Conformation photonic proteins

In addition to photonic switches, photonic proteins were engineered to contain fluorescent moieties that react to changes in a protein s local environment and to conformational changes. In this section, we review several examples of designing photonic probes that goes beyond simple chemical labeling and cysteine mutagenesis. 

Stabo-Eeg F, Lindgren M, Nilsson KPR, Inganas O, Hammarstrdm P (2007) Quantum efficiency and two-photon absorption cross-section of conjugated polyelectrolytes used for protein conformation measurements with applications on amyloid structures. Chem Phys 336 121-126... 

Figure 10 The normalized first moments of the photon echo signal of (a) CA-N3, (b) Hb-N3-, and (c) Hb-CO as a function of delay time T. Note the extended time axis of the Hb-CO data. The inhomogeneity decays with time T due to conformational fluctuations of the proteins.

Multidimentional nonlinear infrared spectroscopy is used for identification of dynamic structures in liquids and conformational dynamics of molecules, peptides and, in principle, small proteins in solution (Asplund et al., 2000 and references herein). This spectroscopy incorporates the ability to control the responses of particular vibrational transitions depending on their couplings to one another. Two and three-pulse IR photon echo techniques were used to eliminate the inhomogeneous broadening in the IR spectrum. In the third-order IR echo methods, three phase-locked IR pulses with wave vectors kb k2, and k3 are focused on the sample at time intervals. The IR photon echo eventually emitted and the complex 2D IR spectrum is obtained with the use of Fourier transformation. The method was applied to the examination of vibrational properties of N-methyl acetamid and a dipeptide, acyl-proline-NH2.in D20. The 2D IR spectrum showed peaks at 1,610 and 1, 670 cm 1, the two frequencies ofthe acyl-proline dipeptide. Geometry and time-ordering of the incoming pulse sequence in fifth-order 2D spectroscopy is shown in Fig. 1.3. 

The fluorescence intensity resolved by wavelength constitutes the fluorescence spectrum. The wavelengths of fluorescence photons contain information about the environment of the fluorophore and the sample heterogeneity. Por example, as described above, buried Trp residues tend to have blue-shifted emission bands (Xmax < 330 mn), whereas Trp residues partially or fully exposed to water have red-shifted emission bands ( max > 340 mn). Therefore, protein conformational changes or unfolding may be accompanied by shifts in the native fluorescence spectra. Pluorescence spectra can be measured on a standard fluorometer, which is available from many manufacturers. 

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