title: The thermal isomerization of the GFP chromophore: A computational study.
abstract: We present a density functional theory (B3LYP) study of the isomerization of 4-hydroxybenzylidene-1,2-dimethyl-imidazolinone (HOBDI), which is to mimic the green fluorescent protein (GFP) chromophore, in the ground state promoted by a nucleophile. Four solvents with different polarity, water, DMSO, methanol, and benzene, have been used to characterize the nucleophile assisted mechanism. The former three solvents have been used as nucleophile to participate in the reaction, while in benzene, we use n-propylamine as the nucleophile. When water, methanol and n-propylamine are used as nucleophile, the isomerization is characterized as a three-step process and the addition of the nucleophile is the rate-determining step. A proton transfer from the nucleophile to the oxygen of imidazolinone (O(1)) is observed during the addition step, which stabilizes the negative charge on O(1) due to the reduction of the C(1)[double bond, length as m-dash]C(2) double bond. The energy barrier to the reaction increases in the order of CH(3)OH <or= water < n-propylamine, which is consistent with the experimental data. Whereas in DMSO, the calculations predict a one-step reaction for the isomerization starting from the zwitterionic state with a high barrier of 26.8 kcal mol(-1), in accord with the slow reaction observed experimentally. Our study suggests that the ability of a nucleophile to assist the thermal isomerization of HOBDI mainly depends on its ability to give a proton upon the addition of the nucleophile to the substrate.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH-8093, Zürich, Switzerland. wfvgn@igc.phys.chem.ethz.ch.
authors.forename: Dongqi
authors.initials: D
authors.lastname: Wang
authors.forename: Thomas
authors.initials: T
authors.lastname: Merz
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
mesh_terms: D003116:Color; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D049452:Green Fluorescent Proteins / Q000737:chemistry*; D007536:Isomerism; D007700:Kinetics; D000432:Methanol / Q000737:chemistry; D008958:Models, Molecular; D011437:Propylamines / Q000737:chemistry; D011487:Protein Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D011437:Propylamines; D012997:Solvents; D014867:Water; D049452:Green Fluorescent Proteins; D000432:Methanol; D004121:Dimethyl Sulfoxide