Calculation of minimum energy pathways in transport proteins

Abstract

Diverse conformations of highly populated protein metastable states are well-studied, but the fleeting transitions between these states cannot be observed by experimental methods or molecular dynamics simulations. To address this, we present a computationally inexpensive algorithm, “cold-inbetweening”, which generates trajectories in torsion angle space, by minimising the overall kinetic energy needed to complete a transition between experimentally determined end-states. Here we demonstrate the application of cold-inbetweening to provide mechanistic insight into the ubiquitous alternate access model of operation in three membrane transporter superfamilies. The model proposes mutually exclusive outward and inward pore opening, allowing ligand translocation but preventing damage from free solvent flow. Here, we study DraNramp fromDeinococcus radiodurians, MalT fromBacillus cereus, and MATE fromPyrococcus furiosus. In MalT, the trajectory demonstrates elevator transport through unwinding of a supporter arm helix, maintaining adequate space to transport maltose. In DraNramp, outward-gate closure occurs prior to inward-gate opening, in agreement with the alternate access model. In the MATE transporter, switching conformation involves obligatory rewinding of an extended N-terminal helix to avoid steric backbone clashes. This concurrently plugs the cavernous ligand-binding site during the conformational change. More generally, cold-inbetweening can be used to inform hypotheses about large functionally relevant conformational changes.