The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations

Karol J Nass,Ioana M Ilie,Manfred J Saller,Arnold J.M Driessen,Amedeo Caflisch,Richard A Kammerer,Xiaodan Li

doi:10.1016/j.bbamem.2021.183825

Abstract

The evolutionary conserved YidC is a unique dual-function membrane protein that adopts insertase and chaperone conformations. The N-terminal helix of Escherichia coli YidC functions as an uncleaved signal sequence and is important for membrane insertion and interaction with the Sec translocon. Here, we report the first crystal structure of Thermotoga maritima YidC (TmYidC) including the N-terminal amphipathic helix (N-AH) (PDB ID: 6Y86). Molecular dynamics simulations show that N-AH lies on the periplasmic side of the membrane bilayer forming an angle of about 15° with the membrane surface. Our functional studies suggest a role of N-AH for the species-specific interaction with the Sec translocon. The reconstitution data and the superimposition of TmYidC with known YidC structures suggest an active insertase conformation for YidC. Molecular dynamics (MD) simulations of TmYidC provide evidence that N-AH acts as a membrane recognition helix for the YidC insertase and highlight the flexibility of the C1 region underlining its ability to switch between insertase and chaperone conformations. A structure-based model is proposed to rationalize how YidC performs the insertase and chaperone functions by re-positioning of N-AH and the other structural elements.

Highlights

YidC belongs to the YidC/Alb3/Oxa1 membrane protein family which is evolutionary conserved from archaea to man [1]
Molecular dynamics (MD) sim ulations of Thermotoga maritima YidC (TmYidC) provide evidence that N-terminal amphipathic helix (N-AH) acts as a membrane recognition helix for the YidC insertase and highlight the flexibility of the C1 region underlining its ability to switch between insertase and chaperone conformations
We propose that N-AH of YidC needs to interact with SecY to allow YidC to perform its function as a chaperone, thereby suggesting a species-specific functional role of N-AH

Summary

Introduction

YidC belongs to the YidC/Alb3/Oxa membrane protein family which is evolutionary conserved from archaea to man [1]. The proteins of this family play an important role in the insertion and folding of membrane proteins in the bacterial, thylakoidal, mitochondrial inner membranes and the eukaryotic endoplasmic reticulum [2,3,4]. The hydrophilic groove within the transmembrane domain (TMD, consisting of the transmembrane helices TM2 to TM6), which represents the catalytic center of the protein. Though sharing rather low sequence similarity, the hydrophilic groove and its ability to form lipid-mediated homo- or hetero-oligomers to promote the efficient protein translocation [2,4] are conserved among the family members. Depletion of the YidC protein results in cell death due to the defective assembly of energy-transducing membrane complexes [5], this makes the YidC protein an attractive antibiotic target

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Results

Conclusion