{
  "abstract": "Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health crisis, further complicated by increasing drug resistance. The mycobacterial membrane protein MmpL3, which is essential for transporting cell wall precursors such as trehalose monomycolate (TMM), is a promising therapeutic target. However, the mechanistic link between proton-driven dynamics and substrate transport in MmpL3 is not fully understood. In this study, we use molecular dynamics simulations to investigate how protonation of conserved Asp-Tyr dyads (Asp256-Tyr646 and Asp645-Tyr257) in Mycobacterium smegmatis (Msmg) MmpL3 regulates conformational changes and TMM binding. Protonation at Asp256 induces an open dyad conformation, increases local water accessibility, and is associated with a tendency toward more open configurations of the periplasmic binding pocket. In contrast, protonation at Asp645 stabilizes a closed dyad conformation, reduces water accessibility, and narrows the transmembrane binding pocket. These findings support a proposed sequential protonation model in which protonation-dependent conformational changes are allosterically coupled to substrate translocation. Author summary: Tuberculosis remains one of the deadliest infectious diseases worldwide, in part because the bacterium builds an unusually strong cell wall that is difficult for drugs to penetrate. MmpL3 is essential for assembling this cell wall and is therefore an important target for new drugs. However, it has not been clear how this transporter uses protons to power lipid movement. In this work, we used molecular dynamics simulations to examine how protonation at two conserved sites controls the structure and behavior of MmpL3. We focused on two conserved sites inside the protein and found that protonation at each site produces different structural effects. One protonation state favors a more open and hydrated local environment, while the other favors a more closed and less hydrated configuration. These changes support a stepwise mechanism in which protonation acts as a molecular switch to coordinate transport. By clarifying how proton-driven conformational changes power MmpL3 function, our work provides insight into a critical process in mycobacterial cell wall construction and may help guide future efforts to develop new tuberculosis therapies.",
  "abstract_shown": true,
  "affiliations": [
    "School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America",
    "Department of Pharmacy Sciences, Creighton University, Omaha, Nebraska, United States of America",
    "Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America",
    "Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America",
    "School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Lixinhao Yang"
    },
    {
      "affs": [
        1
      ],
      "name": "E. Jeffrey North"
    },
    {
      "affs": [
        2
      ],
      "name": "Helen I. Zgurskaya"
    },
    {
      "affs": [
        3
      ],
      "name": "Mary Jackson"
    },
    {
      "affs": [
        0,
        4
      ],
      "name": "James C. Gumbart",
      "orcid": "0000-0002-1510-7842"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0x91wwj2tbytj.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pcbi.1014880",
  "fulltext_url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014880",
  "id": "0x91wwj2tbytj",
  "issns": [
    "1553-7358",
    "1553-734X"
  ],
  "landing_url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014880",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Actinobacteria"
    ],
    [
      "heading",
      "Bacteria"
    ],
    [
      "heading",
      "Bacterial Pathogens"
    ],
    [
      "heading",
      "Biochemical Simulations"
    ],
    [
      "heading",
      "Biochemistry"
    ],
    [
      "heading",
      "Biology and Life Sciences"
    ],
    [
      "heading",
      "Cell Biology"
    ],
    [
      "heading",
      "Cell Walls"
    ],
    [
      "heading",
      "Cellular Structures and Organelles"
    ],
    [
      "heading",
      "Chemistry"
    ],
    [
      "heading",
      "Computational Biology"
    ],
    [
      "heading",
      "Computational Chemistry"
    ],
    [
      "heading",
      "Lipids"
    ],
    [
      "heading",
      "Medical Microbiology"
    ],
    [
      "heading",
      "Medicine and Health Sciences"
    ],
    [
      "heading",
      "Microbial Pathogens"
    ],
    [
      "heading",
      "Microbiology"
    ],
    [
      "heading",
      "Molecular Dynamics"
    ],
    [
      "heading",
      "Mycobacteria"
    ],
    [
      "heading",
      "Mycobacterium Tuberculosis"
    ],
    [
      "heading",
      "Nuclear Physics"
    ],
    [
      "heading",
      "Nucleons"
    ],
    [
      "heading",
      "Organisms"
    ],
    [
      "heading",
      "Pathogens"
    ],
    [
      "heading",
      "Pathology and Laboratory Medicine"
    ],
    [
      "heading",
      "Physical Sciences"
    ],
    [
      "heading",
      "Physics"
    ],
    [
      "heading",
      "Proteins"
    ],
    [
      "heading",
      "Protons"
    ],
    [
      "heading",
      "Research Article"
    ],
    [
      "heading",
      "Transmembrane Transport Proteins"
    ],
    [
      "openalex",
      "2730|Drug Transport and Resistance Mechanisms"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Biochemical simulations"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Lipids"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/Transmembrane transport proteins"
    ],
    [
      "plos",
      "/Biology and life sciences/Cell biology/Cellular structures and organelles/Cell walls"
    ],
    [
      "plos",
      "/Biology and life sciences/Computational biology/Biochemical simulations"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Mycobacteria"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Actinobacteria/Mycobacteria"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Actinobacteria/Mycobacterium tuberculosis"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Mycobacteria"
    ],
    [
      "plos",
      "/Physical sciences/Chemistry/Computational chemistry/Molecular dynamics"
    ],
    [
      "plos",
      "/Physical sciences/Physics/Nuclear physics/Nucleons/Protons"
    ]
  ],
  "openalex": "W7223109806",
  "pdf_url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014880&type=printable",
  "pmcid": "PMC13719056",
  "pmid": "42905872",
  "published": "2026-10-21",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/0x91wwj2tbytj.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:23Z",
      "native_id": "10.1371/journal.pcbi.1014880",
      "source": "plos",
      "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014880"
    },
    {
      "first_seen": "2026-11-02T12:22:58Z",
      "native_id": "PMC13719056",
      "source": "pmc",
      "url": "https://doi.org/10.1371/journal.pcbi.1014880"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "heading:Biochemistry",
      "subfield": "general"
    },
    {
      "field": "biology",
      "origin": "plos:computational biology",
      "subfield": "bioinformatics"
    },
    {
      "field": "biology",
      "origin": "plos:cell biology",
      "subfield": "cell-biology"
    },
    {
      "field": "biology",
      "origin": "plos:microbiology",
      "subfield": "microbiology"
    },
    {
      "field": "chemistry",
      "origin": "heading:Computational Chemistry",
      "subfield": "theoretical"
    }
  ],
  "title": "Proton transport drives allosteric conformational changes in the MmpL3 transporter",
  "title_text": "Proton transport drives allosteric conformational changes in the MmpL3 transporter",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:58Z",
  "url": "https://research.draconitic.com/paper/0x91wwj2tbytj",
  "venue": "PLOS Computational Biology",
  "versions": []
}