title: pH-dependent absorption spectra of rhodopsin mutant E113Q: On the role of counterions and protein.
abstract: The absorption spectra of bovine rhodopsin mutant E113Q in solutions were investigated at the molecular level by using a hybrid quantum mechanics/molecular mechanics (QM/MM) method. The calculations suggest the mechanism of the absorption variations of E113Q at different pH values. The results indicate that the polarizations of the counterions in the vicinity of Schiff base under protonation and unprotonation states of the mutant E113Q would be a crucial factor to change the energy gap of the retinal to tune the absorption spectra. Glu-181 residue, which is close to the chromophore, cannot serve as the counterion of the protonated Schiff base of E113Q in dark state. Moreover, the results of the absorption maximum in mutant E113Q with the various anions (Cl-, Br-, I-and NO3-) manifested that the mutant E113Q could have the potential for use as a template of anion biosensors at visible wavelength.
authors.affiliation: State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China.
authors.forename: Panwang
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Alsaedi
authors.affiliation: State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China. Electronic address: zhangyanhg@dicp.ac.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D065966:Absorption, Physicochemical; D000818:Animals; D002417:Cattle; D002712:Chlorides / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D050505:Mutant Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011522:Protons; D011789:Quantum Theory; D012243:Rhodopsin / Q000737:chemistry*; D012545:Schiff Bases / Q000737:chemistry; D012964:Sodium / Q000737:chemistry
chemical_list: D002712:Chlorides; D050505:Mutant Proteins; D011522:Protons; D012545:Schiff Bases; D012243:Rhodopsin; D012964:Sodium
keywords: Anion biosensor; E113Q rhodopsin; Hydrogen-bond; QM/MM; Spectra tuning