title: QM/MM-Based Calculations of Absorption and Emission Spectra of LSSmOrange Variants.
abstract: The goal of this computational work is to gain new insight into the photochemistry of the fluorescent protein (FP) LSSmOrange. This FP is of interest because besides exhibiting the eponymous large spectral shift (LSS) between the absorption and emission energies, it has been experimentally observed that it can also undergo a photoconversion process, which leads to a change in the absorption wavelength of the chromophore (from 437 to 553 nm). There is strong experimental evidence that this photoconversion is caused by decarboxylation of a glutamate located in the close vicinity of the chromophore. Still, the exact chemical mechanism of the decarboxylation process as well as the precise understanding of structure-property relations in the measured absorption and emission spectra is not yet fully understood. Therefore, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are performed to model the absorption and emission spectra of the original and photoconverted forms of LSSmOrange. The necessary force-field parameters of the chromophore are optimized with CGenFF and the FFToolkit. A thorough analysis of QM methods to study the excitation energies of this specific FP chromophore has been carried out. Furthermore, the influence of the size of the QM region has been investigated. We found that QM/MM calculations performed with time-dependent density functional theory (CAM-B3LYP/D3/6-31G*) and QM calculations performed with the semiempirical ZIndo/S method including a polarizable continuum model can describe the excitation energies reasonably well. Moreover, already a small QM region size seems to be sufficient for the study of the photochemistry in LSSmOrange. Especially, the calculated ZIndo spectra are in very good agreement with the experimental ones. On the basis of the spectra obtained, we could verify the experimentally assigned structures.
authors.affiliation: Department of Chemistry, Quantum Chemistry and Physical Chemistry Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
authors.forename: Maike
authors.identifier: 0000-0003-0944-8605
authors.initials: M
authors.lastname: Bergeler
authors.affiliation: Department of Chemistry, Quantum Chemistry and Physical Chemistry Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Mizuno
authors.affiliation: Department of Chemistry, Quantum Chemistry and Physical Chemistry Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
authors.forename: Eduard
authors.initials: E
authors.lastname: Fron
authors.affiliation: Department of Chemistry, Quantum Chemistry and Physical Chemistry Section ‡Department of Chemistry, Biochemistry, Molecular and Structural Biology Section, §Department of Chemistry, Molecular Imaging and Photonics, KU Leuven , Celestijnenlaan 200F, 3001 Leuven, Belgium.
authors.forename: Jeremy N
authors.identifier: 0000-0002-1728-1596
authors.initials: JN
authors.lastname: Harvey
mesh_terms: D003653:Decarboxylation; D005456:Fluorescent Dyes / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry*; D008027:Light; D056004:Molecular Dynamics Simulation; D055668:Photochemical Processes; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D011789:Quantum Theory; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D005456:Fluorescent Dyes; D011506:Proteins; D011522:Protons; D018698:Glutamic Acid