Universality and Diversity in Science - Festschrift in Honor of Naseem K Rahman's 60th Birthday

The structure and dynamics of the Enhanced Green Fluorescent Protein (EGFP), with the chromophore in the zwitterionic protonation state is analysed. To date there is no direct evidence of its presence within the protein; however, the zwitterionic state of the chromophore may play an important role in the complex photophysics of GFP. In fact it could be linked to the fluorescence fluctuations observed in solution and single molecule experiments whose microscopic origin is still unaccounted for. A force-field molecular dynamics simulation of the whole solvated protein is reported in order to investigate how the amino acid residues around the chromophore adjust themselves upon change in chromophore protonation, from anionic to zwitterionic. We then use ab initio molecular dynamics to test the stability of this conformation and suggest possible paths of transition between the two forms.