Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein

Haley R. Harrington; Matthew H. Zimmer; Laura M. Chamness; Veronica Nash; Wesley D. Penn; Thomas F. Miller; Suchetana Mukhopadhyay; Jonathan P. Schlebach

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. 44, 45 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). 45 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. 44, 46, 47 CGMD simulations of SINV polyprotein biosynthesis suggest the nascent chain samples several different topological isomers (Fig. 5A) , and that its topological heterogeneity persists after the polyprotein has cleared the translocon. TM2 undergoes translocon-mediated membrane integration (Fig. 5A, right) in only 44 ± 4% of the CGMD trajectories in which TM1 is correctly integrated into the membrane. Consistent with expectations, CGMD simulations suggest that the membrane integration efficiency of TM2 is enhanced by the LL mutations (51 ± 4%) and reduced by the EE mutations (11 ± 3%). This finding provides additional evidence that the . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/790444 doi: bioRxiv preprint topological frustration within this domain (see Fig. 3 ) arises primarily from its marginal hydrophobicity.