QM/MM study of the monomeric red fluorescent protein DsRed.M1

Elsa Sanchez-Garcia, Markus Doerr, Ya-Wen Hsiao, Walter Thiel
Journal of Physical Chemistry. B 2009 December 31, 113 (52): 16622-31
We report a combined quantum mechanical/molecular mechanical (QM/MM) study of the DsRed.M1 protein using as QM component the self-consistent charge density functional tight-binding (SCC-DFTB) method in molecular dynamics (MD) simulations and hybrid density functional theory (DFT, B3LYP functional) in QM/MM geometry optimizations. We consider different variants of the chromophore (including the cis- and trans-acylimine and peptide forms) as well as different protonation states of environmental residues. The QM/MM calculations provide insight into the role of nearby residues concerning their interactions with the chromophore and their influence on structural and spectroscopic properties. QM/MM optimizations yield a single conformer for the anionic acylimine chromophore, whereas there are distinct cis- and trans-conformers in the anionic peptide chromophore, the latter being more stable. The calculated vertical excitation energies (DFT/MRCI) for the anionic chromophores agree well with experiment. The published crystal structure of DsRed.M1 with an anionic acylimine chromophore indicates a quinoid structure, while the QM/MM calculations predict the phenolate form to be more stable.

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