Importance of Molecular Dynamics Equilibrium Protocol on Protein-lipid Interactions near Channel Pore

ABSTRACT Multiscale molecular dynamics (MD) simulations using Martini coarse-grained (CG) and all-atom (AA) forcer fields are commonly used in membrane protein studies. In particular, reverse-mapping an equilibrated CG model to an AA model offers an efficient way for preparing large membrane protein systems with complex protein shapes and lipid compositions. Here, we report that this hybrid CG-equilibrium-AA-production protocol may artificially increase lipid density and decrease hydration in ion channel pores walled with transmembrane gaps. To understand the origin of this conundrum, we conducted replicas of CG, AA, and reverse-mapped AA simulations of the pore domain of the mechanosensitive Piezo1 channel in a non-conducting conformation. Lipid/water density analysis and free energy calculations reveal that the lack of initial pore hydration allows adjacent lipids to enter the pore lumen through gaps between pore helices during CG simulation. Due to the mismatch between CG and AA lipid kinetics, these pore lipids remain trapped in the subsequent AA simulations, despite unfavorable binding free energy. We tested several CG equilibrium protocols and found that a protocol restraining the whole lipid produces pore hydration consistent with AA results, thus eliminating this artifact for further studies of lipid gating and protein-lipid interactions. WHY IT MATTERS Membrane-embedded proteins constantly interact with lipid molecules. Computational molecular dynamics simulations have become an indispensable tool for investigating the role of such protein-lipid interactions. Using mechanosensitive Piezo1 channel as model, we found that subtle differences in solvation and equilibrium protocols between coarse-grained and all-atom MD simulations can result in different lipid densities inside the channel pore. We identify the underlying cause of this discrepancy and propose alternative protocols to avoid this artifact.