Retinal Makes Concerted Conformational Changes During Early Stages of Rhodopsin Activation

Abstract

G protein-coupled receptors (GPCRs) are a biomedically important class of integral membrane proteins. Many details of their activation mechanism are still unknown. Notably, the role played by protein-ligand interactions remains elusive. In the present work, we combined microsecond-scale all-atom molecular dynamics (MD) simulations with solid-state 2H NMR to study the behavior of rhodopsin-the mammalian dim-light receptor-in the presence of either 11-cis or all-trans retinal. In order to validate our simulations, we directly calculated the theoretical 2H NMR lineshape for retinal bound to rhodopsin in aligned bilayers [1]. To do this we applied 2H NMR lineshape theory [2] with an iterative refinement procedure. These results corroborate our previous work, [3,4] revealing a highly dynamic ligand. Our data showed that retinal made a dramatic conformational change as the protein transitioned between the dark state and the Meta-I intermediate. A concerted elongation of the ligand defined this change. Simultaneously, (i) the ligand became more torsionally dynamic, (ii) conserved residues in the binding pocket reorganized, and (iii) there was a substantial influx of water into the G protein binding cleft. These changes occur only in simulations containing the all-trans form of retinal, revealing an intriguing picture of the early stages of GPCR activation. Importantly, our results reconcile two disparate experimental crystal structures, where retinal was found in the opposite orientation. [1] Martinez-Mayorga, K., et al., (2006) JACS128,16502. [2] Nevzorov, A., et al., (1999) JACS121, 7636. [3] Struts, A., et al., (2007) JMB372, 50. [4] Struts, A., et al., (2011) PNAS108, 8263.