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Large-Scale Conformational Transitions in Transporters Transporters act as cellular gatekeepers, allowing their small molecule substrates to cross mostly impermeable cellular membranes. Because of their central role in cellular function, transporter malfunction is often associated with disease, and they are also common targets for pharmaceutical drugs. Transporters operate at a
fundamental level through the alternating-access mechanism, in which substrate transport is achieved through a transition between two major functional states, namely the inward-facing (IF) and outward-facing (OF) states. The large-scale conformational changes commonly associated with IF⇌OF transitions are fundamental components of transporters’ function, and an array of advanced molecular dynamics (MD) simulation techniques has previously been developed into a tailored computational recipe to structurally and thermodynamically characterize such IF⇌OF transitions in detail. Within this approach, we start by defining collective variables (i.e., mathematical descriptions of reaction coordinates) that fully describe the major structural differences between the IF and OF states. 

Then, using driven MD simulations, we induce dozens of IF⇌OF transitions through the collective variable space, using work profiles and structural metrics to compare the relative optimality of each transition pathway. Next, we use the string method with swarms of trajectories (SMwST) to structurally relax the most promising pathway. Finally, we run a bias-exchange umbrella sampling (BEUS) simulation along the relaxed pathway and generate a free energy profile from it using the weighted histogram analysis method (WHAM) or multistate Bennett acceptance ratio (MBAR) method. Ultimately, applying this approach to a transporter enables us to identify fundamental connections between the transporter’s structural dynamics and function, which allows us to understand transport mechanisms more deeply and may potentially be leveraged into helping develop new structurally-specific drugs. 

In the primer portion of our presentation, we will introduce the overall approach in more detail, discuss each of its steps, and give some perspectives on recent advances in the approach. In the seminar portion of our presentation, we will talk about a few of our recent applications of this approach to the transporters NaCT, Glt Ph, and GlpT, which will include discussions of some of the practical considerations we made as well as variations to the canonical approach we employed when applying the approach to these transporter systems.