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 Gō-MARTINI model for proteins describes large-amplitude structural dynamics, which has not been possible with the commonly used elastic network model. Using the Gō-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 Gō model. To address this issue, we introduced a simple cutoff scheme and tuned the cutoff distance of the native contacts and the in

SUBMITTER: Mahmood MI 

PROVIDER: S-EPMC7937874 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature