Major facilitator superfamily (MFS) of secondary transporters consists of three classes of proteins: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters. We have performed a variety of equilibrium, non-equilibrium, biased, and unbiased all-atom molecular dynamics (MD) simulations of bacterial proton-coupled oligopeptide transporter GkPOT, human glucose transporter 1 (GLUT1), and bacterial glycerol-3-phosphate transporter (GlpT), representing the symporters, uniporters, and antiporters, respectively. The simulations are specifically performed to compare the similarities and differences of the conformational dynamics of three different classes of transporters in their apo states and thus do not necessarily capture the entire transport mechanism. However, our results suggest very similar conformational transition pathwyas with substantially different energetics. The observed conformational transition pathways involve interbundle salt-bridge formation/disruption events coupled with the orientational changes of transmembrane (TM) helices, specifically the TM helices 1 and 7 on the one hand and the TM helices 5 and 11, on the other hand. These coupled chemomechanical events result in an alternation in the accessibility of binding site at the cyto- vs periplasmic (or intra- vs extracellular) gates. Interestingly, we observe multiple state transitions between the inward- and outward-facing states of GLUT1 within our microsecond-long equilibrium simulations, while the observation of the state transitions requires enhanced sampling techniques in GkPOT and GlpT simulations. The energy barrier associated with the inward- to outward-facing transition is significantly higher in the antiporter (GlpT) relative to symporter (GkPOT) in our apo simulations. This differential behavior in terms of energetics explains the difference in the function of uni-, anti-, and symporters in the MFS superfamily of transporters.

Similarities and differences of conformational transition pathways in uniporters, symporters, and antiporters of the major facilitator superfamily of transporters

ACS Fall 2021

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