Proton Transfer Mechanisms in the MmpL3 Transporter of Mycobacterium tuberculosis Studied by Computer Simulations

The
mycobacterial membrane exporter MmpL3 transports trehalose
monomycolates (TMM) from the cytosol to the outer membrane of Mycobacterium tuberculosis, making it a potential
drug target. Proton influx is believed to drive TMM efflux, suggesting
that disrupting proton transfer (PT) could be therapeutic. However,
the PT mechanism and its relation to function remain unclear. Recent
MmpL3 structures reveal a potential proton channel in its hydrophobic
core, which also binds potential antituberculosis compounds. We investigated
the PT process using hybrid quantum-mechanical/molecular-mechanical
and classical molecular dynamics simulations. We show that transient
water chains form in two connected transmembrane cavities that act
as proton conduits. Four consecutive PT events are necessary to alter
the protonation states of acidic residues in the protein core, triggering
conformational changes that affect the TMM binding site. The process
begins with the tandem movement of two protons through an upper cavity,
protonating two aspartate residues via a classical hydronium migration.
After conformational shifts, PT proceeds through a lower cavity, protonating
two glutamate residues near the cytosolic opening and inducing further
conformational shifts; here, PT occurs sequentially via hydronium
and proton-hole migration. The cycle ends with the release of protons
into the cytosol. Based on the observed conformational changes, we
propose a mechanism for TMM efflux.