Unbiased MD simulations characterize lipid binding pockets in lipid transfer proteins

The molecular characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to the understanding of several aspects of their mechanistic mode of action. However, obtaining lipid-bound structures of LTPs is not straightforward owing to caveats in current experimental structural biology approaches. As a result, several structures of LTPs, and most notably almost all of those that have been proposed to act as bridges between membrane organelles, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. In this work, we develop an in silico protocol based on unbiased coarse grain molecular simulations in which lipids placed in bulk solvent away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the pathway via which lipids enter LTPs. We apply this approach to characterize lipid binding to bridge-like LTPs belonging to the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.