Conformational dynamics of a histidine molecular switch in a cation/proton antiporter
Multisubunit Mrp type sodium proton (Na+/H+) antiporters are indispensable for the growth of alkali and salt tolerant bacteria and archaea under challenging conditions. Several subunits of the membrane protein complex are closely related to the membrane bound subunits of mitochondrial respiratory complex I, a key enzyme in aerobic energy metabolism. The molecular mechanism of ion translocation by complex I and Mrp antiporters has remained largely unknown and is the subject of intense debate. Here, we combine the power of site-directed mutagenesis and large-scale atomistic molecular dynamics simulations to elucidate the molecular basis of proton-conducting function of the MrpA subunit of the antiporter. We show that point mutations directly affect the transport activity by perturbing the conformational dynamics of a key histidine residue that acts as a molecular switch. Importantly, we find that charge and protonation state variations drive hydrogen bonding rearrangements and hydration changes, which result in coupled sidechain and backbone level conformational changes of the histidine and neighboring residues. We propose the histidine switch as a unique functional element central to proton transport function in Mrp antiporters and respiratory complex I. Significance statementEnergy conversion in biology is catalyzed by several membrane-bound enzyme complexes that drive transmembrane charge translocation. A key question is how these charges are moved against a membrane gradient in an efficient manner, i.e., what kind of gating and fail-safe mechanisms are employed by the proteins to ensure charge transfer directionality. By studying cation/proton Mrp antiporter, which shares homology with the mitochondrial complex I, we describe a conserved histidine residue acting as a molecular switch crucial for gating transfer of protons. Our work emphasizes the functional significance of conserved and conformationally mobile motifs in proteins. The results will benefit the mechanistic understanding of naturally existing proteins and design of artificial enzymes.