Dynamic Structure of Retinylidene Ligand of Rhodopsin Probed by Molecular Simulations

Abstract

SummaryRhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the β-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism. We analyzed a total of 23 independent, 100-ns all-atom molecular dynamics simulations for rhodopsin embedded in a lipid bilayer in the microcanonical (N,V,E) ensemble. Analysis of intramolecular fluctuations predicts hydrogen-out-of-plane (HOOP) wagging modes of retinal consistent with those found in Raman vibrational spectroscopy. We show that sampling and ergodicity of the ensemble of simulations are crucial for determining the distribution of conformers of retinal bound to rhodopsin. The polyene chain is rigidly locked into a single, twisted conformation, consistent with the function of retinal as an inverse agonist in the dark state. Most surprisingly, the β-ionone ring is mobile within its binding pocket; interactions are nonspecific and the cavity is sufficiently large to enable structural heterogeneity. We find that retinal occupies two distinct conformations in the dark state, contrary to most previous assumptions. The β-ionone ring can rotate relative to the polyene chain, thereby populating both positively and negatively twisted 6-s-cis enantiomers. This result, while unexpected, strongly agrees with experimental solid-state 2 H NMR spectra. Correlation analysis identifies the residues most critical to controlling mobility of retinal; we find that Trp 265 moves away from the ionone ring prior to any conformational transition. Our findings reinforce how Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. HHS Public Access Graphical AbstractCover. Structure of retinal ligand of G protein-coupled receptor rhodopsin in the inverse agonist form as obtained from molecular simulations.

Retinal Conformation Changes Rhodopsin’s Dynamic Ensemble

“…Our previous work showed that after the 11-cis to all-trans isomerization retinal became more flexible (46,47,67). Here we extend that view to understand how all-trans retinal behaves in the active Meta-II state versus the preactive Meta-I state ( Fig.…”

Location of the Retinal Chromophore in the Activated State of Rhodopsin

“…The absence of line broadening or resonance splitting indicated that we had trapped a spectroscopically well defined Meta II state. Molecular dynamics (MD) simulations and 2 H NMR measurements on rhodopsin have suggested that there are two major conformations of the ␤-ionone ring, one with a positively twisted C6 -C7 single bond and one with a negatively twisted C6 -C7 single bond (33,34). As described below, 13 C chemical shift and DARR NMR measurements suggest that, predominantly, a single conformation exists in rhodopsin and in Meta II.…”

A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-coupled Receptor

“…This follows our protocol previously applied to rhodopsin (30,36,(45)(46)(47). In developing the protocol, we have specifically investigated the consequences of long time constant volume simulations for membrane-GPCR systems, after the volume has been equilibrated to 1 atm of pressure.…”