Premium
Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data
Author(s) -
Miles Andrew J.,
Whitmore Lee,
Wallace B.A.
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041019905
Subject(s) - magnitude (astronomy) , protein secondary structure , circular dichroism , calibration , goodness of fit , scaling , biological system , chemistry , spectral line , vibrational circular dichroism , mathematics , physics , statistics , crystallography , geometry , biology , astronomy , biochemistry
The effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly β‐sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal structures, so it was possible to ascertain the effects of magnitude on both the accuracy of determining the secondary structure and the goodness‐of‐fit of the calculated structures to the experimental data. It was found that most algorithms are highly sensitive to spectral magnitude, and that the goodness‐of‐fit parameter may be a useful tool in assessing the correct scaling of the data. This means that parameters that affect magnitude, including calibration of the instrument, the spectral cell pathlength, and the protein concentration, must be accurately determined to obtain correct secondary structural analyses of proteins from CD data using empirical methods.