1. MD simulations of cotranslational folding of I27.
MD simulations of cotranslational folding of I27. (A) The 50S subunit of the E. coli ribosome (PDB ID code 3OFR) with I27[L = 35] attached via an unstructured linker. (B) Coarse-grained model for I27 (red) and linker (green), with surrounding ribosomal pseudoatoms in blue. Pseudoatoms colored gray are not used in the simulations. The instantaneous force exerted on the AP is calculated from the variation in the distance x between the C-terminal Pro pseudoatom and the next pseudoatom in the linker (Inset). (C) Average forces exerted on the AP by the unfolded state (Fu, empty symbols) and folded state (Ff, filled symbols) of I27 at different linker lengths L. The average fraction folded I27 for different L,Pf, is shown in cyan on the right axis. Free energy profiles at each linker length are shown in SI Appendix, Fig. S11. (D) Experimental (red square) force profiles for cotranslational folding of I27. Force profiles calculated from simulations using the full kinetic scheme or preequilibrium model are shown by blue circles and cyan triangles, respectively. The rmsd of the fFL between experiment and simulation is 0.08.
Pengfei Tian et al. PNAS 2018;115:48:E11284-E11293
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