Exploring the free-energy landscape of GPCR activation

Abstract

G-protein–coupled receptors (GPCRs) are a large group of membrane-bound receptor proteins that are involved in a plethora of diverse processes (e.g., vision, hormone response). In mammals, and particularly in humans, GPCRs are involved in many signal transduction pathways and, as such, are heavily studied for their immense pharmaceutical potential. Indeed, a large fraction of drugs target various GPCRs, and drug-development is often aimed at GPCRs. Therefore, understanding the activation of GPCRs is a challenge of major importance both from fundamental and practical considerations. And yet, despite the remarkable progress in structural understanding, we still do not have a translation of the structural information to an energy-based picture. Here we use coarse-grained (CG) modeling to chart the free-energy landscape of the activation process of the β-2 adrenergic receptor (β2AR) as a representative GPCR. The landscape provides the needed tool for analyzing the processes that lead to activation of the receptor upon binding of the ligand (adrenaline) while limiting constitutive activation. Our results pave the way to better understand the biological mechanisms of action of the β2AR and GPCRs, from a physical chemistry point of view rather than simply by observing the receptor’s behavior physiologically.

A free‐energy landscape for the glucagon‐like peptide 1 receptor GLP1R

“…The open state, however, becomes more dominant when the G protein is bound to the active receptor, as seen in our energy landscape and in the cited studies above. This is in line with the notion that upon binding to the activated receptor, the G protein undergoes the changes required to release GDP and induce signal transduction (separation of the AHD and the RD, termed opening in the current study; and ordering of the α5‐β6 segment; see Reference ). However, there are some discrepancies in this respect between expected trends and our computed energies.…”

“…Interestingly, the G‐protein α subunit conformation in PDB ID 5VAI is very similar to the conformation of the β2AR (the subject of our previous study, PDB ID 3SN6). Consequently, we assume that it should harbor the same conformation for the missing fragments and subunits.…”

“…Consequently, we assume that it should harbor the same conformation for the missing fragments and subunits. Therefore, we took those missing parts of the G protein directly from the models of our previous study . When different fragments were connected, the connections were refined using SWISS‐MODEL, and finally individual missing atoms were added using the CHARMM‐GUI server .…”

“…For the receptor, active and inactive conformations were taken from PDB 5VAI and 5VEX (monomer A), respectively. For the G‐protein: open‐ordered, open‐disordered, and closed states were based on 3SN6, 5JS8, and 1GP2, respectively (see our previous study for more details). All amino‐acid sequences were modified to match the sequences from AAR05444.1 ( Homo sapiens GLP1R; 29‐421) for the receptor; EAX11358.1 ( H. sapiens glucagon; 181‐210) for GLP‐1; and NP_000507.1 ( H. sapiens G(s)α; 9‐394), NP_032168.1 ( Mus musculus G(s)β; 2‐340), and NP_034445.1 ( M. musculus G(s)γ; 5‐62) for G protein subunits α, β, and γ; respectively; all accessions are from NCBI GenBank.…”

“…Here, we conducted extensive studies on GLP1R and its complexes with cellular partners and its agonist, using computational and modeling techniques. We calculated and constructed free‐energy landscapes for GLP1R activation, similar to our recent study on the β 2 AR . The aim of this study was to achieve a high level of understanding of the molecular and energetic details of GLP1R activation.…”