AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP

Abstract

As part of the CASP competition, the protein structure prediction algorithm AlphaFold2 generated multiple models of the proton/drug antiporter LmrP. Previous distance restraints from double electron-electron resonance spectroscopy, a technique which reports distance distributions between spin labels attached to proteins, suggest that one of the lower-ranked models may have captured a conformation that has so far eluded experimental structure determination.

Figure 1.. An inward-facing model of LmrP generated by AlphaFold2 is consistent with experimental data.

A) Outward- and inward-facing conformations determined using X-ray crystallography and modeled by AlphaFold2, respectively. B and C) Experimental DEER distance distributions on the extracellular and intracellular sides of the protein, respectively, overlap with distances predicted by AlphaFold2 model 1. Dashed lines are distance distributions predicted by either the crystal structure (blue) or the model (red). These data have been previously published. D) Average predicted DEER distance of all CASP14 LmrP models on the intracellular side (X-axis) and extracellular side (Y-axis). Solid blue and red circles represent components from the experimental DEER data corresponding to outward- and inward-facing conformations, respectively. The inward-facing AlphaFold2 model shown in panel A is located on the bottom-right.