For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed 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. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

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, maximum information and uniqueness are incorporated into the analysis A constrained regularization method accounts for differences in phase, baseline, and lineshapes between the in vitro and in vivo spectra, and estimates the metabolite concentrations and their uncertainties LCModel is fully automatic in that the only input is the time-domain in vivo data The lack of subjective interaction should help the exchange and comparison of results More than 3000 human brain STEAM spectra from patients and healthy volunteers have been analyzed with LCModel N-acetylaspartate, cholines, creatines, myo-inositol, and glutamate can be reliably determined, and abnormal levels of these or elevated levels of lactate, alanine, scyllo-inositol, glutamine, or glucose clearly indicate numerous pathologies A computer program will be available

Estimation of metabolite concentrations from localized in vivo proton NMR spectra

Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. 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. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.

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Using circular dichroism spectra to estimate protein secondary structure

http://ctrstbio.org.uic.edu/manuals/kellybba.pdf

How to study proteins by circular dichroism

Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set

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.).

J Glöckner

Papers

Estimation of globular protein secondary structure from circular dichroism.