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

The DICHROWEB web server enables on-line analyses of circular dichroism (CD) spectroscopic data, providing calculated secondary structure content and graphical analyses comparing calculated structures and experimental data. The server is located at http://www.cryst.bbk.ac.uk/cdweb and may be accessed via a password-limited user ID, available upon completion of a registration form. The server facilitates analyses using five popular algorithms and (currently) seven different reference databases by accepting data in a user-friendly manner in a wide range of formats, including those output by both commercial CD instruments and synchrotron radiation-based circular dichroism beamlines, as well as those produced by spectral processing software packages. It produces as output calculated secondary structures, a goodness-of-fit parameter for the analyses, and tabular and graphical displays of experimental, calculated and difference spectra. The web pages associated with the server provide information on CD spectroscopic methods and terms, literature references and aids for interpreting the analysis results.

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DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.

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.

http://people.cryst.bbk.ac.uk/~ubcg25a/biopolymers_DW.pdf

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

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

Fourier transform IR (FTIR) spectroscopy is a nondestructive technique for structural characterization of proteins and polypeptides. The IR spectral data of polymers are usually interpreted in terms of the vibrations of a structural repeat. The repeat units in proteins give rise to nine characteristic IR absorption bands (amides A, B and I-VII). Amide I bands (1,700-1,600 cm(-1)) are the most prominent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary structural components. In this protocol, we have detailed the principles that underlie the determination of protein secondary structure by FTIR spectroscopy, as well as the basic steps involved in protein sample preparation, instrument operation, FTIR spectra collection and spectra analysis in order to estimate protein secondary-structural components in aqueous (both H2O and deuterium oxide (D2O)) solution using algorithms, such as second-derivative, deconvolution and curve fitting. Small amounts of high-purity (>95%) proteins at high concentrations (>3 mg ml(-1)) are needed in this protocol; typically, the procedure can be completed in 1-2 d.

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

http://www.nat.vu.nl/~ivo/pub/1990/1990AnalBiochem191_110.pdf

Estimation of protein secondary structure and error analysis from circular dichroism spectra.

Many standards exist in the field of instrumentation. The ever increasing scale of integration of processing power with instrumentation has opened ways to extend and transform the functionality of instruments in software, i.e. create a virtual instrument. Controlling and standardizing this virtual instrument requires a multi-level definition. In this paper we review some of the most relevant developments in this field.

Virtual instrumentation: a survey of standards and their interrelation

We have developed a prototype instrument providing a new way to measure the shape of the cornea. Our approach exploits properties of pseudorandom binary arrays (PRBAs). Encoded in a colored pattern (stimulus) that is mirrored to the eye, a large PRBA allows for unique identification of unambiguously characterized positions both in stimulus and reflected image. This is used to come to an integral reconstruction of the cornea. It is demonstrated that the new technique contributes to a very robust measurement method.

A new instrument to measure the shape of the cornea based on pseudorandom color coding

We have developed a prototype-instrument providing a new way to measure the shape of the cornea. Our approach exploits properties of pseudo random binary arrays (PRBAs). Encoded in a coloured pattern (stimulus) that is mirrored to the eye PRBAs allow for unique characterization of positions both in the stimulus and the reflected image. This is used to come to an integral reconstruction of the cornea. It is demonstrated that the new technique contributes to a very robust measurement method.

A new PRBA-based instrument to measure the shape of the cornea

This paper presents development aspects of a semi-autonomous animated avatar for real-time interactive virtual environment applications.

H.J.W. Spoelder

Papers

Estimation of protein secondary structure and error analysis from circular dichroism spectra.

Virtual instrumentation: a survey of standards and their interrelation

A new instrument to measure the shape of the cornea based on pseudorandom color coding

A new PRBA-based instrument to measure the shape of the cornea

Knowledge-based animation of articulated anthropomorphic models for virtual reality applications