Unraveling Allostery with Simulations of Rhodopsin Photocycle Intermediates

Abstract

G protein-coupled receptors (GPCRs) are a biomedically important class of membrane proteins, accounting for about one third of all FDA approved drugs. They act as molecular transducers, allosterically passing signals across the cell membrane. This allosteric modulation of GPCR signal is vital to their pertinence as drug targets, but the details of the mechanism are not fully understood. Two prominent hypotheses exist to describe how ligands affect changes in signaling. In the induced fit mechanism, the ligand is predicted to drive the protein to a new conformation. Here, the ligand takes an active role, triggering the conformational changes. By contrast, the conformational equilibrium model of allostery states that multiple functional states of the protein are in equilibrium. In this mechanism, the role of the ligand is subtler; it stabilizes a particular protein conformation by preferential binding. We are using unbiased all-atom molecular dynamics simulations of the GPCR rhodopsin to test the relevancy of these hypotheses. Rhodopsin, the visual photoreceptor, is a unique test case; both the active and inactive protein bind the same ligand, retinal. However, retinal adopts different conformations between the states, and the apo-protein, opsin, is outside the normal functional cycle. using simulations of four systems (apo- and holo-protein in the active and inactive states) we will evaluate the applicability of these allosteric models as well as describe how conserved regions of the protein are involved in activation.