Optimizing Go-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane.

ABSTRACT: Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger length and time scales than atomistic MD simulations, providing an attractive alternative to the conventional simulations. Based on the well-known MARTINI CG force field, the recently developed G?-MARTINI model for proteins describes large-amplitude structural dynamics, which has not been possible with the commonly used elastic network model. Using the G?-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. We observe that structural changes of the non-globular protein are largely dependent on the definition of the native contacts in the G? model. To address this issue, we introduced a simple cutoff scheme and tuned the cutoff distance of the native contacts and the interaction strength of the Lennard-Jones potentials in the G?-MARTINI model. With the optimized G?-MARTINI model, we show that it reproduces structural fluctuations of the Pacsin1 dimer from atomistic simulations. We also show that two Pacsin1 dimers properly assemble through lateral interaction on the lipid membrane. Our work presents a first step towards describing membrane remodeling processes in the G?-MARTINI CG framework by simulating a crucial step of protein assembly on the membrane.

SUBMITTER: Mahmood MI 

PROVIDER: S-EPMC7937874 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature