Paper Citing NAMD - Abstract
Bhattacharya, Supriyo; Hall, Spencer E.; Vaidehi, Nagarajan
Agonist-induced conformational changes in bovine rhodopsin: Insight into activation of G-protein-coupled receptors
JOURNAL OF MOLECULAR BIOLOGY, 382:539-555, OCT 3 2008
Activation of G-protein-coupled receptors (GPCRs) is initiated by conformational changes in the transmembrane (TM) helices and the intra- and extracellular loops induced by ligand binding. Understanding the conformational changes in GPCRs leading to activation is imperative in deciphering the role of these receptors in the pathology of diseases. Since the crystal structures of activated GPCRs are not yet available, computational methods and biophysical techniques have been used to predict the structures of GPCR active states. We have recently applied the computational method LITiCon to understand the ligand-induced conformational changes in beta(2)-adrenergic receptor by ligands of varied efficacies. Here we report a study of the conformational changes associated with the activation of bovine rhodopsin for which the crystal structure of the inactive state is known. Starting from the inactive (dark) state, we have predicted the TM conformational changes that are induced by the isomerization of 11-cis retinal to all-trans retinal leading to the fully activated state, metarhodopsin II. The predicted active state of rhodopsin satisfies all of the 30 known experimental distance constraints. The predicted model also correlates well with the experimentally observed conformational switches in rhodopsin and other class A GPCRs, namely the breaking of the ionic lock between R135(3.50) at the intracellular end of TM3 (part of the DRY motif) and E247(6.30) on TM6, and the rotamer toggle switch on W265(6.48) on TM6. We observe that the toggling of the W265(6.48) retainer modulates the bend angle of TN46 around the conserved proline. The rotamer toggling is facilitated by the formation of a water wire connecting S298(7.45), W265(6.48) and H211(5.46). As a result, the intracellular ends of TMs 5 and 6 move outward from the protein core, causing large conformational changes at the cytoplasmic interface. The predicted outward movements of TM5 and TM6 are in agreement with file recently Published crystal structure of opsin, which is proposed to be close to the active-state structure. In the predicted active state, several residues in the intracellular loops, such as R69, V139(3.54), T229, Q237, Q239, S240, T243 and V250(6.33), become more water exposed compared to the inactive state. These residues may be involved in mediating the conformational signal from the receptor to the G protein. From mutagenesis studies, some of these residues, Such as V139(3.54), T229 and V250(6.33), are already implicated in G-protein activation. The predicted active state also leads to the formation of new stabilizing interhelical hydrogen-bond contacts, such as those between W265(6.48) and H211(5.46) and E122(3.37) and C167(4.56). These hydrogen-bond contacts serve as potential conformational switches offering new opportunities for future experimental investigations. The calculated retinal binding energy surface shows that binding of an agonist makes the receptor dynamic and flexible and accessible to many conformations, while binding of an inverse agonist traps the receptor in the incative state and makes the other conformations inaccessible. (C) 2008 Elsevier Ltd. All rights reserved.
