Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques.

Davide Provasi,Juan Carlos Mobarec,Marta Filizola,Ana Negri,Marta Camacho Artacho,Ruth Nussinov

doi:10.1371/journal.pcbi.1002193

Davide Provasi, Juan Carlos Mobarec + Show 4 more

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https://doi.org/10.1371/journal.pcbi.1002193

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Abstract

Extensive experimental information supports the formation of ligand-specific conformations of G protein-coupled receptors (GPCRs) as a possible molecular basis for their functional selectivity for signaling pathways. Taking advantage of the recently published inactive and active crystal structures of GPCRs, we have implemented an all-atom computational strategy that combines different adaptive biasing techniques to identify ligand-specific conformations along pre-determined activation pathways. Using the prototypic GPCR β2-adrenergic receptor as a suitable test case for validation, we show that ligands with different efficacies (either inverse agonists, neutral antagonists, or agonists) modulate the free-energy landscape of the receptor by shifting the conformational equilibrium towards active or inactive conformations depending on their elicited physiological response. Notably, we provide for the first time a quantitative description of the thermodynamics of the receptor in an explicit atomistic environment, which accounts for the receptor basal activity and the stabilization of different active-like states by differently potent agonists. Structural inspection of these metastable states reveals unique conformations of the receptor that may have been difficult to retrieve experimentally.

Highlights

G-protein coupled receptors (GPCRs) are versatile signaling proteins that functionally couple a host of extracellular stimuli to intracellular effectors, mediating several vital cellular responses
Compelling evidence referred to as ‘functional selectivity’ shows that ligands with varied efficacies can stabilize different GPCR conformations that may selectively interact with different intracellular proteins, and induce different biological responses
We propose here a computational strategy that enables identification of the specific conformations assumed by a GPCR when interacting with ligands that elicit different physiological responses

Summary

Introduction

G-protein coupled receptors (GPCRs) are versatile signaling proteins that functionally couple a host of extracellular stimuli to intracellular effectors, mediating several vital cellular responses. Very recently have high-resolution crystal structures of agonist-bound GPCRs started to appear in the literature [10,11,12,13,14,15]. Possibly restrained by crystallization conditions, not all these agonist-bound structures present the features that are usually attributed to an active GPCR conformation, most typically: the large outward movement of transmembrane helix 6 (TM6) with respect to the center of the receptor helical bundle, which is accompanied by the disruption of an important salt bridge between the conserved D/E3.49-R3.50 pair and E6.30, commonly referred to as the ‘‘ionic lock’’. We direct the reader elsewhere (e.g., [17,18]) for recent reviews of all the relevant structural changes that have been attributed by various biophysical techniques to active forms of GPCRs

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