Calculation of minimum energy pathways in transport proteins

Although static structures of protein metastable states are well-studied, the fleeting transitions between these states are difficult to experimentally observe or predict. We present a computationally inexpensive algorithm, “cold-inbetweening”, which generates trajectories between experimentally determined end-states. Here we apply cold-inbetweening to provide mechanistic insight into the ubiquitous alternate access model of operation in three membrane transporter superfamilies. Here, we study DraNramp from Deinococcus radiodurans, MalT from Bacillus cereus, and MATE from Pyrococcus 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 accordance with the alternate access hypothesis. In the MATE transporter, switching conformation involves obligatory rewinding of the N-terminal helix to avoid steric backbone clashes. This concurrently plugs the cavernous ligand-binding site mid-conformational change. Cold-inbetweening can generate hypotheses about large functionally relevant protein conformational changes.