Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy.
A simple approach to estimate the number of alpha-helical and beta-strand segments from protein circular dichroism spectra is described. The alpha-helix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given alpha-helix or beta-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-helix and two residues per beta-strand may be considered distorted in proteins. The number of alpha-helical and beta-strand segments and their average length in a given protein were estimated from the fraction of distorted alpha-helix and beta-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.
Sreerama
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Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523, USA.
Venyaminov
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SY
Woody
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RW
D000818:Animals; D002942:Circular Dichroism; D003087:Colicins / Q000032:analysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D049452:Green Fluorescent Proteins; D008164:Luminescent Proteins / Q000032:analysis; D017433:Protein Structure, Secondary; D051381:Rats
D003087:Colicins; D008164:Luminescent Proteins; D049452:Green Fluorescent Proteins