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- W2059638277 abstract "Rhodopsin is one of the primary systems for computational studies of G-protein coupled receptor (GPCR) activation pathways [1,2]. Activation occurs through isomerization of its covalently bound ligand, retinal, from an 11-cis to an all-trans conformation. FTIR spectroscopy studies indicated the importance of retinal methyl groups, clearly demonstrating that retinal desmethyl analogs caused a backshift in the activation pathway [3]. Additionally, recent 2H nuclear magnetic resonance (NMR) studies on retinal bound to rhodopsin hint towards a much lower methyl rotation activation barrier than observed in previous MD simulations [4]. Here we report quantum chemical calculations of torsional surfaces of model compounds and molecular dynamics (MD) simulations of the proteolipid complex in full atomic detail, to aid in the interpretation of the body of experimental data. Specifically, by using larger retinal fragments and a higher level of theory (MP2/cc-pVDZ), we are able to accurately reproduce the rotational behavior observed from 2H NMR relaxation data [4]. For example, the relaxation data indicate an unusually low activation energy (Ea) for C9-methyl rotation, due to intraretinal interactions with H7 and H11 of the retinal polyene chain. These results in turn should lead to the ability to begin to simulate the coupling of small- to large-scale motions in rhodopsin activation. Ultimately, these efforts are aimed towards modeling more accurate comparisons to other GPCR proteins. [1] P.-W. Lau et al. (2007) J. Mol. Biol. 372(4) 906-917. [2] K. Martinez-Mayorga et al. (2006) J. Amer. Chem. Soc. 128(51) 16502-16503. [3] R. Vogel et al. (2006) Biochemistry 45(6), 1640-1652. [4] M.F. Brown et al. (2009) Biochim. Biophys. Acta, in press." @default.
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- W2059638277 date "2010-01-01" @default.
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- W2059638277 title "Computational Insights into Retinal Dynamics in Rhodopsin" @default.
- W2059638277 doi "https://doi.org/10.1016/j.bpj.2009.12.3072" @default.
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