Abstract
An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large- and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments.
Highlights
Knowledge of a detailed picture of the events occurring in the chromophore-containing domains of photosensing proteins at atomic resolution is important for a rational design of novel fluorescent proteins with improved properties
Multiple attempts to apply inexpensive TD density functional theory (DFT) [33] and ZINDO [34] methods to evaluate vertical excitation energies for model systems composed of the chromophore and small fractions of the environmental molecular groups of protein have often resulted in uncertain conclusions
The ZINDO results for the absorption band maxima of the isolated chromophores are 556 nm for the trans isomer and 569 nm for the cis isomer
Summary
Knowledge of a detailed picture of the events occurring in the chromophore-containing domains of photosensing proteins at atomic resolution is important for a rational design of novel fluorescent proteins with improved properties. Elaborate approaches based on quantum mechanics-molecular mechanics (QM/MM) optimization of geometry coordinates in the chromophore-containing domains, followed by expensive ab initio calculations of excitation energies (e.g., by using versions of configuretion interaction (CI) and perturbation theory-based methods, CASPT2 and MCQDPT2), are described in the literature [4,10,13,14,20,22,27,30,31,32] The significance of these approaches is highly recognized; time and computational resources are quite demanding for these approaches to be routinely applied to a series of calculations. Since the first calculations for the DsRed protein [1], in which the authors demonstrated that ZINDO provided reasonable estimates for absorption bands, and TD DFT was highly inferior to ZINDO, the progress along this line has been fairly slow
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