Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon

The Sec translocon, a protein-conducting channel, consists of a heterotrimeric complex (SecYEG in bacteria and Sec61 alpha beta gamma in eukaryotes) that provides a pathway for secretary proteins to cross membranes, or for membrane proteins to integrate into the membrane. The Sec translocon alone is a passive channel, and association with channel partners, including the ribosome or SecA ATPase in bacteria, is needed for protein translocation. Three recently published crystal structures of SecY are considered to represent the closed (resting state), pre-open (transitional state determined with the bound Fab fragment mimicking SecA interaction), and SecA-bound forms. To elucidate mechanisms of transition between closed and pre-open forms, we performed all-atom molecular dynamics simulations for the pre-open form of Thermus thermophilus SecYE and the closed form of Methanococcus janaschii SecYE beta in explicit solvent and membranes. We found that the closed form of SecY is stable, while the pre-open form without the Fab fragment undergoes large conformational changes toward the closed form. The pre-open form of SecY with Fab remains unchanged, suggesting that the cytosolic interaction mimicking SecA binding stabilizes the pre-open form of SecY. Importantly, a lipid molecule at the lateral gate region appears to be required to maintain the pre-open form in the membrane. We propose that the conformational transition from closed to pre-open states of SecY upon association with SecA facilitates intercalation of phospholipids at the lateral gate, inducing initial entry of the positively charged signal peptide into the channel.