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

Hiroshi Watanabe, Yoshiharu Mori, Takashi Tada, Shozo Yokoyama, Takahisa Yamato

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)67-78
Number of pages12
JournalBiophysics
Volume6
DOIs
Publication statusPublished - 2010 Dec 1
Externally publishedYes

Fingerprint

Rhodopsin
Color
Amino Acids
Mutation
Retinal Pigments
Molecular Dynamics Simulation
Principal Component Analysis
Computer Simulation
Spectrum Analysis

Keywords

  • CASPT2
  • Color-tuning mechanism
  • G protein-coupled-receptor
  • Retinal
  • Spectral broadening

ASJC Scopus subject areas

  • Biophysics

Cite this

Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. / Watanabe, Hiroshi; Mori, Yoshiharu; Tada, Takashi; Yokoyama, Shozo; Yamato, Takahisa.

In: Biophysics, Vol. 6, 01.12.2010, p. 67-78.

Research output: Contribution to journalArticle

Watanabe, Hiroshi ; Mori, Yoshiharu ; Tada, Takashi ; Yokoyama, Shozo ; Yamato, Takahisa. / Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. In: Biophysics. 2010 ; Vol. 6. pp. 67-78.
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