Accuracy of protein secondary structure determination from circular dichroism spectra based on immunoglobulin examples

Sergey Y. Tetin, Franklyn G. Prendergast, Sergei Yu Venyaminov

Research output: Contribution to journalArticlepeer-review

30 Scopus citations

Abstract

Strong contribution of the aromatic amino acid side chain chromophores to the far-UV circular dichroism (CD) spectra substantially distorts a relatively weak CD signal originating from β sheet, the main type of immunoglobulin secondary structure. In this study we compared the secondary structure calculated from the far-UV CD spectra with the X-ray data for three antibody Fab fragments. Calculations were performed with three different algorithms, using two sets of reference proteins. Low standard deviations between all six estimates indicate stable mathematical solutions. Despite pronounced differences in the shape and amplitude of the CD spectra, we found a strong correlation between CD and X-ray data in the secondary structure for every protein studied. The number and average length of the secondary structure elements estimated from the CD spectra closely resemble those of the X-ray data. Agreement between spectroscopic and crystallographic results demonstrates that modern methods of secondary structure calculation are resilient to distortions of the far-UV CD spectra of immunoglobulins caused by aromatic side chain chromophores.

Original languageEnglish (US)
Pages (from-to)183-187
Number of pages5
JournalAnalytical Biochemistry
Volume321
Issue number2
DOIs
StatePublished - Oct 15 2003

Keywords

  • Comparison of circular dichroism and X-ray analysis
  • Monoclonal antibody
  • Secondary structure

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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