QM/MM study of the monomeric red fluorescent protein DsRed.M1.
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.
Sanchez-Garcia
Elsa
E
Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr.
Doerr
Markus
M
Hsiao
Ya-Wen
YW
Thiel
Walter
W
D006860:Hydrogen Bonding; D007536:Isomerism; D008164:Luminescent Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
D008164:Luminescent Proteins; C413663:fluorescent protein 583; D014867:Water