An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

Abstract

YidC is a membrane protein that facilitates the insertion of newly synthesized proteins into lipid membranes. Through YidC, proteins are inserted into the lipid bilayer via the SecYEG-dependent complex. Additionally, YidC functions as a chaperone in protein folding processes. Several studies have provided evidence of its independent insertion mechanism. However, the mechanistic details of the YidC independent protein insertion mechanism remain elusive at the molecular level. This study elucidates the insertion mechanism of YidC at an atomic level through a combination of equilibrium and non-equilibrium molecular dynamics (MD) simulations. Different docking models of YidC-Pf3 in the lipid bilayer were built in this study to better understand the insertion mechanism. To conduct a complete investigation of the conformational difference between the two docking models developed, we used classical molecular dynamics simulations supplemented with a non-equilibrium technique. Our findings indicate that the YidC transmembrane (TM) groove is essential for this high-affinity interaction and that the hydrophilic nature of the YidC groove plays an important role in protein transport across the cytoplasmic membrane bilayer to the periplasmic side. At different stages of the insertion process, conformational changes in YidC’s TM domain and membrane core have a mechanistic effect on the Pf3 coat. Furthermore, during the insertion phase, the hydration and dehydration of the YidC’s hydrophilic groove are critical. These demonstrate that Pf3 interactions with the membrane and YidC vary in different conformational states during the insertion process. Finally, this extensive study directly confirms that YidC functions as an independent insertase.

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

“…Previous studies have revealed that the YidC transmembrane (TM) region is crucial for membrane protein insertion mechanism 19,75,76 . In order to examine the impact of deleting the PD and C2 loop on the TM helices, the helical angle between each pair of TMs was measured in this work (Fig.…”

“…Å. The interhelical angles were determined as the angle between the third main axes of the respective helices 19,60,67,70,71 . The selection of the TM helices and other sub-domains are as indicated: TM1 (355-388); TM2 (423-442); TM3 (466-479); TM4 (497-508); TM5 (511-528);…”

“…A VMD plugin was used to analyze salt bridge interactions by measuring the distance between the oxygen atoms of acidic residues and the nitrogen atoms of basic residues with a cut-off distance of 4 Å. The interhelical angles were determined as the angle between the third main axes of the respective helices 19,60,67,70,71 . The selection of the TM helices and other sub-domains are as indicated: TM1 (355-388); TM2 (423-442); TM3 (466-479); TM4 (497-508); TM5 (511-528); C1 area (380-420); C2 loop (480-492); and PD (49-326) (Fig.…”

“…To analyze the water inside the groove region, we counted the number of water molecules within 5 Å of R366. Principle component analysis (PCA) was performed for each trajectory using PRODY 19,60,72 , taking only protein C α atoms into account.…”

“…In the past, gram-positive bacterial YidC insertase has been widely researched 15,19,45,46 . The significance of the extra PD region in gram-negative YidC is not fully understood, yet.…”