Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin

Abstract

The synergetic effects of multiple rhodopsin mutations on color tuning need to be completely elucidated. Systematic genetic studies and spectroscopy have demonstrated an interesting example of synergetic color tuning between two amino acid residues in conger rhodopsin’s ancestral pigment (p501): — a double mutation at one nearby and one distant residue led to a significant λmax blue shift of 13 nm, whereas neither of the single mutations at these two sites led to meaningful shifts.To analyze the molecular mechanisms of this synergetic color tuning, we performed homology modeling, molecular simulations, and electronic state calculations. For the double mutant, N195A/A292S, in silico mutation analysis demonstrated conspicuous structural changes in the retinal chromophore, whereas that of the single mutant, A292S, was almost unchanged. Using statistical ensembles of QM/MM optimized structures, the excitation energy of retinal chromophore was evaluated for the three visual pigments. As a result, the λmax shift of double mutant (DM) from p501 was −8 nm, while that of single mutant (SM) from p501 was +1 nm. Molecular dynamics simulation for DM demonstrated frequent isomerization between 6-s-cis and 6-s-trans conformers. Unexpectedly, however, the two conformers exhibited almost identical excitation energy, whereas principal component analysis (PCA) identified the retinal-counterion cooperative change of BLA (bond length alternation) and retinal-counterion interaction lead to the shift.

Atomistic design of microbial opsin-based blue-shifted optogenetics tools

“…2 ). The C 6 –C 7 bond can be easily twisted, that is, the potential energy curve along the torsional coordinate is flat 29 30 31 ( Supplementary Fig. 2 ).…”

Structural Model of Channelrhodopsin

“…In the first step, we build a homology model using the DChR sequence and the characteristic sequence pattern of helices A and B. Homology modeling has been successfully applied for structure prediction when the template sequence has high homology with that of the target protein, as recently shown for G protein-coupled receptors (12,13), which have seven transmembrane helices similar to the microbial rhodopsins. Based on the ASR structural template, we construct a three-dimensional structural model, which is subjected to extensive molecular dynamics (MD) simulations to examine its stability and dynamical features.…”

Normal mode analysis and beyond

“…performed time-structure independent component analysis (tICA) [19]. In 2010, Watanabe, H. C., et al performed extended PCA study on the color tuning mechanism of rhodopsin [20]. They added an electronic excitation energy as an additional "coordinate", and successfully illustrated the molecular mechanism of the shift of optical absorption maximum of conger rhodopsin.…”