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Proc Natl Acad Sci U S A. 2018 Dec 3. pii: 201812526. doi: 10.1073/pnas.1812526115. [Epub ahead of print]

Structure and activity of lipid bilayer within a membrane-protein transporter.

Author information

1
Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298.
2
Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219.
3
Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032.
4
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.
5
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032; jf2192@cumc.columbia.edu wah2@cumc.columbia.edu yguo4@vcu.edu.
6
Department of Biological Sciences, Columbia University, New York, NY 10027.
7
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032.
8
New York Structural Biology Center, New York, NY 10027.
9
Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298; jf2192@cumc.columbia.edu wah2@cumc.columbia.edu yguo4@vcu.edu.

Abstract

Membrane proteins function in native cell membranes, but extraction into isolated particles is needed for many biochemical and structural analyses. Commonly used detergent-extraction methods destroy naturally associated lipid bilayers. Here, we devised a detergent-free method for preparing cell-membrane nanoparticles to study the multidrug exporter AcrB, by cryo-EM at 3.2-Å resolution. We discovered a remarkably well-organized lipid-bilayer structure associated with transmembrane domains of the AcrB trimer. This bilayer patch comprises 24 lipid molecules; inner leaflet chains are packed in a hexagonal array, whereas the outer leaflet has highly irregular but ordered packing. Protein side chains interact with both leaflets and participate in the hexagonal pattern. We suggest that the lipid bilayer supports and harmonizes peristaltic motions through AcrB trimers. In AcrB D407A, a putative proton-relay mutant, lipid bilayer buttresses protein interactions lost in crystal structures after detergent-solubilization. Our detergent-free system preserves lipid-protein interactions for visualization and should be broadly applicable.

KEYWORDS:

AcrB; cryo-EM; nanoparticle; phospholipid; styrene maleic acid copolymer

PMID:
30509977
DOI:
10.1073/pnas.1812526115

Conflict of interest statement

The authors declare no conflict of interest.

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