Glycerol transport through the aquaglyceroporin GlpF: bridging dynamics and kinetics with atomic simulation.

ABSTRACT: The aquaglyceroporin GlpF is a member of the aquaporin family. It selectively conducts small molecules, such as glycerol, across the cell membrane under a concentration gradient of the substrate. Atomistic molecular dynamics (MD) simulation would provide great insight into the substrate transport mechanism of GlpF and membrane channels alike. Ideally, non-equilibrium simulations under various concentration gradients of glycerol are desired to emulate the transportation in cells, but this kind of simulation is difficult due to a complicated system setup and high computational cost. Here, we present a new strategy to extract non-equilibrium kinetic information from equilibrium MD simulation. We first performed long-time (totally 22.5 μs) multi-copy equilibrium MD simulations of glycerol cond

SUBMITTER: Wang D 

PROVIDER: S-EPMC6685356 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature