Elsevier

Analytical Biochemistry

Volume 287, Issue 2, 15 December 2000, Pages 243-251
Analytical Biochemistry

Regular Article
Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Inclusion of Denatured Proteins with Native Proteins in the Analysis

https://doi.org/10.1006/abio.2000.4879Get rights and content

Abstract

We have expanded our reference set of proteins used in the estimation of protein secondary structure by CD spectroscopy from 29 to 37 proteins by including 3 additional globular proteins with known X-ray structure and 5 denatured proteins. We have also modified the self-consistent method for analyzing protein CD spectra, SELCON3, by including a new selection criterion developed by W. C. Johnson, Jr. (Proteins Struct. Funct. Genet. 35, 307–312, 1999). The secondary structure corresponding to the denatured proteins was approximated to be 90% unordered, owing to the spectral similarity of the denatured proteins and unordered structures. We examined the thermal denaturation of ribonuclease T1 by CD using both the original and expanded sets of reference proteins and obtained more consistent results with the expanded set. The expanded set of reference proteins will be helpful for the determination of protein secondary structure from protein CD spectra with higher reliability, especially of proteins with significant unordered structure content and/or in the course of denaturation.

References (43)

  • S.Y. Venyaminov et al.

    Circular dichroic analysis of denatured proteins: Inclusion of denatured protein in the reference set

    Anal. Biochem.

    (1993)
  • P.L. Privalov et al.

    Heat capacity and conformation of proteins in the denatured state

    J. Mol. Biol.

    (1989)
  • L.A. Compton et al.

    Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication

    Anal. Biochem.

    (1986)
  • K. Wüthrich

    NMR assignments as a basis for structural characterization of denatured states of globular proteins

    Curr. Opin. Struct. Biol.

    (1994)
  • H. Fabian et al.

    Secondary structure and temperature induced unfolding and refolding of ribonuclease T1 in aqueous solution—A Fourier transform spectroscopic study

    J. Mol. Biol.

    (1993)
  • N. Greenfield et al.

    Computed circular dichroism spectra for the evaluation of protein conformation

    Biochemistry

    (1969)
  • V.P. Saxena et al.

    A new basis for interpreting the circular dichroism spectra of proteins

    Proc. Natl. Acad. Sci. USA

    (1971)
  • Y.H. Chen et al.

    Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion

    Biochemistry

    (1972)
  • I.A. Bolotina et al.

    Determination of the secondary structure of proteins from the circular dichroism spectra. 1. Protein reference spectra for α-, β- and irregular structures

    Mol. Biol.

    (1980)
  • S.W. Provencher et al.

    Estimation of protein secondary structure from circular dichroism

    Biochemistry

    (1981)
  • J.P. Hennessey et al.

    Information content in the circular dichroism of proteins

    Biochemistry

    (1981)
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