Visualizing small molecule binding in membrane protein by single particle cryo-EM

[Speaker] Yifan Cheng:1
1:Biochemistry and Biophysics, HHMI/University of California San Francisco, USA

In the last few years, major technological breakthroughs, particularly the development of new direct electron detection cameras and associated technologies, have enabled single particle cryogenic electron microscopy (cryo-EM) to become the technique of choice for high-resolution structure determination of many challenging biological macromolecules. Atomic structures of many membrane proteins, particularly ion channels, that are refractory to crystallization have now determined by this method, including our own work of determining the atomic structures of TRPV1, TRPA1 and TPRM4. A recent technological development in single particle cryo-EM of integral membrane protein is to enable atomic structure determination of integral membrane proteins in a native or native-like lipid bilayer environment. In many recent cryo-EM studies, integral membrane proteins are reconstituted into native like lipid bilayer environment, using various lipid-protein nanoparticle techniques including lipid nanodisc, saposin based Salipro nanoparticles, or the styrene-maleic acid (SMA) copolymer based native lipid nanodisc. By reconstituting integral membrane proteins into artificial or near native lipid bi-layer environment, it is now feasible to use single particle cryo-EM for studying specific protein - lipid interactions, and to visualize binding of small pharmacological substances in membrane protein in lipid environment.

Recently, we determined atomic structures of nanodisc-embedded TRPV1 in three different conformations. These structures revealed locations of some annular and regulatory lipids that form specific interactions with the channel. Such specific phospholipid interactions enhance binding of a spider toxin to TRPV1 through formation of a tripartite complex. Our structures also reveal that, in the absence of vanilloid agonist, a phosphatidylinositol lipid occupies the capsaicin-binding site of TRPV1, providing important clues about physiological mechanisms of channel regulation.
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