Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome
Figure 9
Folding of the Two-Domain Protein SFVP
(A) Evolution of QN, QC, and QINT during a typical refolding trajectory of the serine protease module of SFVP.
(B) The most populated points in (QN, QC, QINT) space during 100 refolding trajectories. Each point in the (QN, QC, QINT) space is counted only once per trajectory in order to prevent repeated revisiting of the same region in a trajectory from biasing the results. Symbol size and color reflect relative population (large, red symbols being populated in 100% of simulations).
(C) Same as (B), but for ten coupled synthesis–folding simulations.
(D) Snapshot of the moment that native structure is cotranslationally formed; the green chain extending back to the peptidyltransferase active site represents the approximately 28 residues synthesized after the protease module's final residue.