YidC Insertase of Escherichia coli: Water Accessibility and Membrane Shaping

• Published in: Structure (London) 2017-09, Vol.25 (9), p.1403-1414.e3
• Main Authors: Chen, Yuanyuan, Capponi, Sara, Zhu, Lu, Gellenbeck, Patrick, Freites, J. Alfredo, White, Stephen H., Dalbey, Ross E.
• Format: Article
• Language: English
• Subjects: Alkylation; aqueous access; Cell Membrane - metabolism; Crystallography, X-Ray; Cysteine - chemistry; cysteine-scanning mutagenesis; Escherichia coli - chemistry; Escherichia coli - enzymology; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; membrane protein folding; membrane protein insertion; membrane thinning; Membrane Transport Proteins - chemistry; Membrane Transport Proteins - metabolism; Models, Molecular; molecular dynamics; Molecular Dynamics Simulation; Protein Stability; Protein Structure, Secondary; Water - metabolism; YidC
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2017.07.008

The YidC/Oxa1/Alb3 family of membrane proteins function to insert proteins into membranes in bacteria, mitochondria, and chloroplasts. Recent X-ray structures of YidC from Bacillus halodurans and Escherichia coli revealed a hydrophilic groove that is accessible from the lipid bilayer and the cytoplasm. Here, we explore the water accessibility within the conserved core region of the E. coli YidC using in vivo cysteine alkylation scanning and molecular dynamics (MD) simulations of YidC in POPE/POPG membranes. As expected from the structure, YidC possesses an aqueous membrane cavity localized to the membrane inner leaflet. Both the scanning data and the MD simulations show that the lipid-exposed transmembrane helices 3, 4, and 5 are short, leading to membrane thinning around YidC. Close examination of the MD data reveals previously unrecognized structural features that are likely important for protein stability and function. [Display omitted] •In vivo water accessibility of E. coli YidC was determined using NEM labeling•Accessibility of YidC determined from all-atom MD simulations agrees with NEM results•Compared with crystal structure, YidC structure in POPE:POPG is much more compact•YidC thins the bilayer locally due to interface aromatic residues and salt bridges Chen et al. have measured the in vivo water accessibility of the E. coli YidC insertase and carried out MD simulations of YidC in POPE:POPG bilayers. Water accessibilities are similar for the two approaches. The simulations reveal important structural features that stabilize YidC in membranes.