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 experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency.

Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein

“…New beads are translated at a rate of 5 amino acids per second, and emerge from the ribosome-translocon complex into an environment with an implicit representation of the bilayer and cytosol (Supplemental Movie 1). 39 These simulations were previously found to sufficiently recapitulate several aspects of cotranslational membrane protein folding including the formation of topological isomers and the generation of tension on the nascent chain. 38,40,41 CGMD simulations of SINV polyprotein biosynthesis suggest the nascent chain samples several different topological isomers (Fig.…”

“…To further explore the interplay between sequence, topology, and force, we carried out coarsegrained molecular dynamics (CGMD) simulations of the translation and translocon-mediated membrane integration of the nascent structural polyprotein. 38,39 In these simulations, three-residue segments of the nascent chain are modeled as individual beads with physicochemical properties based on their constituent amino acids. New beads are translated at a rate of 5 amino acids per second, and emerge from the ribosome-translocon complex into an environment with an implicit representation of the bilayer and cytosol (Supplemental Movie 1).…”

“…Coarse-grained molecular dynamics (CGMD) simulations are based on a previously developed and tested approach. 38,39 Briefly, simulations are carried out in the context of a coarsened representation of the ribosome exit tunnel, Sec translocon, and nascent chain. The nascent chain is composed of beads that each represent three amino acids, and new beads are sequentially added to the nascent chain in order to explicitly simulate translation.…”

Improving membrane protein expression by optimizing integration efficiency

“…This explanation leaves open the possibility that improvements to the CG model in terms of its description of tertiary IMP interactions could lead to more robust measures of simulated integration efficiency (34).…”

Molecular simulations of cellular processes

“…Simulating macromolecule stability and interactions in a eukaryotic-like cell requires a large effort for the presence of localized and pervasive structures (Neri et al 2013;Smith et al 2014;Unterberger and Holzapfel 2014;Mak et al 2015Mak et al , 2016Gao et al 2015;Nguyen et al 2016;Popov et al 2016;Reddy and Sansom 2016;Chavent et al 2016;Foffano et al 2016;Niesen et al 2017;Tachikawa and Mochizuki 2017). Future investigations will be devoted to simulating dynamical processes involving the cytoskeleton and the membranes, such as the trafficking of macromolecules and vesicles to their sub-cellular localization (Miller et al 2016).…”