithium-Acetate Transformation\nof Intact Yeast-Cells Using Single-Stranded Nucleic-Acids as Carrier","volume":"7","author":"Gietz","year":"1991","journal-title":"Yeast"},{"key":"2026081008105599500_cit36","doi-asserted-by":"publisher","first-page":"29151","DOI":"10.1074\/jbc.M504247200","article-title":"Mutations in MTO2\nrelated to tRNA modification impair mitochondrial gene expression\nand protein synthesis in the presence of a paromomycin resistance\nmutation in mitochondrial 15 S rRNA","volume":"280","author":"Yan","year":"2005","journal-title":"J. Biol.\nChem."},{"key":"2026081008105599500_cit37","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1111\/j.1432-1033.1970.tb01086.x","article-title":"Adenine nucleotide\ntranslocation\nof mitochondria. Identification of carrier sites","volume":"16","author":"Weidemann","year":"1970","journal-title":"Eur. J. Biochem."},{"key":"2026081008105599500_cit38","doi-asserted-by":"publisher","first-page":"7701","DOI":"10.1128\/MCB.22.21.7701-7711.2002","article-title":"A human mitochondrial\nGTP binding protein related to\ntRNA modification may modulate phenotypic expression of the deafness-associated\nmitochondrial 12S rRNA mutation","volume":"22","author":"Li","year":"2002","journal-title":"Mol. Cell.\nBiol."},{"key":"2026081008105599500_cit39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.biocel.2016.05.012","article-title":"The defective expression of gtpbp3\nrelated to tRNA modification alters the mitochondrial function and\ndevelopment of zebrafish","volume":"77","author":"Chen","year":"2016","journal-title":"Int. J. Biochem. Cell\nBiol."},{"key":"2026081008105599500_cit40","doi-asserted-by":"publisher","first-page":"3662","DOI":"10.1128\/aem.62.10.3662-3667.1996","article-title":"Controlled\ngene expression systems\nfor Lactococcus lactis with the food-grade inducer nisin","volume":"62","author":"deRuyter","year":"1996","journal-title":"Appl. Environ. Microbiol."},{"key":"2026081008105599500_cit41","doi-asserted-by":"publisher","first-page":"2621","DOI":"10.1128\/aem.55.10.2621-2626.1989","article-title":"Improved\nelectroporation efficiency of intact Lactococcus-lactis\nsubsp lactis cells grown in defined media","volume":"55","author":"McIntyre","year":"1989","journal-title":"Appl.\nEnviron. Microbiol."},{"key":"2026081008105599500_cit42","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1007\/978-1-4939-3637-3_6","article-title":"Membrane Protein\nProduction in Lactococcus lactis for Functional Studies","volume":"1432","author":"Seigneurin-Berny","year":"2016","journal-title":"Methods in molecular biology (Clifton, N.J.)"},{"key":"2026081008105599500_cit43","doi-asserted-by":"publisher","first-page":"11499","DOI":"10.1074\/jbc.M010586200","article-title":"Expression\nof the mitochondrial ADP\/ATP carrier in Escherichia coli. Renaturation,\nreconstitution, and the effect of mutations on 10 positive residues","volume":"276","author":"Heimpel","year":"2001","journal-title":"J. Biol. Chem."},{"key":"2026081008105599500_cit44","doi-asserted-by":"publisher","first-page":"16144","DOI":"10.1021\/bi960668j","article-title":"Probing the\nrole of positive residues in the ADP\/ATP carrier from yeast. The effect\nof six arginine mutations on transport and the four ATP versus ADP\nexchange modes","volume":"35","author":"Heidka\u0308mper","year":"1996","journal-title":"Biochemistry"},{"key":"2026081008105599500_cit45","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adp7725","article-title":"Membrane potential stimulates ADP import and ATP export\nby the mitochondrial ADP\/ATP carrier due to its positively charged\nbinding site","volume":"10","author":"Mavridou","year":"2024","journal-title":"Sci. Adv."},{"key":"2026081008105599500_cit46","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1016\/j.bbabio.2016.02.006","article-title":"The switching\nmechanism of the mitochondrial ADP\/ATP carrier explored by free-energy\nlandscapes","volume":"1857","author":"Pietropaolo","year":"2016","journal-title":"Bba-Bioenergetics"},{"key":"2026081008105599500_cit47","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.3390\/molecules27031071","article-title":"Investigating the Broad\nMatrix-Gate Network in the Mitochondrial ADP\/ATP Carrier through Molecular\nDynamics Simulations","volume":"27","author":"Yao","year":"2022","journal-title":"Molecules"}],"container-title":["Journal of\nChemical Information\nand Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c01006","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/15\/9328\/65120335\/acs.jcim.6c01006.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/15\/9328\/65120335\/acs.jcim.6c01006.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T12:17:27Z","timestamp":1786364247000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/66\/15\/9328\/5159024\/Structural-Basis-for-Stepwise-Substrate-Transport"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,17]]},"references-count":47,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,6,17]]},"published-print":{"date-parts":[[2026,8,10]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c01006","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,17]]}}}