ABSTRACT
Opening and closure of certain mechanosensitive ion channels has recently been linked with the presence of lipids in or near their pores. Although non-conducting structures of mechanosensitive Piezo channels do not show the presence of lipids in the pore, computational simulations suggest whole phospholipids enter the Piezo1 pore in the closed state. Here, to probe this phenomenon, we conduct coarse-grained (CG) and all-atom (AA) simulations of Piezo1 with different solvation algorithms and equilibrium protocols, including CG-to-AA reverse mapping from Martini CG force field to CHARMM AA force field. Our results show that the lack of initial hydration of the upper pore region, enabled by common CG but not AA solvation algorithms, allows entry of whole lipids through gaps between pore helices during subsequent equilibrium simulations. Absolute binding free energy calculations show that these lipids are thermodynamically unfavorable, indicating they are likely kinetically trapped in the pore during microsecond-long AA simulations. An alternative equilibrium protocol is proposed to avoid such simulation artifact for channels whose pores are walled with transmembrane gaps. This work underscores the notion that, as simulated systems become increasingly complex, interpretation of simulated data in physiological contexts requires extra precautions. When no experimental data is available, free energy approaches such as those implemented here appear as trustworthy validations of results observed from MD trajectories.
SIGNIFICANCE STATEMENT 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. Recent simulation studies suggest the presence of lipids in the nonconducting pore of mechanosensitive Piezo1 channels. Here, we show that certain computational protocols at the initial equilibrium stage enable lipids to be trapped in the pore despite a large free energy cost, suggesting these lipids are kinetically trapped and likely entered the pore as a result of a computational artifact rather than from a physiological process. This work emphases the need for additional validations of membrane protein simulation outcomes and proposes alternative protocols to avoid such artifact.
Competing Interest Statement
The authors have declared no competing interest.