scholarly journals Structure Analysis of Proteins by Synchrotron Radiation Circular Dichroism: Challenge of CD Spectroscopy to Structural Biology

2009 ◽  
Vol 49 (1) ◽  
pp. 023-024
Author(s):  
Koichi MATSUO
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Structural Biology ◽  
Structure Analysis ◽  
Cd Spectroscopy ◽  
Circular Dichroïsm

Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions

2010 ◽  
Vol 38 (4) ◽  
pp. 861-873 ◽  
Author(s):  
B.A. Wallace ◽  
Robert W. Janes
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Protein Interactions ◽  
Structural Information ◽  
Data Bank ◽  
Cd Spectroscopy ◽  
Circular Dichroism Spectroscopy ◽  
Protein Conformations ◽  
Mutant Proteins ◽  
Circular Dichroïsm

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein–protein complex formation involving either induced-fit or rigid-body mechanisms, and protein–lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery

2003 ◽  
Vol 31 (3) ◽  
pp. 631-633 ◽  
Author(s):  
B.A. Wallace ◽  
Robert W. Janes
Keyword(s):  
Circular Dichroism ◽  
Drug Discovery ◽  
Synchrotron Radiation ◽  
High Throughput ◽  
Conformational Changes ◽  
High Throughput Screening ◽  
Cd Spectroscopy ◽  
Drug Binding ◽  
Apoptosis Protein ◽  
Circular Dichroïsm

CD spectroscopy is an established and valuable technique for examining protein structure, dynamics and folding. Because of its ability to sensitively detect conformational changes, it has important potential for drug discovery, enabling screening for ligand and drug binding, and detection of potential candidates for new pharmaceuticals. The binding of the anti-tumour agent Taxol to the anti-apoptosis protein Bcl-2 [Rodi, Janes, Sanganee, Holton, Wallace and Makowski (1999) J. Mol. Biol. 285, 197–204] and the binding of the anti-epileptic drug lamotrigine to voltage-gated sodium channels [Cronin, O'Reilly, Duclohier and Wallace (2003) J. Biol. Chem. 278, 10675–10682] are used as examples to show changes detectable by CD involving secondary structure, and are contrasted with the binding of the agonist carbamylcholine to acetylcholine receptors [Mielke and Wallace (1988) J. Biol. Chem. 263, 8177–8182], an example where binding does not involve a secondary structural change. Synchrotron radiation CD spectroscopy offers significant enhancements with respect to conventional CD spectroscopy, which will enable its usage for high-throughput screening and as a tool in ‘chemical genomics’ or ‘reverse chemical genetics’ strategies for ligand identification. The lower wavelength data available enable more detailed, sensitive and accurate detection, the higher light intensity permits much smaller amounts of both proteins and drug candidates to be used in the screening, and future technological developments in sample handling and detection should enable automated high-throughput screening to be performed.

Circular dichroism beamline B23 at the Diamond Light Source

2011 ◽  
Vol 19 (1) ◽  
pp. 132-135 ◽  
Author(s):  
Rohanah Hussain ◽  
Tamás Jávorfi ◽  
Giuliano Siligardi
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Light Source ◽  
Structural Biology ◽  
Third Generation ◽  
User Community ◽  
Recent Advances ◽  
Synchrotron Facility ◽  
Circular Dichroïsm ◽  
Established Technique

Synchrotron radiation circular dichroism (SRCD) is a well established technique in structural biology. The first UV-VIS beamline, dedicated to circular dichroism, at Diamond Light Source Ltd, a third-generation synchrotron facility in south Oxfordshire, UK, has recently become operational and it is now available for the user community. Herein the main characteristics of the B23 SRCD beamline, the ancillary facilities available for users, and some of the recent advances achieved are summarized.

JCAMP-DX for circular dichroism spectra and metadata (IUPAC Recommendations 2012)

2012 ◽  
Vol 84 (10) ◽  
pp. 2171-2182 ◽  
Author(s):  
Benjamin Woollett ◽  
Daniel Klose ◽  
Richard Cammack ◽  
Robert W. Janes ◽  
B. A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Data Exchange ◽  
Data Bank ◽  
Cd Spectroscopy ◽  
Public Repository ◽  
Data Format ◽  
The Public ◽  
Compare And Contrast ◽  
Circular Dichroïsm

Circular dichroism (CD) spectroscopy is a widely used technique for the characterisation of proteins. A number of CD instruments are currently on the market, and there are more than a dozen synchrotron radiation circular dichroism (SRCD) beamlines in operation worldwide. All produce different output formats and contents. In order for users of CD and SRCD data to be able simply to compare and contrast data and the associated recorded or unrecorded metadata, it is essential to have a common data format. For this reason, the JCAMP-DX-CD format for CD spectroscopy has been developed, based on extensive consultations with users and senior representatives of all the instrument manufacturers and beamlines, and under the auspices of IUPAC, based on the Joint Committee on Atomic and Physical Data Exchange protocols. The availability of a common format is also important for deposition to, and access from, the Protein Circular Dichroism Data Bank, the public repository for CD and SRCD data and metadata. The JCAMP-DX-CD format can be read by standard JCAMP programs such as JSpecView. We have also created a series of parsers, available at the DichroJCAMP web site (http://valispec.cryst.bbk.ac.uk/formatConverter/dichroJCAMPDX-CD.html), which will enable the conversion between instrument and beamline formats and the JCAMP-DX-CD format.

Protein characterisation by synchrotron radiation circular dichroism spectroscopy

2009 ◽  
Vol 42 (4) ◽  
pp. 317-370 ◽  
Author(s):  
B. A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Protein Structures ◽  
Light Flux ◽  
Cd Spectroscopy ◽  
Drug Binding ◽  
Disordered Proteins ◽  
Wide Range ◽  
New Applications ◽  
Circular Dichroïsm

AbstractCircular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational/bioinformatics resources for secondary structure analyses that take advantage of the improved data quality available from SRCD. In summary, this review discusses how SRCD can be used for a wide range of structural and functional studies of proteins.

scholarly journals Calibration and standardisation of synchrotron radiation and conventional circular dichroism spectrometers. Part 2: Factors affecting magnitude and wavelength

2005 ◽  
Vol 19 (1) ◽  
pp. 43-51 ◽  
Author(s):  
Andrew J. Miles ◽  
Frank Wien ◽  
Jonathan G. Lees ◽  
B.A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Secondary Structure ◽  
Optical Rotation ◽  
Good Practice ◽  
Protein Secondary Structure ◽  
Cd Spectroscopy ◽  
Synchrotron Source ◽  
Calibration Methods ◽  
Circular Dichroïsm

Circular dichroism (CD) spectroscopy is an important tool in structural biology, especially for protein secondary structure analyses. Synchrotron radiation circular dichroism (SRCD) spectroscopy is a modified version of the technique that uses the intense light from a synchrotron source to enable the collection of data to much lower wavelengths than possible on conventional circular dichroism (cCD) instruments. There is a need for standardization of calibration methods amongst and between cCD and SRCD instruments to ensure consistency and the ability to use common reference databases for empirical secondary structural analyses. In a previous study (Spectroscopy17(2003), 653–661), we compared optical rotation measurements on several cCD and SRCD instruments, whilst holding constant other experimental factors. In this study, other experimental parameters which contribute to the spectral magnitude, such as cell pathlength and protein concentration determinations, are examined. In addition, the extent of wavelength calibration variations between instruments and their effects on secondary structure calculations have been examined. Hence, this paper provides additional practical guidance for “good practice” in the measurement of CD data.

scholarly journals Calibration and Standardisation of Synchrotron Radiation Circular Dichroism and Conventional Circular Dichroism Spectrophotometers

2003 ◽  
Vol 17 (4) ◽  
pp. 653-661 ◽  
Author(s):  
Andrew J. Miles ◽  
Frank Wien ◽  
Jonathan G. Lees ◽  
A. Rodger ◽  
Robert W. Janes ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Secondary Structure ◽  
Structural Biology ◽  
Optical Rotation ◽  
Protein Secondary Structure ◽  
Reference Database ◽  
Calibration Methods ◽  
Circular Dichroïsm ◽  
Representative Protein

Synchrotron radiation circular dichroism (SRCD) is an emerging technique in structural biology with particular value in protein secondary structure analyses since it permits the collection of data down to much lower wavelengths than conventional circular dichroism (cCD) instruments. Reference database spectra collected on different SRCD instruments in the future as well as current reference datasets derived from cCD spectra must be compatible. Therefore there is a need for standardization of calibration methods to ensure quality control. In this study, magnitude and optical rotation measurements on four cCD and three SRCD instruments were compared at 192.5, 219, 290 and 490 nm. At high wavelengths, all gave comparable results, however, at the lower wavelengths, some variations were observable. The consequences of these differences on the spectrum, and the calculated secondary structure, of a representative protein (myoglobin) are demonstrated. A method is proposed for standardising spectra obtained on any CD instrument, conventional or synchrotron‒based, with respect to existing and future databases.

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