NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study.
We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.
Röhrig
Ute F
UF
Ludwig Institute for Cancer Research, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland.
Sebastiani
Daniel
D
D002244:Carbon / Q000737:chemistry; D003624:Darkness; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D011522:Protons; D012243:Rhodopsin / Q000737:chemistry*
D011522:Protons; C015017:bathorhodopsin; D002244:Carbon; D012243:Rhodopsin