Techniques are presented to develop spectroscopic factors directly from circular dichroism spectra of proteins using singular value decomposition on a small database. Four spectra of maximum spectral variability are chosen to characterize the database. These selected protein spectra are then factored by singular values into component spectra, which are collected as comparative vector characteristics used as factor fractions. The necessary standardization for comparison is achieved using unit normalized spectra. Those spectra are used to quantify the parameter uncertainties as a means for comparison. The difference between the fit spectrum and the data spectrum for each protein is analyzed by least square to obtain parameter uncertainties due to the model. The sum of the factor fractions over the database is within the theoretical predictions.
Cite this paper
Haner, D. A. (2020). Selection and Analysis of Protein Circular Dichroism Spectra Using an Expansion of Spectral Factors. Open Access Library Journal, 7, e7049. doi: http://dx.doi.org/10.4236/oalib.1107049.
Compton, L.A. and Johnson, W.C. (1986) Analysis of Protein Circular Dichroism Spectra for Secondary Structures Using a Simplified Matrix Multiplication. Analytical Biochemistry, 155, 155-167. https://doi.org/10.1016/0003-2697(86)90241-1
Mulkerrin, M.G. (1996) Protein Structure Analysis Using Circular Dichroism. In: Henry, A.H., Ed., Spectroscopic Methods for Determining Protein Structures in Solution, VCH Publishers, New York, 5-27.
Kliger, D.S., Louis, J.W. and Randall, C.E. (1990) Polarized Light in Optics and Spectroscopy. Academic Press, San Diego, 237-274.
https://doi.org/10.1016/B978-0-08-057104-1.50011-9
Hennessey, J.P. and Johnson, W.C. (1981) Information Content in the Circular Dichroism of Proteins. Biochemistry, 20, 1085-1094.
https://doi.org/10.1021/bi00508a007
Haner, D.A. and Mobley, P.W. (2018) Error Analysis for Protein Conformation Quantities in Circular Dichroism Spectrum. Open Access Library Journal, 5, e4966.
Press, W.H., Flannery, P.P., Teukolsky, S.A., Vetterling, W.T., et al. (1986) Numerical Recipes, the Art of Scientific Computing. Cambridge University Press, New York, 489.
Oberg, K.S., Ruysschaert, J.M. and Goormaghtigh, E. (2003) Rationally Selected Basis Proteins: A New Approach to Selecting Protein Spectroscopic Secondary Structure Analysis. Protein Science, 12, 2015-2031. https://doi.org/10.1110/ps.0354703
Oberg, K.S., Ruysschaert, J.M. and Goormaghtigh, E. (2004) The Optimization of Proteins Secondary Structure Determination with Infrared and Dichroism Spectra. European Journal of Biochemistry, 271, 2937-2948.
https://doi.org/10.1111/j.1432-1033.2004.04220.x
Khrapunov, S. (2009) CD Spectroscopy Has Intrinsic Limits for Protein Secondary Structures. Analytical Biochemistry, 389, 174-176.
https://doi.org/10.1016/j.ab.2009.03.036
Rozett, R.W. and Peterson, E.M. (1975) Methods of Factor Analysis of Mass Spectra. Analytical Chemistry, 47, 1301-1308. https://doi.org/10.1021/ac60358a032
Haner, D.A. and Mobley, P.W. (2015) Simulations Relating to the Determination of Protein Secondary Structure Fraction from Circular Dichroism Spectra. Open Access Library Journal, 2, e1601. https://doi.org/10.4236/oalib.1101601
