Simulations Relating to the Determination of Protein Secondary Structure Fractions from Circular Dichroism Spectra - Open Access Library Journal

OALibJ > Vol.2 No.6, June 2015

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

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DOI: 10.4236/oalib.1101601 963 Downloads 1,782 Views Citations

Author(s)

David A. Haner, Patrick W. Mobley^*

Affiliation(s)

Department of Chemistry and Biochemistry, California State Polytechnic University, Pomona, USA.

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

Share and Cite:

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.

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