Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration.

ABSTRACT: We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces

SUBMITTER: Niesen MJ 

PROVIDER: S-EPMC5381951 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature