title: Color tuning in binding pocket models of the chlamydomonas-type channelrhodopsins.
abstract: We examined the shift of absorption maxima between the chlamydomonas-type channelrhodopsins (ChRs) and bacteriorhodopsin (BR). Starting from the BR X-ray structure, we modeled the color tuning in the binding pockets of the ChRs by mutating up to 28 amino acids in the vicinity of the chromophore. By applying the efficient self-consistent charge density functional tight binding (SCC-DFTB) method in a quantum mechanical/molecular mechanical (QM/MM) framework, including explicit polarization and calculating excitation energies with the semiempirical OM2/MRCI method and the ab initio SORCI method, we have shown that multiple mutations in the binding pocket of BR causes large hypsochromic shifts that are of the same order as the experimentally observed shifts of the absorption maxima between BR and the ChRs. This study further demonstrates that mutations in the proximity of the Schiff base and complex counterion lead to a stronger but more flexible interaction with the retinal, which could serve as a possible explanation for the spectral patterns found in the ChRs.
authors.affiliation: Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Kai
authors.initials: K
authors.lastname: Welke
authors.forename: Jan S
authors.initials: JS
authors.lastname: Frähmcke
authors.forename: Hiroshi C
authors.initials: HC
authors.lastname: Watanabe
authors.forename: Peter
authors.initials: P
authors.lastname: Hegemann
authors.forename: Marcus
authors.initials: M
authors.lastname: Elstner
mesh_terms: D000042:Absorption; D000595:Amino Acid Sequence; D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D002138:Calibration; D002696:Chlamydomonas; D003116:Color; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D011789:Quantum Theory; D025603:Sensory Rhodopsins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D044446:Volvox
chemical_list: D010940:Plant Proteins; D025603:Sensory Rhodopsins; D001436:Bacteriorhodopsins