Journal ArticleDOI
Estimation of globular protein secondary structure from circular dichroism.
S W Provencher,J Glöckner +1 more
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TLDR
In this article, a linear combination of the CD spectra (from 190 to 240 nm) of 16 proteins whose secondary structures are known from X-ray crystallography was used to characterize helix, beta sheet, beta turn, and remainder.Abstract:
A new method is developed in which a circular dichroism (CD) spectrum is analyzed directly as a linear combination of the CD spectra (from 190 to 240 nm) of 16 proteins whose secondary structures are known from X-ray crystallography. This avoids the dilemma encountered in previous methods of trying to define single reference CD spectra that were supposed to characterize such broad and variable classes as helix, beta sheet, beta turn, and "remainder". It also permits a more accurate and flexible analysis. The usual instability in using so many parameters is automatically controlled by a simple constrained statistical regularization procedure (similar to ridge regression). Sixteen tests were made by removing 1 spectrum at a time from the set of 16 and analyzing it in terms of the other 15. The product moment correlation coefficients between the computed fractions of helix, beta sheet, beta turn, and remainder and the fractions from the X-ray data were 0.96, 0.94, 0.31,, and 0.49, respectively. Thus, the helix and beta-sheet accuracy is very good. (The corresponding values calculated by a previous method with four reference spectra were 0.85, 0.25, --0.31, and 0.46.).read more
Citations
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Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Journal ArticleDOI
Estimation of metabolite concentrations from localized in vivo proton NMR spectra
TL;DR: The LCModel method analyzes an in vivo spectrum as a Linear Combination of Model spectra of metabolite solutions in vitro by using complete model spectra, rather than just individual resonances, to ensure maximum information and uniqueness are incorporated into the analysis.
Journal ArticleDOI
Using circular dichroism spectra to estimate protein secondary structure
TL;DR: This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins.
Journal ArticleDOI
How to study proteins by circular dichroism
TL;DR: The basis of the CD approach and its application to the study of proteins, and clear guidelines on how reliable data can be obtained and analysed are presented.
Journal ArticleDOI
Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set
TL;DR: Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions, and three programs are provided in CDPro software package and have been modified for easier use with the different reference sets described in this paper.
References
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Journal ArticleDOI
Determination of the helix and beta form of proteins in aqueous solution by circular dichroism.
Journal ArticleDOI
Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion.
Journal ArticleDOI
Circular dichroic analysis of protein conformation: inclusion of the beta-turns.
TL;DR: In this paper, the mean residue ellipticity, [theta], at any wavelength, lambda, of a protein in aqueous solution is expressed as ε = fH[theta]H infinity(1-k/n) + f beta[thet]beta + ft[thetea]t + fR[ theta]R with two constraints: 1 > or = fj > 0 and sigma fj = 1.
Journal ArticleDOI
Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism
S. Brahms,J.G. Brahms +1 more
TL;DR: By including all types of secondary structure and by enlarging substantially the spectral region, the method permits analysis of the conformation of a variety of proteins, such as nucleic acid-binding proteins, immunoglobulins and β-pleated sheet-rich proteins.
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