Excited states of GFP chromophore and active site studied by the SAC‐CI method: Effect of protein‐environment and mutations

Abstract

Excited states of fluorescent proteins were studied using symmetry-adapted cluster-configuration interaction (SAC-CI) method. Protein-environmental effect on the excitation and fluorescence energies was investigated. In green fluorescent protein (GFP), the overall protein-environmental effect on the first excitation energy is not significant. However, glutamine (Glu) 94 and arginine (Arg96) have the red-shift contribution as reported in a previous study (Laino et al., Chem Phys 2004, 298, 17). The excited states of GFP active site (GFP-W22-Ser205-Glu222-Ser65) were also calculated. Such large-scale SAC-CI calculations were performed with an improved code containing a new algorithm for the perturbation selection. The SAC-CI results indicate that a charge-transfer state locates at 4.19 eV, which could be related to the channel of the photochemistry as indicated in a previous experimental study. We also studied the excitation and fluorescence energies of blue fluorescent protein, cyan fluorescent protein, and Y66F. The SAC-CI results are very close to the experimental ones. The protonation state of blue fluorescent protein was determined. Conformation of cyan fluorescent protein indicated by the present calculation agrees to the experimentally observed structure.

Fluorescence of a Histidine-Modified Enhanced Green Fluorescent Protein (EGFP) Effectively Quenched by Copper(II) Ions. Part II. Molecular Determinants

“…The results regarding to planar geometries are in good agreement with those reported in previous studies [20,35]. It can be seen, that the HOMO orbital has π-bonding and antibonding character on the γ and β bond, respectively.…”

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

“…When performing such simulations, questions of accuracy and speed of calculations are the important issues for quick prediction of spectral bands in mutated proteins, which is a typical request from experimentalists. At one extreme, 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; however, time and computational resources are quite demanding for these approaches to be routinely applied to a series of calculations.…”

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

“…Similar conclusions were drawn in a SAC-CI based QM/MM study in ref. [262], which dealt with excitation and fluorescence energies of a variety of GFP-like proteins. ONIOM-based studies of GFP mutants are presented in ref.…”