Adherence to the conservation of momentum to elucidate membrane transporter mechanisms

The conformational landscape of proteins and associated dynamics is an essential component of function. Diverse conformations of highly populated metastable states are well-studied, but transitions between these states are rare, fleeting events. Neither molecular dynamics simulations nor experimental methods provide information about these. To address this conundrum, we present a computationally inexpensive algorithm, “cold-inbetweening”, which generates trajectories in torsion angle space. This minimises the overall kinetic energy needed to complete a transition between experimentally determined end-states. We use this method to provide mechanistic insight into three transporter superfamilies. This method allows interrogation of structural transitions, provides unique insights into coupled motion and hypotheses of action. The alternate access model of operation [1] is ubiquitous among many superfamilies of membrane transporters [2]. The model proposes that outward and inward pore opening is mutually exclusive, allowing ligand translocation but preventing damage from free solvent flow. Here, we study DraNramp (MntH) from Deinococcus radiodurians [3], MalT (bcMalT) from Bacillus cereus [4], and MATE (PfMATE) from Pyrococcus furiosus [5]. In MalT, the trajectory demonstrates elevator transport through unwinding of a supporter arm helix, maintaining the necessary and sufficient space to transport maltose. In DraNramp, this trajectory exhibited outward-gate closure prior to inward-gate opening, suggesting that the timing of gate closure is an inherent property of the protein architecture. In the MATE transporter, switching conformation involves the rewinding of an extended N-terminal helix. We suggest that the necessary motions to avoid steric backbone clashes forces this helix to plug the cavernous ligand-binding site during the conformational change. We propose helix unwinding as a general structural mechanism in membrane transporter function due to ease of helix register slippage in the lipid bilayer.