title: Conformational and Thermodynamic Landscape of GPCR Activation from Theory and Computation.
abstract: We present a hybrid computational methodology to predict multiple energetically accessible conformations for G protein-coupled receptors (GPCRs) that might play a role in binding to ligands and different signaling partners. To our knowledge, this method, termed ActiveGEnSeMBLE, enables the first quantitative energy profile for GPCR activation that is consistent with the qualitative profile deduced from experiments. ActiveGEnSeMBLE starts with a systematic coarse grid sampling of helix tilts/rotations (∼13 trillion transmembrane-domain conformations) and selects the conformational landscape based on energy. This profile identifies multiple potential active-state energy wells, with the TM3-TM6 intracellular distance as an approximate activation coordinate. These energy wells are then sampled locally using a finer grid to find locally minimized conformation in each energy well. We validate this strategy using the inactive and active experimental structures of β2 adrenergic receptor (hβ2AR) and M2 muscarinic acetylcholine receptor. Structures of membrane-embedded hβ2AR along its activation coordinate are subjected to molecular-dynamics simulations for relaxation and interaction energy analysis to generate a quantitative energy landscape for hβ2AR activation. This landscape reveals several metastable states along this coordinate, indicating that for hβ2AR, the agonist alone is not enough to stabilize the active state and that the G protein is necessary, consistent with experimental observations. The method's application to somatostatin receptor SSTR5 (no experimental structure available) shows that to predict an active conformation it is better to start from an inactive structure template based on a close homolog than to start from an active template based on a distant homolog. The energy landscape for hSSTR5 activation is consistent with hβ2AR in the role of the G protein. These results demonstrate the utility of the ActiveGEnSeMBLE method for predicting multiple conformations along the pathways for activating GPCRs and the corresponding energy landscapes, thereby providing detailed structural insights into the initial molecular events of GPCR function that are not easily accessible by experiments.
authors.affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, California.
authors.forename: Sijia S
authors.initials: SS
authors.lastname: Dong
authors.affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, California. Electronic address: wag@wag.caltech.edu.
authors.forename: William A
authors.initials: WA
authors.lastname: Goddard
authors.affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, California; Department of Biomedical Sciences and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California. Electronic address: abrolr@csmc.edu.
authors.forename: Ravinder
authors.initials: R
authors.lastname: Abrol
mesh_terms: D058666:Adrenergic beta-2 Receptor Agonists / Q000378:metabolism; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D009010:Monte Carlo Method; D011485:Protein Binding; D011487:Protein Conformation; D055550:Protein Stability; D017433:Protein Structure, Secondary; D043585:Receptor, Muscarinic M2 / Q000378:metabolism; D018343:Receptors, Adrenergic, beta-2 / Q000378:metabolism; D043562:Receptors, G-Protein-Coupled / Q000378:metabolism*; D017481:Receptors, Somatostatin / Q000378:metabolism; D012399:Rotation; D013816:Thermodynamics
chemical_list: D058666:Adrenergic beta-2 Receptor Agonists; D043585:Receptor, Muscarinic M2; D018343:Receptors, Adrenergic, beta-2; D043562:Receptors, G-Protein-Coupled; D017481:Receptors, Somatostatin; C094573:somatostatin receptor 5