Vibrational Spectroscopy of Fluorescent Proteins: A Tool to Investigate the Structure of the Chromophore and Its Environment - Fluorescent Proteins: From Understanding to Design - page 130

Fig. 1 (a) Molecular structures of an analogues of the chromophore of GFP in its cis form (cGFP)
[HBDI: (Z)-4-(4-hydroxybenzylidene)-1,2-dimethyl-1 H-imidazol-5(4 H)-one]. In the figure are
also labeled the angles , and the PDB

nomenclature for some of the atoms. (b) Example of a delocalized mode on cGFP (calculated
mode at 612 cm 1 , corresponding to the experimental peak at 606 cm 1 ); the chromophore is
represented in stick mode, with different colors for different atoms; the arrows indicate the relative
displacement (or velocity) of the atoms within the vibrational mode. (c) Top : schematic represen-
tation of the quantum transitions involved in IR absorption spectroscopy, Raman, and resonance
Raman scattering. Up -( down -) arrows represent the energy of the photons of impinging (scattered)
radiation; in the central panel, dotted lines schematize the fact that all transitions are summed in
the calculation of the dynamic electronic polarizability responsible for the Raman scattering.
Bottom : comparison of IR-absorption, Raman, and resonance Raman spectra of the model chro-
mophore HDBI

t (involved in the “ cis - trans ” isomerization) and '

presentation of some of the results obtained by vibrational spectroscopy on GFP
mutants: in the first part, the techniques used to interpret the vibrational spectrum of
the chromophore and the influence of the protein environment on its vibrational
modes will be discussed; in the second part, some examples will help to explain in
which ways vibrational spectroscopy can help in understanding structural changes
and dynamics of the chromophore and how these affect the spectroscopy properties
and in general the physical behavior of GFP mutants.