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Proceedings Paper

Modeling trans-cis chromophore isomerization for the asFP595 kindling protein
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Paper Abstract

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.

Paper Details

Date Published: 3 February 2007
PDF: 5 pages
Proc. SPIE 6449, Genetically Engineered and Optical Probes for Biomedical Applications IV, 64490O (3 February 2007); doi: 10.1117/12.699356
Show Author Affiliations
Bella L. Grigorenko, M.V. Lomonosov Moscow State Univ. (Russia)
Alexander V. Nemukhin, M.V. Lomonosov Moscow State Univ. (Russia)
N.M. Emanuel Institute of Biochemical Physics (Russia)

Published in SPIE Proceedings Vol. 6449:
Genetically Engineered and Optical Probes for Biomedical Applications IV
Samuel Achilefu; Alexander Pavlovich Savitsky; Rebekka M. Wachter; Darryl J. Bornhop; Ramesh Raghavachari, Editor(s)

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