Predicting Cholesterol Interaction Sites on GPCRs using Coarse-Grained MD

ORAL

Abstract

Cholesterol has been shown to be important to the function of G-protein coupled receptors (GPCRs), the largest class of signaling membrane proteins and the largest class of drug targets in the human genome. However, experiments cannot always reveal how a specific GPCR and cholesterol molecule interact. We developed a method based on molecular dynamics (MD) simulations to predict sites on the protein where the cholesterol may interact. A limitation of all-atom MD is the computational cost to sample even a few \textmu s of simulation time. In order to sample longer time scales (tens of \textmu s), coarse-grained MD simulations were preformed and analyzed for several GPCRs, including the beta-2 adrenergic receptor and the cannabinoid receptors CB1 and CB2. The computed off rates ($k_{\mathrm{off}})$ or equivalently, the average waiting time in the bound state, show a difference in cholesterol binding for CB1R and CB2R, where CB1R has been shown to bind to cholesterol and CB2R does not. For the proteins in which cholesterol binds, we identified several residues of interest that agree with electron densities from crystallographic measurements and known cholesterol binding motifs. In summary, we developed a physics-based method to predict cholesterol binding sites in GPCRs (and potentially other membrane proteins) and validated it using experimental data.

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Authors

  • Rick Sexton

    Arizona State University, Department of Physics

  • James Geiger

    Arizona State University, Biodesign Institute, Center for Applied Structural Discovery

  • John Spence

    Brigham Young University, Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, Department of Scientific Research, The Metropolitan Museum of Art, New York, NY 10028, Century Darkroom, Toronto, ON M4M 2S1, Canada, Colorado State University, University of Waterloo, Southern Connecticut State University, Clemson University, Oak Ridge National Laboratory, University of Bordeaux, BYU REU Program, New Mexico State University, Arizona State University, Biodesign Institute, Center for Applied Structural Discovery, University of Utah, University of Hawaii, Johns Hopkins University, Embry-Riddle Aeronautical University, Arizona State University, Utah State University, Department of Physics, United States Air Force Academy, Department of Chemistry, Case Western Reserve University, Air Force Research Laboratory, Wright-Patterson Air Force Base, United States Air Force Academy, Lousiana State University, Brigham Young University - Provo, The University of New Mexico, Department of Physics and Astronomy, Brigham Young University, SLAC National Accelerator Laboratory, Department of Chemistry, Brigham Young University, Department of Materials, Devices, and Energy Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA, Department of Physics, New Mexico State University, Las Cruces, New Mexico 88003, USA, Center for Memory and Recording research, UCSD, Advanced Photon Source, Argonne National Laboratory, University of New Mexico, Los Alamos National Laboratory, University of Chicago

  • John Spence

    Brigham Young University, Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, Department of Scientific Research, The Metropolitan Museum of Art, New York, NY 10028, Century Darkroom, Toronto, ON M4M 2S1, Canada, Colorado State University, University of Waterloo, Southern Connecticut State University, Clemson University, Oak Ridge National Laboratory, University of Bordeaux, BYU REU Program, New Mexico State University, Arizona State University, Biodesign Institute, Center for Applied Structural Discovery, University of Utah, University of Hawaii, Johns Hopkins University, Embry-Riddle Aeronautical University, Arizona State University, Utah State University, Department of Physics, United States Air Force Academy, Department of Chemistry, Case Western Reserve University, Air Force Research Laboratory, Wright-Patterson Air Force Base, United States Air Force Academy, Lousiana State University, Brigham Young University - Provo, The University of New Mexico, Department of Physics and Astronomy, Brigham Young University, SLAC National Accelerator Laboratory, Department of Chemistry, Brigham Young University, Department of Materials, Devices, and Energy Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA, Department of Physics, New Mexico State University, Las Cruces, New Mexico 88003, USA, Center for Memory and Recording research, UCSD, Advanced Photon Source, Argonne National Laboratory, University of New Mexico, Los Alamos National Laboratory, University of Chicago

  • John Spence

    Brigham Young University, Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, Department of Scientific Research, The Metropolitan Museum of Art, New York, NY 10028, Century Darkroom, Toronto, ON M4M 2S1, Canada, Colorado State University, University of Waterloo, Southern Connecticut State University, Clemson University, Oak Ridge National Laboratory, University of Bordeaux, BYU REU Program, New Mexico State University, Arizona State University, Biodesign Institute, Center for Applied Structural Discovery, University of Utah, University of Hawaii, Johns Hopkins University, Embry-Riddle Aeronautical University, Arizona State University, Utah State University, Department of Physics, United States Air Force Academy, Department of Chemistry, Case Western Reserve University, Air Force Research Laboratory, Wright-Patterson Air Force Base, United States Air Force Academy, Lousiana State University, Brigham Young University - Provo, The University of New Mexico, Department of Physics and Astronomy, Brigham Young University, SLAC National Accelerator Laboratory, Department of Chemistry, Brigham Young University, Department of Materials, Devices, and Energy Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA, Department of Physics, New Mexico State University, Las Cruces, New Mexico 88003, USA, Center for Memory and Recording research, UCSD, Advanced Photon Source, Argonne National Laboratory, University of New Mexico, Los Alamos National Laboratory, University of Chicago

  • Wei Liu

    Arizona State University, Biodesign Institute, Center for Applied Structural Discovery

  • Oliver Beckstein

    Arizona State University, USA, Arizona State University, Department of Physics and Center for Biological Physics, Arizona State Univ.