Retinal Flips the Script

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Understanding the link between dynamics and function stands as a grand challenge in molecular-scale protein biophysics. The G protein-coupled receptor (GPCR) rhodopsin provides an important case study in this context. Upon absorption of a photon, rhodopsin’s covalently bound ligand retinal is converted from 11-cis to all-trans, which changes the ligand from an inverse agonist to an agonist. Although structures of both the dark state (1) and the activated (Meta-II) state of rhodopsin have been solved (2), exactly how the local conformational change of the ligand is transduced to a global conformational change of the protein and ultimately into transducin activation remains unknown. A surprising development is provided by recently published structures of the active, Meta-II state, which reveal an all-trans retinal rotated 180° about its long axis.

The combination of structural data and molecular-dynamics (MD) simulation has provided key insights into GPCR function, including ligand binding (3) and dynamics (4), the dynamics of the ionic lock motif (5), and the role of lipids in modulating function (6,7). However, direct access to the activation mechanism is not possible by brute-force MD on commodity computing resources, because the physical timescale for the dark state → Meta-II transition exceeds the MD timescale by roughly three orders of magnitude.

Building on previous work (8), Feng et al. (9) have made this problem more tractable through a clever combination of recently published structural data (2), manipulation of the lipid environment, and control of the protonation state of the protein. Beginning from a structure of Meta-II with a flipped, all-trans retinal, the authors selected protonation states and a lipid environment that are expected to back-shift the protein toward the Meta-I conformation. Remarkably, they observe spontaneous back-flip of the retinal under these conditions in two of three simulations. Under conditions (protonation state and lipid environment) that stabilize the Meta-II conformation, they do not observe back-flip of the retinal. They have thus directly corroborated the flip of retinal as a step along the activation pathway of the protein. In addition, this observation reconciles published spectroscopic (10) data by showing that retinal is more dynamic in the Meta-II state than in the dark state, and that the spectroscopic data therefore need to be understood in terms of an ensemble of active conformations.

This last point mirrors recent simulations of both the β2 adrenergic receptor (3) and the A_2A adenosine receptor (4,11) in which some ligands were found to be surprisingly dynamic, even when bound to the protein. We now know that many GPCRs signal via non-G protein pathways in a ligand-dependent way, a phenomenon known as “functional selectivity” (12). The observation that some ligands admit a broader range of protein conformations suggests a possible dynamic mechanism for functional selectivity—activation of one pathway may require a narrower range of conformations, while others respond to a more structurally diverse presentation of the cytoplasmic face. Feng et al. (9) provide a template by which a combination of MD and carefully selected experimental information will together connect GPCR dynamics to function. Considering differences in dynamics under different ligation states offers a potential route to extend the approach toward the problem of functional selectivity.

Editor: Scott Feller.