Simulations Relating to the Determination of Protein Secondary Structure Fractions from Circular Dichroism Spectra

Patrick W.  Mobley; David A.  Haner

doi:10.4236/oalib.1101601

Journals by Subject

Journals by Title

OALibJ Vol.2 No.6 , June 2015

Simulations Relating to the Determination of Protein Secondary Structure Fractions from Circular Dichroism Spectra

David A. Haner, Patrick W. Mobley^*

Abstract: Test problem simulations are presented of the matrix equation, D = BF, equivalent to least squares data fitting, where the matrices are rectangular with D and F being experimental data. The chosen application is finding fractions of secondary structures of proteins from circular dichroism (CD) spectra employing singular value decomposition, SVD, to obtain the matrix B and its pseudo-reciprocal. In practice the first step of the analysis is to select the reduced noise representation of the CD spectra which sets the bounds for subsequent computation and the development of the CD noise spectra. The conclusion from analysis is to obtain the structural component spectra summarizing the database and all the structural fractions and their uncertainties. The database noise spectrum can be used to prepare the reduced noise CD spectrum for a new protein to yield its structural fractions and their uncertainties.

Keywords: Singular Value Decomposition, Circular Dichroism, Protein Structure

Cite this paper: Haner, D. and Mobley, P. (2015) Simulations Relating to the Determination of Protein Secondary Structure Fractions from Circular Dichroism Spectra. Open Access Library Journal, 2, 1-10. doi: 10.4236/oalib.1101601.

References

[1] Bevington, P. (1969) Data Reduction and Error Analysis for the Physical Sciences. McGraw-Hill, New York, 154.

[2] Forsythe, G.E., Malcolm, M.A. and Moler, C.B. (1977) Computer Methods for Mathematical Computations. Prentice-Hall, Inc., Englewood Cliffs, 192.

[3] Malinowski, E.R. (1991) Factor Analysis in Chemistry. 2nd Edition, John Wiley and Sons, New York, 58, 85, 95, 111.

[4] Olver, P.J. and Shakiban, C. (2006) Applied Linear Algebra. Pearson Prentice Hall, New Jersey, 425.

[5] Perrin, C.L. (1970) Mathematics for Chemists. John Wiley & Sons Inc., New York, 247.

[6] Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1986) Numerical Recipes. Cambridge University Press, Cambridge, 52, 60, 172.

[7] Compton, L.A. and Johnson, W.C. (1986) Analysis of Protein Circular Dichroism Spectra for Secondary Structure Using a Simple Matrix Multiplication. Analytical Biochemistry, 155, 155-167.
http://dx.doi.org/10.1016/0003-2697(86)90241-1

[8] Hennessey, J.P. and Johnson, W.C. (1981) Information Content in the Circular Dichroism of Proteins. Biochemistry, 20, 1085-1094.
http://dx.doi.org/10.1021/bi00508a007

[9] Hennessey, J.P. and Johnson, W.C. (1982) Experimental Errors and Their Effect on Analyzing Circular Dichroism Spectra of Proteins. Analytical Biochemistry, 125, 177-188.
http://dx.doi.org/10.1016/0003-2697(82)90400-6

[10] Miles, A.J., Whitmore, L. and Wallace, B.A. (2005) Spectral Magnitude Effects on the Analyses of Secondary Structure from Circular Dichroism Spectroscopic Data. Protein Science, 14, 368-374.
http://dx.doi.org/10.1110/ps.041019905

[11] Whitmore, L. (2001) DichroWeb—Online Circular Dichroism Analysis.
http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

[12] Sreerama, N. (2004) CDPro—A Software Package for Analyzing Protein CD Spectra.
http://lamar.colostate.edu/~sreeram/CDPro/