QM/MM Study of the Monomeric Red Fluorescent Protein DsRed.M1

Abstract

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.

Molecular dynamics study of taxadiene synthase catalysis

“…The simulation system consisted of 23,641 atoms (TXS: 6133; cation: 53; PPi: 9; Mg 2+ : 3; Na + : 10; water: 17,433). The chosen MD setup is analogous to that of previous studies reported in the literature …”

“…The chosen MD setup is analogous to that of previous studies reported in the literature. [32,33,41,45] Three MD simulations with different initial velocity distributions (referred to as MD1, MD2, and MD3) were performed for each complex to enhance sampling. [30][31][32][33][34][35] All MD simulations were done with the CHARMM software package (version 35b2).…”

Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant

“…Proteins (2 mg/ml) were incubated in 15 µl gel filtration buffer, acidic buffer (0.1 M HCl) and alkaline buffer (0.1 M NaOH) for 10 min at room temperature [36]. Samples were incubated at 95°C for 10 min before loading on a 12% SDS-PAGE.…”

“…However, recent hybrid quantum/classical (QM/MM) studies on, for example, DsRed.M1 [36], [37] and HcRed [23], [38] provide detailed insights into the protonation states of the chromophore and surrounding residues, as well as the spectrosopic properties of these red fluorescent proteins. Together, these studies highlight the potential of computational approaches to elucidate the molecular mechanism that contribute to spectral properties of fluorescent proteins and that are not always obvious from crystallographic and spectral analysis alone.…”

Isomerization mechanism of the HcRed fluorescent protein chromophore

“…38 Our groups have previously studied the structural and energetic properties as well as the absorption spectra of some RFPs (DsRed.M1 and HcRed). [39][40][41][42] In recent years, there has been much progress in theoretical research on electronically excited states, with MS-CASPT2 (multi-state complete-active-space second-order perturbation theory) 43,44 and coupled cluster methods (CC2, CCSD, CC3) [45][46][47] being well established for small molecules. Moreover, time-dependent density functional theory (TD-DFT) 48 has become popular for calculations on medium-sized molecules, giving reasonable results for various (but not all) types of excited states at relatively low computational cost.…”