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Journal of Biosciences

, Volume 8, Issue 1–2, pp 141–149 | Cite as

Protein secondary structure from circular dichroism spectra

  • Parthasarathy Manavalan
  • W. Curtis Johnson
Article

Abstract

Circular dichroism spectra of proteins are extremely sensitive to secondary structure. Nevertheless, circular dichroism spectra should not be analyzed for protein secondary structure unless they are measured to at least 184 nm. Even if all the various types ofβ-turns are lumped together, there are at least 5 different types of secondary structure in a protein (α-helix, antiparallelβ-sheet, parallelβ-sheet,β-turn, and other structures not included in the first 4 categories). It is not possible to solve for these 5 parameters unless there are 5 equations. Singular value decomposition can be used to show that circular dichroism spectra of proteins measured to 200 nm contain only 2 pieces of information, while spectra measured to 190 nm contain about 4. Adding the constraint that the sum of secondary structures must equal 1 provides another piece of information, but even with this constraint, spectra measured to 190 nm simply do not analyze well for the 5 unknowns in secondary structure. Spectra measured to 184 nm do contain 5 pieces of information and we have used such spectra successfully to analyze a variety of proteins for their component secondary structures.

Keywords

Circular dichroism proteins secondary structure singular value decomposition information content 

Abbreviations used

CD

Circular dichroism

SVD

singular value decomposition

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Copyright information

© Indian Academy of Sciences 1985

Authors and Affiliations

  • Parthasarathy Manavalan
    • 1
  • W. Curtis Johnson
    • 1
  1. 1.Department of Biochemistry and BiophysicsOregon State UniversityCorvallisUSA

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