Green fluorescent proteins: Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamics simulation's of the wild type and S65T mutant

CHARMM force field parameters are reported for the neutral and anionic form of the p-hydroxybenzylidene-imidazolinone chromophore of green fluorescent protein (GFP). They were derived by fitting against ab initio (RHF/6-31G*) and density functional (B3LYP/6-31G*) reference data for the isolated chromophore model compounds and their complexes with water. More specifically, the parameters for the bonded interactions were calibrated against B3LYP geometries and rotational barriers of the model compounds, the atomic charges for the nonbonded Coulomb interactions were fitted against RHF geometries and binding energies of the complexes, and the van der Waals parameters were taken from related CHARMM residues. The optimized parameters reproduce the reference data well. For further validation, molecular dynamics (MD) simulations were carried out for wild-type GFP with a neutral chromophore and for the S65T mutant with an anionic chromophore. The average MD structures from 400 ps production runs are generally in reasonable agreement with the available X-ray structures, e.g., concerning the geometry of the chromophore in the protein and the hydrogen bonding network around the chromophore. In some aspects, however, the present MD simulations differ from the published X-ray results: in particular, they raise the issue whether the residue Glu222 might be deprotonated in the S65T mutant, contrary to the conclusions from the X-ray work.