Modeling the dynamics and regulation of Sec-facilitated protein translocation and membrane integration

We present a novel modeling approach that spans the nanosecond- to minute-timescale dynamics of co-translational protein translocation. Based on detailed all-atom simulations, the method enables direct simulation of both integral membrane protein topogenesis and transmembrane domain (TM) stop-transfer efficiency. Simulations reveal multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the exptl. obsd. dependence of protein topol. on ribosomal translation rate and protein length. We further demonstrate that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon lateral gate, and it is predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equil. and nonequil. processes in protein targeting, and it provides insight into the mol. regulation of the Sec translocon.