{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T13:32:05Z","timestamp":1791984725343,"version":"4.4.0"},"reference-count":76,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218514\/Z\/19\/Z"],"award-info":[{"award-number":["218514\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/X035603\/1"],"award-info":[{"award-number":["EP\/X035603\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Proton-coupled oligopeptide transporters (POTs) are of great pharmaceutical interest owing to their promiscuous substrate binding site that has been linked to improved oral bioavailability of several classes of drugs. Members of the POT family are conserved across all phylogenetic kingdoms and function by coupling peptide uptake to the proton electrochemical gradient. Cryo-EM structures and alphafold models have recently provided new insights into different conformational states of two mammalian POTs, SLC15A1, and SLC15A2. Nevertheless, these studies leave open important questions regarding the mechanism of proton and substrate coupling, while simultaneously providing a unique opportunity to investigate these processes using molecular dynamics (MD) simulations. Here, we employ extensive unbiased and enhanced-sampling MD to map out the full SLC15A2 conformational cycle and its thermodynamic driving forces. By computing conformational free energy landscapes in different protonation states and in the absence or presence of peptide substrate, we identify a likely sequence of intermediate protonation steps that drive inward-directed alternating access. These simulations identify key differences in the extracellular gate between mammalian and bacterial POTs, which we validate experimentally in cell-based transport assays. Our results from constant-PH MD and absolute binding free energy (ABFE) calculations also establish a mechanistic link between proton binding and peptide recognition, revealing key details underpining secondary active transport in POTs. This study provides a vital step forward in understanding proton-coupled peptide and drug transport in mammals and pave the way to integrate knowledge of solute carrier structural biology with enhanced drug design to target tissue and organ bioavailability.<\/jats:p>","DOI":"10.7554\/elife.96507","type":"journal-article","created":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T13:27:25Z","timestamp":1713274045000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.96507","source":"Crossref","is-referenced-by-count":10,"title":["The mechanism of mammalian proton-coupled peptide transporters"],"prefix":"10.7554","volume":"13","author":[{"given":"Simon M","family":"Lichtinger","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford","place":["Oxford, United Kingdom"]},{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"The Kavli Institute for Nanoscience Discovery, University of Oxford","place":["Oxford, United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Joanne L","family":"Parker","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford","place":["Oxford, United Kingdom"]},{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"The Kavli Institute for Nanoscience Discovery, University of Oxford","place":["Oxford, United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7432-2270","authenticated-orcid":true,"given":"Simon","family":"Newstead","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford","place":["Oxford, United Kingdom"]},{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"The Kavli Institute for Nanoscience Discovery, University of Oxford","place":["Oxford, United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5100-8836","authenticated-orcid":true,"given":"Philip C","family":"Biggin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"publisher"}],"name":"Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford","place":["Oxford, United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2024,7,23]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","type":"journal-article","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"29931","DOI":"10.1074\/jbc.M115.675603","type":"journal-article","article-title":"Salt bridge swapping in the EXXERFXYY motif of proton-coupled oligopeptide transporters","volume":"290","author":"Aduri","year":"2015","journal-title":"The Journal of Biological Chemistry"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"6148","DOI":"10.1021\/acs.jctc.2c00516","type":"journal-article","article-title":"Scalable constant pH molecular dynamics in GROMACS","volume":"18","author":"Aho","year":"2022","journal-title":"Journal of Chemical Theory and Computation"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1039\/c5sc02678d","type":"journal-article","article-title":"Accurate calculation of the absolute free energy of binding for drug molecules","volume":"7","author":"Aldeghi","year":"2016","journal-title":"Chemical Science"},{"key":"bib5","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-7756-7","type":"journal-article","article-title":"Absolute alchemical free energy calculations for ligand binding: a beginner\u2019s guide: in Computational drug discovery and design","volume":"1762","author":"Aldeghi","year":"2018","journal-title":"Methods in Molecular Biology"},{"key":"bib6","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-022-00721-4","type":"journal-article","article-title":"Evaluating the use of absolute binding free energy in the fragment optimisation process","volume":"5","author":"Alibay","year":"2022","journal-title":"Communications Chemistry"},{"key":"bib7","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.100.020603","type":"journal-article","article-title":"Well-tempered metadynamics: a smoothly converging and tunable free-energy method","volume":"100","author":"Barducci","year":"2008","journal-title":"Physical Review Letters"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"6433","DOI":"10.1021\/acs.jctc.9b00524","type":"journal-article","article-title":"Exploring conformational transitions and free-energy profiles of proton-coupled oligopeptide transporters","volume":"15","author":"Batista","year":"2019","journal-title":"Journal of Chemical Theory and Computation"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"1889","DOI":"10.1016\/j.str.2015.07.016","type":"journal-article","article-title":"Crystal structures of the extracellular domain from PepT1 and PepT2 provide novel insights into mammalian peptide transport","volume":"23","author":"Beale","year":"2015","journal-title":"Structure"},{"key":"bib10","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-015-0167-8","type":"journal-article","article-title":"Role of electrostatic interactions for ligand recognition and specificity of peptide transporters","volume":"13","author":"Boggavarapu","year":"2015","journal-title":"BMC Biology"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"9535","DOI":"10.1021\/jp0217839","type":"journal-article","article-title":"Absolute binding free energies:a quantitative approach for their calculation","volume":"107","author":"Boresch","year":"2003","journal-title":"The Journal of Physical Chemistry B"},{"key":"bib12","doi-asserted-by":"publisher","DOI":"10.1063\/1.2408420","type":"journal-article","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"The Journal of Chemical Physics"},{"key":"bib13","volume-title":"Amber","author":"Case","year":"2022","type":"book"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"2773","DOI":"10.1074\/jbc.274.5.2773","type":"journal-article","article-title":"Stoichiometry and kinetics of the high-affinity H+-coupled peptide transporter PepT2","volume":"274","author":"Chen","year":"1999","journal-title":"The Journal of Biological Chemistry"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1006\/bbrc.2000.2851","type":"journal-article","article-title":"Functional roles of histidine and tyrosine residues in the H(+)-peptide transporter PepT1","volume":"272","author":"Chen","year":"2000","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1152\/physiol.00054.2005","type":"journal-article","article-title":"From bacteria to man: archaic proton-dependent peptide transporters at work","volume":"21","author":"Daniel","year":"2006","journal-title":"Physiology"},{"key":"bib17","doi-asserted-by":"publisher","DOI":"10.1063\/1.2829861","type":"journal-article","article-title":"Adaptive biasing force method for scalar and vector free energy calculations","volume":"128","author":"Darve","year":"2008","journal-title":"The Journal of Chemical Physics"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"1726","DOI":"10.1021\/acs.jctc.1c01217","type":"journal-article","article-title":"Lipid21: complex lipid membrane simulations with AMBER","volume":"18","author":"Dickson","year":"2022","journal-title":"Journal of Chemical Theory and Computation"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"11343","DOI":"10.1073\/pnas.1301079110","type":"journal-article","article-title":"Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT","volume":"110","author":"Doki","year":"2013","journal-title":"PNAS"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/368563a0","type":"journal-article","article-title":"Expression cloning of a mammalian proton-coupled oligopeptide transporter","volume":"368","author":"Fei","year":"1994","journal-title":"Nature"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1021\/bi962058p","type":"journal-article","article-title":"Identification of the histidyl residue obligatory for the catalytic activity of the human H+\/peptide cotransporters PEPT1 and PEPT2","volume":"36","author":"Fei","year":"1997","journal-title":"Biochemistry"},{"key":"bib22","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/S0005-2736(99)00046-2","type":"journal-article","article-title":"Preferential recognition of zwitterionic dipeptides as transportable substrates by the high-affinity peptide transporter PEPT2","volume":"1418","author":"Fei","year":"1999","journal-title":"Biochimica et Biophysica Acta (BBA) - Biomembranes"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.str.2014.12.012","type":"journal-article","article-title":"Gating topology of the proton-coupled oligopeptide symporters","volume":"23","author":"Fowler","year":"2015","journal-title":"Structure"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/embor.2013.107","type":"journal-article","article-title":"Structural insights into substrate recognition in proton-dependent oligopeptide transporters","volume":"14","author":"Guettou","year":"2013","journal-title":"EMBO Reports"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1038\/nsmb.2860","type":"journal-article","article-title":"Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2","volume":"21","author":"Guettou","year":"2014","journal-title":"Nature Structural & Molecular Biology"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1016\/j.bbamem.2017.10.033","type":"journal-article","article-title":"Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations","volume":"1860","author":"Harpole","year":"2018","journal-title":"Biochimica et Biophysica Acta. Biomembranes"},{"key":"bib27","doi-asserted-by":"publisher","DOI":"10.48550\/ARXIV.2202.04164","type":"preprint","article-title":"Enhanced sampling methods for molecular dynamics simulations","volume-title":"arXiv","author":"H\u00e9nin","year":"2022"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/978-3-642-58360-5","type":"book-chapter","article-title":"Steered molecular Dynamics","volume-title":"Computational molecular dynamics: challenges, methods, ideas","author":"Izrailev","year":"1999"},{"key":"bib29","doi-asserted-by":"publisher","first-page":"3164","DOI":"10.1021\/jp212503e","type":"journal-article","article-title":"Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids","volume":"116","author":"J\u00e4mbeck","year":"2012","journal-title":"The Journal of Physical Chemistry. B"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"282","DOI":"10.2174\/092986612799363109","type":"journal-article","article-title":"Functional investigation of conserved membrane-embedded glutamate residues in the proton-coupled peptide transporter YjdL","volume":"19","author":"Jensen","year":"2012","journal-title":"Protein and Peptide Letters"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1093\/pcp\/pcv145","type":"journal-article","article-title":"A functional EXXEK motif is essential for proton coupling and active glucosinolate transport by NPF2.11","volume":"56","author":"J\u00f8rgensen","year":"2015","journal-title":"Plant & Cell Physiology"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","type":"journal-article","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","type":"journal-article","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"bib34","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abk3259","type":"journal-article","article-title":"Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes","volume":"7","author":"Killer","year":"2021","journal-title":"Science Advances"},{"key":"bib35","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2023.112831","type":"journal-article","article-title":"Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition","volume":"42","author":"Kotov","year":"2023","journal-title":"Cell Reports"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1007\/s00424-003-1101-4","type":"journal-article","article-title":"The proton oligopeptide cotransporter family SLC15 in physiology and pharmacology","volume":"447","author":"Kottra","year":"2004","journal-title":"Pfl\u00fcgers Archiv: European Journal of Physiology"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"2266","DOI":"10.1016\/j.bpj.2022.05.029","type":"journal-article","article-title":"Proton coupling and the multiscale kinetic mechanism of a peptide transporter","volume":"121","author":"Li","year":"2022","journal-title":"Biophysical Journal"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"3705","DOI":"10.1021\/acs.jctc.3c00140","type":"journal-article","article-title":"Tackling hysteresis in conformational sampling: how to be forgetful with MEMENTO","volume":"19","author":"Lichtinger","year":"2023","journal-title":"Journal of Chemical Theory and Computation"},{"key":"bib39","type":"software","article-title":"Pymemento","volume-title":"Software Heritage","author":"Lichtinger","year":"2024","unstructured":"Lichtinger S. 2024. Pymemento. Software Heritage. swh:1:rev:cf8a6ef48fd95f2c64bc8e14a4534d85dd3864c5. https:\/\/archive.softwareheritage.org\/swh:1:dir:740593dbeabd11476e4bc62f43405d5b1799a133;origin=https:\/\/github.com\/simonlichtinger\/PyMEMENTO;visit=swh:1:snp:f87d46d48a7d33b9f17043764bac3816a6fa34f1;anchor=swh:1:rev:cf8a6ef48fd95f2c64bc8e14a4534d85dd3864c5."},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.1063\/1.4890371","type":"journal-article","article-title":"Accelerated weight histogram method for exploring free energy landscapes","volume":"141","author":"Lindahl","year":"2014","journal-title":"The Journal of Chemical Physics"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"886","DOI":"10.15252\/embr.201338403","type":"journal-article","article-title":"Structural basis for polyspecificity in the POT family of proton-coupled oligopeptide transporters","volume":"15","author":"Lyons","year":"2014","journal-title":"EMBO Reports"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","type":"journal-article","article-title":"ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"Journal of Chemical Theory and Computation"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1016\/j.str.2018.01.005","type":"journal-article","article-title":"Multispecific substrate recognition in a proton-dependent oligopeptide transporter","volume":"26","author":"Martinez Molledo","year":"2018","journal-title":"Structure"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1073\/pnas.1813715116","type":"journal-article","article-title":"Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters","volume":"116","author":"Minhas","year":"2019","journal-title":"PNAS"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/emboj.2010.309","type":"journal-article","article-title":"Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2","volume":"30","author":"Newstead","year":"2011","journal-title":"The EMBO Journal"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.sbi.2016.10.018","type":"journal-article","article-title":"Recent advances in understanding proton coupled peptide transport via the POT family","volume":"45","author":"Newstead","year":"2017","journal-title":"Current Opinion in Structural Biology"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1248\/bpb.b20-01013","type":"journal-article","article-title":"Protonation state of a histidine residue in human oligopeptide transporter 1 (hPEPT1) regulates hPEPT1-mediated efflux activity","volume":"44","author":"Omori","year":"2021","journal-title":"Biological & Pharmaceutical Bulletin"},{"key":"bib48","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.04273","type":"journal-article","article-title":"Thermodynamic evidence for a dual transport mechanism in a POT peptide transporter","volume":"3","author":"Parker","year":"2014","journal-title":"eLife"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature13116","type":"journal-article","article-title":"Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1","volume":"507","author":"Parker","year":"2014","journal-title":"Nature"},{"key":"bib50","doi-asserted-by":"publisher","first-page":"13182","DOI":"10.1073\/pnas.1710727114","type":"journal-article","article-title":"Proton movement and coupling in the POT family of peptide transporters","volume":"114","author":"Parker","year":"2017","journal-title":"PNAS"},{"key":"bib51","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abh3355","type":"journal-article","article-title":"Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals","volume":"7","author":"Parker","year":"2021","journal-title":"Science Advances"},{"key":"bib52","doi-asserted-by":"publisher","first-page":"7182","DOI":"10.1063\/1.328693","type":"journal-article","article-title":"Polymorphic transitions in single crystals: a new molecular dynamics method","volume":"52","author":"Parrinello","year":"1981","journal-title":"Journal of Applied Physics"},{"key":"bib53","doi-asserted-by":"publisher","first-page":"2784","DOI":"10.1111\/febs.15531","type":"journal-article","article-title":"A guide to plasma membrane solute carrier proteins","volume":"288","author":"Pizzagalli","year":"2021","journal-title":"The FEBS Journal"},{"key":"bib54","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1016\/j.jmb.2011.02.008","type":"journal-article","article-title":"The alternating-access mechanism of MFS transporters arises from inverted-topology repeats","volume":"407","author":"Radestock","year":"2011","journal-title":"Journal of Molecular Biology"},{"key":"bib55","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1006\/bbrc.2000.3546","type":"journal-article","article-title":"Cloning and characterization of the gene encoding the mouse peptide transporter PEPT2","volume":"276","author":"Rubio-Aliaga","year":"2000","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","type":"journal-article","article-title":"Comparative protein modelling by satisfaction of spatial restraints","volume":"234","author":"Sali","year":"1993","journal-title":"Journal of Molecular Biology"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1021\/acscentsci.8b00330","type":"journal-article","article-title":"Free energy landscape of the complete transport cycle in a key bacterial transporter","volume":"4","author":"Selvam","year":"2018","journal-title":"ACS Central Science"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1016\/j.str.2022.04.011","type":"journal-article","article-title":"Extracellular domain of PepT1 interacts with TM1 to facilitate substrate transport","volume":"30","author":"Shen","year":"2022","journal-title":"Structure"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"3411","DOI":"10.1038\/emboj.2012.157","type":"journal-article","article-title":"Alternating access mechanism in the POT family of oligopeptide transporters","volume":"31","author":"Solcan","year":"2012","journal-title":"The EMBO Journal"},{"key":"bib60","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-022-00636-0","type":"journal-article","article-title":"Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor","volume":"5","author":"Stauffer","year":"2022","journal-title":"Communications Chemistry"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1113\/jphysiol.1997.sp021883","type":"journal-article","article-title":"Stoichiometry and pH dependence of the rabbit proton\u2010dependent oligopeptide transporter PepT1","volume":"498","author":"Steel","year":"1997","journal-title":"The Journal of Physiology"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1016\/B978-0-444-63772-7.00019-1","type":"book-chapter","article-title":"Membrane transport","volume-title":"An Introduction to Biological Membranes","author":"Stillwell","year":"2016"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1023\/A:1008202821328","type":"journal-article","article-title":"Di\ufb00erential evolution \u2013 a simple and e\ufb03cient heuristic for global optimization over continuous spaces","volume":"11","author":"Storn","year":"1997","journal-title":"Journal of Global Optimization"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"1765","DOI":"10.1093\/bioinformatics\/btz828","type":"journal-article","article-title":"QMEANDisCo-distance constraints applied on model quality estimation","volume":"36","author":"Studer","year":"2020","journal-title":"Bioinformatics"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/nrd3187","type":"journal-article","article-title":"Coexistence of passive and carrier-mediated processes in drug transport","volume":"9","author":"Sugano","year":"2010","journal-title":"Nature Reviews. Drug Discovery"},{"key":"bib66","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/nature13074","type":"journal-article","article-title":"Crystal structure of the plant dual-affinity nitrate transporter NRT1.1","volume":"507","author":"Sun","year":"2014","journal-title":"Nature"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1021\/ct401042b","type":"journal-article","article-title":"Constant pH replica exchange molecular dynamics in explicit solvent using discrete protonation states: implementation, testing, and validation","volume":"10","author":"Swails","year":"2014","journal-title":"Journal of Chemical Theory and Computation"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/0014-5793(96)00952-0","type":"journal-article","article-title":"Identification of the histidine residues involved in substrate recognition by a rat H+\/peptide cotransporter, PEPT1","volume":"394","author":"Terada","year":"1996","journal-title":"FEBS Letters"},{"key":"bib69","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/0021-9991(77)90121-8","type":"journal-article","article-title":"Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling","volume":"23","author":"Torrie","year":"1977","journal-title":"Journal of Computational Physics"},{"key":"bib70","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1016\/j.cpc.2013.09.018","type":"journal-article","article-title":"PLUMED 2: new feathers for an old bird","volume":"185","author":"Tribello","year":"2014","journal-title":"Computer Physics Communications"},{"key":"bib71","doi-asserted-by":"publisher","first-page":"1911","DOI":"10.1023\/b:pham.0000008036.05892.e9","type":"journal-article","article-title":"Biophysical evidence for His57 as a proton-binding site in the mammalian intestinal transporter hPepT1","volume":"20","author":"Uchiyama","year":"2003","journal-title":"Pharmaceutical Research"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"2404","DOI":"10.1021\/jacs.8b11343","type":"journal-article","article-title":"Structure of prototypic peptide transporter DtpA from E. coli in complex with valganciclovir provides insights into drug binding of human PepT1","volume":"141","author":"Ural-Blimke","year":"2019","journal-title":"Journal of the American Chemical Society"},{"key":"bib73","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","type":"journal-article","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nature Methods"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"1997","DOI":"10.1002\/jcc.23702","type":"journal-article","article-title":"CHARMM-GUI Membrane Builder toward realistic biological membrane simulations","volume":"35","author":"Wu","year":"2014","journal-title":"Journal of Computational Chemistry"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1016\/j.str.2014.06.008","type":"journal-article","article-title":"Crystal structure of the E. coli peptide transporter YbgH","volume":"22","author":"Zhao","year":"2014","journal-title":"Structure"},{"key":"dataset1","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.10561418","type":"dataset","article-title":"Supplementary data for: The mechanism of mammalian proton-coupled peptide transporters","volume-title":"Zenodo","author":"Lichtinger","year":"2024","unstructured":"Lichtinger S, Parker J, Newstead S, Biggin PC. 2024. Supplementary data for: The mechanism of mammalian proton-coupled peptide transporters. Zenodo."}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/96507\/elife-96507-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/96507\/elife-96507-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/96507","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:17:14Z","timestamp":1787566634000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/96507"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,23]]},"references-count":76,"alternative-id":["10.7554\/eLife.96507"],"URL":"https:\/\/doi.org\/10.7554\/elife.96507","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.02.04.578827","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.96507.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.96507.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.96507.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"doi","id":"10.5281\/zenodo.10561418","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:740593dbeabd11476e4bc62f43405d5b1799a133;origin=https:\/\/github.com\/simonlichtinger\/PyMEMENTO;visit=swh:1:snp:f87d46d48a7d33b9f17043764bac3816a6fa34f1;anchor=swh:1:rev:cf8a6ef48fd95f2c64bc8e14a4534d85dd3864c5","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,23]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP96507"}}