Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase

YidC is a membrane protein that plays an important role in inserting newly generated proteins into lipid membranes. The Sec-dependent complex is responsible for inserting proteins into the lipid bilayer, and this process is facilitated by YidC in bacteria. In addition, YidC acts as a chaperone during the folding process of proteins. Multiple investigations have conclusively shown that the gram-positive bacterial YidC has Sec-independent insertion mechanisms. Through the use of microsecond-level allatom molecular dynamics (MD) simulations, we have carried out the first in-depth investigation of the YidC protein originating from gram-negative bacteria. This research sheds light on the significance of multiple domains of YidC structure at an atomic level by utilizing equilibrium MD simulations. Specifically, in this research, multiple models of YidC embedded in the lipid bilayer were constructed to characterize the critical role of the C2 loop and the periplasmic domain present in gram-negative YidC, which is absent in its gram-positive counterpart. Based on our results, the C2 loop is responsible for the overall stabilization of the protein, most notably in the transmembrane region, and it also has an allosteric influence on the periplasmic domain. We have found critical inter- and intra-domain interactions that contribute to the stability of the protein and its function. Finally, our study provides a hypothetical Sec-independent insertion mechanism for gram-negative bacterial YidC.