Experimental and theoretical study of formation of polyproline II helix by means of Raman optical activity
V. Profant1*, P. Bouř2, V. Baumruk1
1Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16, Prague, Czech Republic
2Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám 2, 166 10, Prague, Czech Republic
Polyproline-II helix (PPII) represents a less common protein secondary structure motif. Its structure is rather specific due to absence of internal stabilizing hydrogen bonds. The stability of the helix is caused only by sterical reasons and the interaction with surrounding solvent molecules. Number of recently discovered evidences  has lead to a presupposition that the PPII helix is the dominant element of the structure of unfolded proteins.
In our experiment we measured Raman and Raman optical activity (ROA) spectra of several oligo- and poly-L-proline samples in a wide frequency range between 120 cm-1 and 1800 cm-1 and analyzed them with respect to the length of the proline chain. The relatively new technique of ROA [2,3], which is based on a different interaction of a specimen with the right- and left-handed circularly polarized laser light, represented an ideal methodology for this type of observation due to its high sensitivity to the conformational stability and rigidity of peptide chain backbone. There is also a strong link to previous experiments  which were focused on the characterization of proline side chain conformation and its interaction with solvent.
The stress was laid on the interconnection between experiments and simulations. For that purpose we performed ab initio calculations of Raman and ROA spectral bands and their intensities for all measured samples in order to obtain more accurate interpretation of recorded spectra and observed phenomena. Computations were done in Gaussian program, whose latest implementation enables analytical calculations of optical activity tensors leading to the significant decrease of computational time.
So far, we were able to determine the characteristic spectral peaks associated with formation of stable PPII helical conformation in studied systems. The most relevant peaks were found at 405, 535 and 945 cm-1. Based on our experimental data analysis we were able to determine the minimal length of (L-proline)N chain necessary for formation of the stable PPII conformation as N=6 . Moreover, based on the results of calculation we managed to assign specific vibrations to the most proliferating spectral peaks and discuss the influence of various peptide bond and side chain conformers in experimental spectra.
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The work was supported by the Grant Agency of the Czech Republic (grant No. P208/11/0105) and by the Charles University in Prague (projects SVV-2010-261304 and SVV-2011-263304).