An Investigation of the YidC-Mediated Membrane Insertion of a Pf3 Coat Protein Using MD Simulations

Abstract

YidC is a bacterial member of the YidC/Alb3/Oxa1 insertase family which mediates the insertion of newly synthesized peptides and proteins in the membrane. Proteins can be inserted into lipid bilayers via the SecYEG complex or through Sec-independent mechanisms. In this molecular dynamics (MD) study, we have developed different docking models of YidC with a nascent Pf3 coat protein in a POPE membrane. Our equilibrium MD simulations show that sequential global conformational changes occur in the transmembrane (TM) helices, cytoplasmic loops and EH1 domains of the YidC which have a prominent role at different stages of insertion mechanism. We have also performed a steered molecular dynamics (SMD) simulation to characterize these conformational changes, using our docking models as a reference. The SMD simulations reveal that a positively charged arginine residue in the hydrophilic groove establishes strong electrostatic interactions with negatively charged Pf3 coat residues over the course of insertion process. Therefore, we propose that the formation of strong interactions between the Pf3 coat protein and YidC hydrophilic groove are essential for the insertion of Pf3 into the lipid bilayer. In addition, our results from equilibrium simulations, such as Pf3 coat interactions with lipids, global, and local conformational changes in YidC domains at different conformational stages are also reappeared in SMD simulation process very similarly. This study thus characterizes the local conformational dynamics of the YidC-Pf3 interaction in the context of a Sec-independent insertion mechanism.