Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics.
A major current focus of structural work on G-protein-coupled receptors (GPCRs) pertains to the investigation of their active states. However, for virtually all GPCRs, active agonist-bound intermediate states have been difficult to characterize experimentally owing to their higher conformational flexibility, and thus intrinsic instability, as compared to inactive inverse agonist-bound states. In this work, we explored possible activation pathways of the prototypic GPCR bovine rhodopsin by means of biased molecular dynamics simulations. Specifically, we used an explicit atomistic representation of the receptor and its environment, and sampled the conformational transition from the crystal structure of a photoactivated deprotonated state of rhodopsin to the low pH crystal structure of opsin in the presence of 11-trans-retinal, using adiabatic biased molecular dynamics simulations. We then reconstructed the system free-energy landscape along the predetermined transition trajectories using a path collective variable approach based on metadynamics. Our results suggest that the two experimental endpoints of rhodopsin/opsin are connected by at least two different pathways, and that the conformational transition is populated by at least four metastable states of the receptor, characterized by a different amplitude of the outward movement of transmembrane helix 6.
Provasi
Davide
D
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, USA.
Filizola
Marta
M
D019943:Amino Acid Substitution; D000818:Animals; D002417:Cattle; D003198:Computer Simulation; D003459:Crystallins; D006863:Hydrogen-Ion Concentration; D008565:Membrane Proteins / Q000737:chemistry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation / Q000706:statistics & numerical data*; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D043562:Receptors, G-Protein-Coupled / Q000819:agonists / Q000737:chemistry* / Q000378:metabolism; D017948:Retinal Rod Photoreceptor Cells / Q000737:chemistry*; D012172:Retinaldehyde / Q000737:chemistry*; D012243:Rhodopsin / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
D003459:Crystallins; D008565:Membrane Proteins; D043562:Receptors, G-Protein-Coupled; D012243:Rhodopsin; D012172:Retinaldehyde