Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation

Abstract

Rhodopsin has served as the primary model for studying G protein-coupled receptors (GPCRs)—the largest group in the human genome, and consequently a primary target for pharmaceutical development. Understanding the functions and activation mechanisms of GPCRs has proven to be extraordinarily difficult, as they are part of a complex signaling cascade and reside within the cell membrane. Although X-ray crystallography has recently solved several GPCR structures that may resemble the activated conformation, the dynamics and mechanism of rhodopsin activation continue to remain elusive. Notably solid-state 2H NMR spectroscopy provides key information pertinent to how local dynamics of the retinal ligand change during rhodopsin activation. When combined with molecular mechanics simulations of proteolipid membranes, a new paradigm for the rhodopsin activation process emerges. Experiment and simulation both suggest that retinal isomerization initiates the rhodopsin photocascade to yield not a single activated structure, but rather an ensemble of activated conformational states.

Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy

“…Solid-state NMR spectroscopy has been particularly useful in characterizing the structure of dark rhodopsin and its intermediates. Deuterium NMR spectroscopy along with molecular dynamics has provided insights into the structure and dynamics of the retinal chromphore [41], while 13 C and 1 H NMR correlation spectroscopy has been used to probe the retinal structure and its interaction with surrounding amino acids [42, 43] The use of selective pairs of 13 C labels has been useful for characterizing the conformation of the retinal [44] and internuclear 13 C.. 13 C distances in the protein [45]. The receptor structure can be probed in a membrane environment using the native protein sequence or site directed mutants, and low temperature [46] provides a way to trap intermediates.…”

Investigation of Rhodopsin Dynamics in Its Signaling State by Solid-State Deuterium NMR Spectroscopy

“…Once the structure is available, one might qualitatively analyze the dynamical parameters with respect to steric hindrances (10,30), or apply molecular mechanics or quantum mechanical simulations to calculate potential barriers. The results can be compared with experimentally obtained activation energies (31) and used to improve the force field, or refine the protein structure.…”

The G Protein-Coupled Receptor Rhodopsin: A Historical Perspective

“…How this receptor and these waters reorganize during activation needs to be solved. Perhaps a combination of computational [85, 86] and NMR studies [68, 87] will dominate in this area of investigation.…”