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

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.Author summary: Ubiquitous across all kingdoms of life, the Sec translocon is an essential piece of molecular machinery for protein biosynthesis. The translocon is a transmembrane channel that enables the secretion of newly synthesized proteins across the lipid membrane, as well as the integration of protein domains into the membrane interior. Understanding the function and regulation of the translocon is necessary for developing a refined view of early stage protein folding and targeting in the cell. Although computational methods are well suited to elucidating the interactions of the translocon with newly synthesized proteins, conventional simulation techniques are unable to reach the exceedingly long timescales (i.e., minutes) that are relevant for protein biosynthesis. In this work, we present a novel coarse-grained approach that realistically models the ribosome/translocon/nascent-protein complex, while also allowing for the efficient simulation of biological timescales. The coarse-grained model is parameterized on the basis of extensive molecular dynamics simulations and enables the simulation of any nascent protein with only amino-acid sequence information as input. To validate the model, we perform over 26,000 simulations of protein biosynthesis, enabling direct comparison and demonstrating good agreement with a range of experimental studies describing this minute-timescale process.