Electrostatics inside the SecY Translocon

Abstract

SecY constitutes the core of the highly conserved SecYEG translocon complex that governs the translocation or integration of proteins across or into cytoplasmic membranes. Besides its role of guiding nascent membrane protein chains into the lipid bilayer, it also plays an important role in determining transmembrane topology via the so-called positive-inside rule. Site-directed mutations of translocons are known to modify the topology of nascent α-helical segments [1]. We performed molecular dynamics simulations of SecYE from Pyrococcus furiosus [2] embedded in a POPC bilayer. In this structure, SecY is in a partially open ‘primed’ state. It conveniently remained open over the course of a 450 ns simulation due to the presence of lipids wedged between helices TM2b and TM7 (the lateral gate), thus allowing close examination of the electrostatics within the translocon. Within the channel, water dipoles exhibit a preferred orientation, which affects the electrostatic (ES) potential. Time-averaged ES maps reveal a largely positive potential relative to the bulk aqueous phase within the channel except for a strong negative peak at the N-terminus of TM2b. This has implications for the entry of signal sequences into the translocon channel.Research supported by NIH grants RO1 GM74637 and PO1 GM86685.