Deciphering the\nInterdomain Coupling in a Gram-Negative\nBacterial Membrane Insertase

YidC is a membrane protein that plays an important role\nin inserting\nnewly generated proteins into lipid membranes. The Sec-dependent complex\nis responsible for inserting proteins into the lipid bilayer in bacteria.\nYidC facilitates the insertion and folding of membrane proteins, both\nin conjunction with the Sec complex and independently. Additionally,\nYidC acts as a chaperone during the folding of proteins. Multiple\ninvestigations have conclusively shown that Gram-positive bacterial\nYidC has Sec-independent insertion mechanisms. Through the use of\nmicrosecond-level all-atom molecular dynamics (MD) simulations, we\nhave carried out an in-depth investigation of the YidC protein originating\nfrom Gram-negative bacteria. This research sheds light on the significance\nof multiple domains of the YidC structure at a detailed molecular\nlevel by utilizing equilibrium MD simulations. Specifically, multiple\nmodels of YidC embedded in the lipid bilayer were constructed to characterize\nthe critical role of the C2 loop and the periplasmic domain (PD) present\nin Gram-negative YidC, which is absent in its Gram-positive counterpart.\nBased on our results, the C2 loop plays a role in the overall stabilization\nof the protein, most notably in the transmembrane (TM) region, and\nit also has an allosteric influence on the PD region. We have found\ncritical inter- and intradomain interactions that contribute to the\nstability of the protein and its function. Finally, our study provides\na hypothetical Sec-independent insertion mechanism for Gram-negative\nbacterial YidC.