Analysis of secondary alpha helix and beta sheet conformations of peptides through the modeling of their electrophoretic mobility

MARÍA V. PIAGGIO; MARTA B. PEIROTTI; JULIO A. DEIBER

Buenos Aires

Simposio; 18 th Latin-American Symposium on Biotechnology, Biomedical, Biopharmaceutical and Industrial Applications of Capillary Electrophoresis and Microchip Technology; 2012

AES- Electrophoresis Society, USA

The interplay between the electrophoretic mobility of peptides and their possible secondary structures was described in [1]. In this regard, linear expressions of semi-empirical models were fitted to experimental electrophoretic mobility data of peptides as a function of the effective charge-to-size ratio parameter. Therefore the correlation coefficient value was used as the controlling parameter to detect those peptides that could present secondary structure. This interesting proposal was discussed and justified by using the electrophoretic mobility of a series of different synthetic peptides obtained via free solution high-performance capillary zone electrophoresis. It was shown that the divergence from the linear expressions of these models possibly occurred due to the proclivity of specific arrangements of peptide amino acid sequences to assume preferred alpha-helix and beta-sheet conformations at the specific protocol conditions. It was then indicated that electrophoretic mobility may provide useful information concerning conformational differences of similar peptides. Based on these results, here we have studied these peptides through simple theoretical models of the polyampholyte-polypeptide electrophoretic mobility already proposed in the literature [2], where aspherical and spherical hard particles with occluded water are considered. It was found that there exist several physicochemical parameter values like particle asphericity, hydration and effective charge, among others, that may also lead one to similar conclusions as those described in [1]. Also hydrated chain fractal dimensions defined in [3] and evaluated in this framework are shown to be important for this specific purpose.   Acknowledgments   Authors wish to thank the financial aid received from Universidad Nacional del Litoral, Santa Fe, Argentina (CAI+D 2009) and CONICET (PIP 112-200801-01106).   References   [1] Sitaram BR, Keah HH, Hearn MTW. J. Chromatography A 1999, 857, 263-273. [2] Piaggio MV, Peirotti MB, Deiber JA. J. Sep. Sci. 2010, 33, 2423-2429. [3] Deiber JA, Piaggio MV, Peirotti MB. Electrophoresis 2011, 32, 2779-2787.