Infrared spectroscopy experiments that measure properties of the vibration-vibration couplings in molecules are emerging as powerful tools to provide structural, reactive and dynamic information of proteins. Interpreting the resulting spectra requires detailed knowledge of the strength, direction and coupling of transition dipole vectors.Using ONIOM(QM:MM) methodology we are able to reduce the expense of computing the Hessian of Green Fluorescent Protein (GFP) (4367 atoms). Further developments have enabled environment electronic polarization of the chromophore and surrounding residues (>100 atoms) to be routinely included in frequency calculations. While mechanical coupling will increase mode delocalization through covalent and hydrogen bonds, the electrostatic environment results in transition dipole coupling and Stark tuning. We are thus able to examine the hierarchical effects of the environment, separating electronic and mechanical properties.In this talk I will present our study of the harmonic vibrational modes of the entire GFP molecule. These modes, their associated frequencies and dipole derivative vectors have been used to interpret experimental difference spectra (GFPI2 -GFPA), chromophore vibrational Stark shifts, and changes in the experimentally measured angle between electronic and vibrational transition dipole (mode angles).

Analytical harmonic vibrational frequencies for the green fluorescent protein computed with ONIOM: Chromophore mode character and its response to environment

247th National Meeting (2014)

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