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.