Prediction of protein conformation.

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

Infrared spectroscopy is one of the oldest and well established experimental techniques for the analysis of secondary structure of polypeptides and proteins. It is convenient, non-destructive, requires less sample preparation, and can be used under a wide variety of conditions. This review introduces the recent developments in Fourier transform infrared (FTIR) spectroscopy technique and its applications to protein structural studies. The experimental skills, data analysis, and correlations between the FTIR spectroscopic bands and protein secondary structure components are discussed. The applications of FTIR to the secondary structure analysis, conformational changes, structural dynamics and stability studies of proteins are also discussed.

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Fourier Transform Infrared Spectroscopic Analysis of Protein Secondary Structures

PARTIAL TABLE OF CONTENTS: Circular Dichroism: An Introduction (G. Snatzke). From Pasteur to Parity Nonconservation: Theories of the Origin of Molecular Chirality (S. Mason). Theoretical Approach to Electronic Optical Activity (A. Koslowski, et al.). Vibrational Optical Acivity Theory (L. Nafie & T. Freedman). Fast Time-Resolved Circular Dichroism Measurements (D. Kliger & J. Lewis). The Octant Rule (D. Lightner). Circular Dichroism and Chirality of Dienes (J. Gawroski). Exciton Chirality Method: Principles and Applications (N. Berova & K. Nakanishi). A Model for How Polymers Amplify Chirality (M. Green). Induced CD or Polymers (E. Yashima & Y. Okamoto). Application of CD to the Study of Some Cholesteric Mesophase (G. Gottarelli & G. Spada). Circular Dichroism of Inorganic Complexes: Interpretation and Applications (R. Kuroda). Circular Dichroism of Peptides and Proteins (N. Sreerama & R. Woody). Peptide and Protein Conformational Studies with Vibrational Circular Dichroism and Related Spectroscopies (T. Keiderling). HPLC-CD: Stereochemical Analysis at Work (P. Salvadori, et al.). Applications of Chiroptical Spectroscopy in the Characterization of Compounds Having Pharmaceutical Importance (H. Brittain). Index.

Circular Dichroism: Principles and Applications

A Self-Consistent Method for the Analysis of Protein Secondary Structure from Circular Dichroism

Publisher Summary Circular dichroism (CD) is a spectroscopic method which depends on the fact that certain molecules interact differently with right and left circularly polarized light. Circularly polarized light is chiral—that is, it occurs in two nonsuperimposable forms that are mirror images of one another. To discriminate between the two chiral forms of light, a molecule must be chiral, including the vast majority of biological molecules. A method that can discern the subtle differences between non superimposable mirror image molecules (enantiomers) must be highly sensitive to the three-dimensional features of molecules—that is, to conformation. Binding of ligands or protein-protein and protein–DNA interactions can also alter the circular dichroism spectrum of the protein and/or nucleic acid. These changes in CD can be used to determine equilibrium constants, and they can also provide evidence for conformational changes. Thus, CD can provide information about the secondary structure of proteins and nucleic acids and about the binding of ligands to these types of macromolecule.

[4] Circular dichroism

A simple approach to estimate the number of alpha-helical and beta-strand segments from protein circular dichroism spectra is described. The alpha-helix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given alpha-helix or beta-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-helix and two residues per beta-strand may be considered distorted in proteins. The number of alpha-helical and beta-strand segments and their average length in a given protein were estimated from the fraction of distorted alpha-helix and beta-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.

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Robert W. Woody

Papers

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

Circular Dichroism: Principles and Applications

A Self-Consistent Method for the Analysis of Protein Secondary Structure from Circular Dichroism

[4] Circular dichroism

Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy.