Exploring the Thermodynamics of Activation Pathways of Bovine Rhodopsin with Fast Molecular Dynamics Simulations

Abstract

Recent progress made in the understanding of the structure and function of G-protein coupled receptors (GPCRs) points to compelling biophysical and crystallographic evidence for distinct conformational changes of the prototypical family member bovine rhodopsin/opsin upon illumination. To investigate possible activation pathways of bovine rhodopsin from an early inactive intermediate (lumirhodopsin) produced by the cis-trans photoisomerization of its retinal chromophore to an activated ligand-bound opsin-like conformation of the protein, we carried out several independent biased molecular dynamics simulations of the receptor in an explicit dipalmitoylphosphatidylcholine (DPPC) membrane bilayer. The simulations revealed significantly different activation pathways between inactive and opsin-like activated forms of bovine rhodopsin, whose thermodynamic behavior was evaluated by metadynamics using as reaction coordinates both the position along the identified representative pathways, and the distance from them. The results point to three common metastable states that are likely to correspond to a photoactivated deprotonated Meta I-380/Meta IIa, and two different Meta IIb-like intermediates of bovine rhodopsin. Inferences from these molecular models are expected to shed new light into mechanisms of allosteric modulation of rhodopsin function.