{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T05:46:49Z","timestamp":1788932809802,"version":"build-2803163510"},"reference-count":59,"publisher":"American Chemical Society (ACS)","issue":"8","license":[{"start":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T00:00:00Z","timestamp":1594339200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T00:00:00Z","timestamp":1594339200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T00:00:00Z","timestamp":1594339200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM121275"],"award-info":[{"award-number":["GM121275"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Dopamine (DA) transporter (DAT) is a major target for psychostimulant drugs of abuse such as cocaine that competitively binds to DAT, inhibits DA reuptake, and consequently increases synaptic DA levels. In addition to the central binding site inside DAT, the available experimental evidence suggests the existence of alternative binding sites on DAT, but detection and characterization of these sites are challenging by experiments alone. Here, we integrate multiple computational approaches to probe the potential binding sites on the wild-type Drosophila melanogaster DAT and identify a new allosteric site that displays high affinity for cocaine. This site is located on the surface of DAT, and binding of cocaine is primarily dominated by interactions with hydrophobic residues surrounding the site. We show that cocaine binding to this new site allosterically reduces the binding of DA\/cocaine to the central binding pocket, and simultaneous binding of two cocaine molecules to a single DAT seems infeasible. Furthermore, we find that binding of cocaine to this site stabilizes the conformation of DAT but alters the conformational population and thereby reduces the accessibility by DA, providing molecular insights into the inhibitory mechanism of cocaine. In addition, our results indicate that the conformations induced by cocaine binding to this site may be relevant to the oligomerization of DAT, highlighting a potential role of this new site in modulating the function of DAT.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00346","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T13:03:10Z","timestamp":1594386190000},"page":"3958-3968","source":"Crossref","is-referenced-by-count":12,"title":["Identification of a New Allosteric Binding Site for\nCocaine in Dopamine Transporter"],"prefix":"10.1021","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6556-7521","authenticated-orcid":true,"given":"Liang","family":"Xu","sequence":"first","affiliation":[{"name":"University of Texas at San Antonio , , One UTSA Circle , , ,","place":["San Antonio, Texas, United States, 78249"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liao Y.","family":"Chen","sequence":"additional","affiliation":[{"name":"University of Texas at San Antonio , , One UTSA Circle , , ,","place":["San Antonio, Texas, United States, 78249"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,7,10]]},"reference":[{"key":"2026081805104971300_cit1","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1038\/s41594-019-0253-7","article-title":"Monoamine Transporters:\nStructure, Intrinsic Dynamics and Allosteric\nRegulation","volume":"26","author":"Cheng","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026081805104971300_cit2","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1111\/j.1471-4159.2011.07335.x","article-title":"Dopamine Release\nMediated by the Dopamine Transporter, Facts and Consequences","volume":"118","author":"Leviel","year":"2011","journal-title":"J. Neurochem."},{"key":"2026081805104971300_cit3","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1016\/j.tips.2013.07.005","article-title":"Mechanisms of Dopamine\nTransporter Regulation in Normal\nand Disease States","volume":"34","author":"Vaughan","year":"2013","journal-title":"Trends Pharmacol. Sci."},{"key":"2026081805104971300_cit4","doi-asserted-by":"publisher","first-page":"227","DOI":"10.9758\/cpn.2015.13.3.227","article-title":"Classic Studies\non the Interaction of Cocaine and the Dopamine Transporter","volume":"13","author":"Verma","year":"2015","journal-title":"Clin. Psychopharmacol. Neurosci."},{"key":"2026081805104971300_cit5","doi-asserted-by":"publisher","first-page":"80","DOI":"10.3389\/fmolb.2019.00080","article-title":"Structure\nand Gating\nDynamics of Na+\/Cl\u2013 Coupled Neurotransmitter Transporters","volume":"6","author":"Joseph","year":"2019","journal-title":"Front. Mol. Biosci."},{"key":"2026081805104971300_cit6","doi-asserted-by":"publisher","first-page":"10338","DOI":"10.1073\/pnas.0804659105","article-title":"Mechanism\nfor Alternating Access\nin Neurotransmitter Transporters","volume":"105","author":"Forrest","year":"2008","journal-title":"Proc. Natl.\nAcad. Sci. 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Neurosci."},{"key":"2026081805104971300_cit10","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1016\/j.molcel.2008.05.008","article-title":"The Mechanism of a Neurotransmitter:Sodium\nSymporter\ue5f8Inward\nRelease of Na+ and Substrate Is Triggered by Substrate in a Second\nBinding Site","volume":"30","author":"Shi","year":"2008","journal-title":"Mol. 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Physiol."},{"key":"2026081805104971300_cit21","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nature03978","article-title":"Crystal Structure\nof a Bacterial Homologue of Na+\/Cl--Dependent Neurotransmitter Transporters","volume":"437","author":"Yamashita","year":"2005","journal-title":"Nature"},{"key":"2026081805104971300_cit22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016350","article-title":"The Substrate-Driven\nTransition to an Inward-Facing Conformation in the Functional Mechanism\nof the Dopamine Transporter","volume":"6","author":"Shan","year":"2011","journal-title":"PLoS One"},{"key":"2026081805104971300_cit23","doi-asserted-by":"publisher","first-page":"134","DOI":"10.3389\/fneur.2015.00134","article-title":"Insights into the Modulation\nof Dopamine\nTransporter Function by Amphetamine, Orphenadrine, and Cocaine Binding","volume":"6","author":"Cheng","year":"2015","journal-title":"Front. 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Comput.\nChem."},{"key":"2026081805104971300_cit37","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1002\/(sici)1096-987x(19981115)19:14&lt;1639::aid-jcc10&gt;3.0.co;2-b","article-title":"Automated\nDocking Using a Lamarckian\nGenetic Algorithm and an Empirical Binding Free Energy Function","volume":"19","author":"Morris","year":"1998","journal-title":"J. Comput. Chem."},{"key":"2026081805104971300_cit38","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM\nGeneral Force Field: A Force\nField for Drug-Like Molecules Compatible with the CHARMM All-Atom\nAdditive Biological Force Fields","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput.\nChem."},{"key":"2026081805104971300_cit39","doi-asserted-by":"publisher","first-page":"2714","DOI":"10.1038\/s41467-019-10449-w","article-title":"Substrate-Induced\nConformational Dynamics of the Dopamine Transporter","volume":"10","author":"Nielsen","year":"2019","journal-title":"Nat. Commun."},{"key":"2026081805104971300_cit40","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1093\/bioinformatics\/btk023","article-title":"OPM: Orientations\nof Proteins in Membranes Database","volume":"22","author":"Lomize","year":"2006","journal-title":"Bioinformatics"},{"key":"2026081805104971300_cit41","doi-asserted-by":"publisher","first-page":"D370","DOI":"10.1093\/nar\/gkr703","article-title":"OPM Database\nand PPM Web Server: Resources for Positioning of Proteins in Membranes","volume":"40","author":"Lomize","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2026081805104971300_cit42","doi-asserted-by":"publisher","first-page":"7830","DOI":"10.1021\/jp101759q","article-title":"Update of the CHARMM\nAll-Atom Additive Force Field\nfor Lipids: Validation on Six Lipid Types","volume":"114","author":"Klauda","year":"2010","journal-title":"J.\nPhys. Chem. B"},{"key":"2026081805104971300_cit43","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.20945","article-title":"CHARMM-GUI: A Web-Based Graphical\nUser Interface for CHARMM","volume":"29","author":"Jo","year":"2008","journal-title":"J. Comput. Chem."},{"key":"2026081805104971300_cit44","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1021\/acs.jctc.5b00935","article-title":"CHARMM-GUI Input Generator\nfor NAMD, GROMACS, AMBER, OpenMM, and CHARMM\/OpenMM Simulations Using\nthe CHARMM36 Additive Force Field","volume":"12","author":"Lee","year":"2015","journal-title":"J. Chem.\nTheory Comput."},{"key":"2026081805104971300_cit45","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable Molecular\nDynamics with NAMD","volume":"26","author":"Phillips","year":"2005","journal-title":"J. Comput. Chem."},{"key":"2026081805104971300_cit46","doi-asserted-by":"publisher","first-page":"4613","DOI":"10.1063\/1.470648","article-title":"Constant Pressure\nMolecular Dynamics Simulation: The Langevin Piston Method","volume":"103","author":"Feller","year":"1995","journal-title":"J. Chem. Phys."},{"key":"2026081805104971300_cit47","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/jcc.540040211","article-title":"CHARMM: A Program for Macromolecular Energy, Minimization,\nand Dynamics Calculations","volume":"4","author":"Brooks","year":"1983","journal-title":"J. Comput. Chem."},{"key":"2026081805104971300_cit48","doi-asserted-by":"publisher","first-page":"10606","DOI":"10.1063\/1.1480013","article-title":"Novel Generalized\nBorn Methods","volume":"116","author":"Lee","year":"2002","journal-title":"J. Chem. 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