Unbiased MD simulations identify lipid binding sites in lipid transfer proteins.

ABSTRACT: The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, 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. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid

SUBMITTER: Srinivasan S 

PROVIDER: S-EPMC11303870 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature