Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases

Abstract

Circular dichroism (CD) spectroscopy has been a valuable method for the analysis of protein secondary structures for many years. With the advent of synchrotron radiation circular dichroism (SRCD) and improvements in instrumentation for conventional CD, lower wavelength data are obtainable and the information content of the spectra increased. In addition, new computation and bioinformatics methods have been developed and new reference databases have been created, which greatly improve and facilitate the analyses of CD spectra. This article discusses recent developments in the analysis of protein secondary structures, including features of the DICHROWEB analysis webserver. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 392–400, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

The lambda spanin components Rz and Rz1 undergo tertiary and quaternary rearrangements upon complex formation

“…24 Spectra of the individual sRz and sRz1 proteins were also fit using the CONTINLL 25,26 and CDSSTR 27 programs available on the DICHROWEB server. 28 To determine the molar ratio of sRz to sRz1 in the complex, a 10 lM solution of sRz in 10 mM sodium phosphate, 100 mM NaCl, pH 7.5, at 25 C was titrated, in 2.5 lM increments, with a stock solution of sRz1 supplemented with 10 lM sRz. The change in ellipticity due to binding was corrected for the sRz1 stock solution alone and dilution from 200 to 350 lL.…”

Small Molecule Screening Identifies Regulators of the Transcription Factor ΔFosB

“…CD spectra were recorded at RT on an Aviv-202 spectrometer from 190 to 260 nm in a 1.0 mm path length quartz cuvette using an average time of 2 s at the spectral bandwidth of 1.0 nm. Final background cleared averaged spectra were analyzed and deconvoluted using "dichroweb" 50,51 (see Supporting Information).…”

Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold

“…Prior to deconvolution, control buffer spectra were subtracted and the data Zacharchenko et al, 2016 8 zeroed using the CD signal at λ=260nm. Data were deconvoluted using the Dichroweb server with the CDSSTR method [26,27]. To measure thermal stability, CD spectra were collected in the spectral range λ=180-260 nm and in the temperature range 20-90 o C.…”