We report the results of quantum mechanical - molecular mechanical (QM/MM) simulations aiming to elucidate the mechanism of kindling of the initially non-fluorescent protein asFP595, which is a mutated variant of the chromoprotein asCP from the sea anemone Anemonia sulcata. asFP595 becomes brightly fluorescent (kindles) with emission at 595 nm in response to intense light irradiation at 568 nm. In simulations, we use the flexible effective fragment QM/MM method with the complete active space self-consistent field (CASSCF) wavefunctions in the quantum part and the AMBER force field parameters in the molecular mechanical part. We analyze the computed scans over potential energy surfaces of the ground and excited electronic states and consider details of the working hypothesis that the trans-cis isomerization of the chromophore group inside the protein is responsible for kindling.
Computational approaches to describe optical spectra of biological chromophores in proteins, in solutions and in the gas phase are discussed. Recently, accurate measurements of spectral properties for the series of chromophores in different media allowed the authors to estimate the positions of the bands with a high accuracy and to challenge theoreticians by stating that the measured S0-S1 transition wavelengths may be used as new benchmark values for the theory. The novel computational approaches based on the multiconfigurational quasidegenerate perturbation theory present the practical means how to adapt the high level methodology for calculations of accurate excitation energies in large biological chromophores. The theory is illustrated for a series of model compounds for which experimental data are available: the retinal molecule in the protonated Shiff-base form, the chromophores from the Green Fluorescent Protein family including the kindling protein asFP595, and the chromophore from the BLUF domain containing photoreceptor proteins.
KEYWORDS: Chromophores, Proteins, Chemical species, Crystals, Systems modeling, Chemistry, Fluorescent proteins, Quantum physics, Quantum computing, Green fluorescent protein
We present the results of modeling properties of the chromophore, 2-acetyl-4-(p-hydroxybenzylidene)-1-methyl-5-
imidazolone (AHBMI), from the newly discovered fluorescent protein asFP595 inside the protein environment by using
the combined quantum mechanical - molecular mechanical (QM/MM) method. In this approach, the chromophore unit
and the side chains of the nearest amino acid residues are assigned to the quantum subsystem. The starting coordinates
of heavy atoms were taken from the relevant crystal structures of the protein. Hydrogen atoms were added manually,
and the structure of the model protein system was optimized by using QM/MM energy minimization for the trans-form
of the chromophore. The Hartree-Fock/6-31G quantum chemical approximation and the AMBER force field parameters
were employed in geometry optimization. The points on potential energy surfaces of the ground and first and second
excited electronic states were computed with the complete active space self-consistent field approximation in the
quantum subsystem under different choices of the QM/MM partitioning. Possible pathways for the trans-cis photo
isomerization presumably responsible for the kindling properties of asFP595 as well as other mechanisms of photo
excitation are discussed.
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