A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space

Journal Article · Sun Jan 01 04:00:00 EST 2006 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btl327· OSTI ID:929795

Lees, J; Miles, A; Wien, F; Wallace, B

Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.

• Research Organization: Brookhaven National Laboratory (BNL) National Synchrotron Light Source
• Sponsoring Organization: Doe - Office Of Science
• DOE Contract Number: AC02-98CH10886
• OSTI ID: 929795
• Report Number(s): BNL--80342-2008-JA
• Journal Information: Bioinformatics, Journal Name: Bioinformatics Vol. 22
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
43 PARTICLE ACCELERATORS
CRYSTAL STRUCTURE
DATA
DICHROISM
MOLECULAR BIOLOGY
PROTEINS
SPACE
SPECTRA
SPECTROSCOPY
SYNCHROTRON RADIATION
WAVELENGTHS
national synchrotron light source