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.

Predicted structure of fully activated human bitter taste receptor TAS2R4 complexed with G protein and agonists

“…The constructed protein was immersed into 1-palmitoyl-2-oleoylsn-glycero-3-phosphocholine (POPC) lipid bilayer, using a preequilibrated bilayer structure with 277 molecules (Dong et al, 2016). The protein and lipid membrane were placed in a~100 Â 100 Â 140 Å 3 box, with water molecules and 100 mM concentration of ions (sodium and chloride).…”

Vibrational Energy in Proteins Correlates with Topology

“…This might be associated with the fact that the inactive state features larger thermodynamic stability than the active one. 21 These larger CDT i values in the inactive state can be ascribed to larger vibrational mode frequencies in such states (Figure S2). This determines larger energy gaps between the harmonic oscillators, which in turn hampers Evib_xc processes.…”

“…The inactive state ones are larger and hence the Evib_xc processes are slower. This might be associated with the fact that the inactive state features larger thermodynamic stability than the active one 21 .…”

Functional Amyloids and their Possible Influence on Alzheimer Disease

“…Through studying the binding of octreotide with SSTR2, it was discovered that Asn276 and Phe294 in transmembrane domains VI and VII stabilize the interaction with Phe7, Trp8 and Thr10 within the SST binding epitope, as well as the Cys3-Cys14 disulfide bridge. Binding is further stabilized by an electrostatic interaction between Lys9 on SST-14 and Asp137 on transmembrane domain III of the receptor 148,179 .…”