Hostname: page-component-8448b6f56d-wq2xx Total loading time: 0 Render date: 2024-04-20T11:59:26.874Z Has data issue: false hasContentIssue false
  • English
  • Français

Protein characterisation by synchrotron radiation circular dichroism spectroscopy

Published online by Cambridge University Press:  10 May 2010

B. A. Wallace
B. A. Wallace*
Affiliation:
Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
*
*Author for correspondence: B. A. Wallace, Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, LondonWC1E 7HX, UK. Tel.:44-207-631-6800; Fax: 44-207-631-6803; Email: b.wallace@mail.cryst.bbk.ac.uk
Get access Rights & Permissions [Opens in a new window]

Abstract

Circular 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.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 42 , Issue 4 , November 2009 , pp. 317 - 370
Copyright
Copyright © Cambridge University Press 2010

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Andrade, M. A., Chacón, P., Merelo, J. J. & Morán, F. (1993). Evaluation of secondary structure of proteins from UV circular dichroism using an unsupervised learning neural network. Protein Engineering 6, 383–390.CrossRefGoogle ScholarPubMed
Arndt, E. R. & Stevens, E. S. (1993). Vacuum-ultraviolet circular dichroism studies of simple saccharides. Journal of the American Chemical Society 115, 7849–7853.CrossRefGoogle Scholar
Bagger, H. L., Hoffmann, S. V., Fuglsang, C. C. & Westh, P. (2007). Glycoprotein-surfactant interactions: a calorimetric and spectroscopic investigation of the phytase-SDS system. Biophysical Chemistry 129, 251–258.CrossRefGoogle ScholarPubMed
Balasubramanian, S., Schneider, T., Gerstein, M. & Regan, L. (2000). Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome. Nucleic Acids Research 28, 3075–3082.CrossRefGoogle Scholar
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research 28, 235–242.CrossRefGoogle ScholarPubMed
Besley, N. A. & Hirst, J. D. (1999). Theoretical studies toward quantitative protein circular dichroism calculations. Journal of the American Chemical Society 121, 9636–9644.CrossRefGoogle Scholar
Bulheller, B. M. & Hirst, J. D. (2009). Ab initio calculations for circular dichroism and synchrotron radiation circular dichroism spectroscopy of proteins. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 202–215. Amsterdam: IOS Press.Google Scholar
Bulheller, B. M., Miles, A. J., Wallace, B. A. & Hirst, J. (2008). Charge-transfer transitions in the vacuum ultraviolet of protein circular dichroism spectra. Journal of Physical Chemistry B 112, 1866–1874.CrossRefGoogle ScholarPubMed
Cascio, M. & Wallace, B. A. (1995). Effects of local environment on the circular dichroism spectra of polypeptides. Analytical Biochemistry 227, 90–100.CrossRefGoogle ScholarPubMed
Cerasoli, E., Kelly, S., Coggins, J. R., Boam, D. J., Clarke, D. T. & Price, N. C. (2002). The refolding of type II shikamate kinase from Erwinia chrysanthemi after denaturation in urea. European Journal of Biochemistry 269, 2124–2132.CrossRefGoogle ScholarPubMed
Chen, Y. & Wallace, B. A. (1997). Secondary solvent effects on the circular dichroism spectra of polypeptides: influence of polarisation effects on the far ultraviolet spectra of alamethicin. Biophysical Chemistry 65, 65–74.CrossRefGoogle ScholarPubMed
Clarke, D. T. & Jones, G. R. (1999). Extended circular dichroism measurements using synchrotron radiation show that the assembly of clatherin coats requires no change in secondary structure. Biochemistry 38, 10457–10462.CrossRefGoogle Scholar
Clarke, D. T. & Jones, G. R. (2004). CD12: a new high-flux beamline for ultraviolet and vacuum-ultraviolet circular dichroism on the SRS, Daresbury. Journal of Synchrotron Radiation 11, 142–149.CrossRefGoogle ScholarPubMed
Clarke, D. T., Doig, A. J., Stapeley, B. J. & Jones, G. R. (1999). The alpha-helix folds on a millisecond time scale. Proceedings of the National Academy of Sciences USA 96, 7232–7237.CrossRefGoogle ScholarPubMed
Clarke, D. T., Bowler, M. A., Fell, B. D., Flaherty, J. V., Grant, A. F., Jones, G. R., Martin-Fernandez, M. L., Shaw, D. A., Todd, B., Wallace, B. A. & Towns-Andrews, E. (2000). A high aperature beamline for vacuum ultraviolet circular dichroism on the SRS. Synchrotron Radiation News 13, 21–27.CrossRefGoogle Scholar
Compton, L. A. & Johnson, W. C. Jr., (1986). Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Analytical Biochemistry 155, 155–167.CrossRefGoogle ScholarPubMed
Cowieson, N. P., Miles, A. J., Robin, G., Forwood, J. K., Kobe, B., Martin, J. L. & Wallace, B. A. (2008). Evaluating protein: protein complex formation using synchrotron radiation circular dichroism spectroscopy. Proteins: Structure, Function, and Bioinformatics 70, 1142–1146.CrossRefGoogle ScholarPubMed
Cronin, N., O'Reilly, A., Duclohier, H. & Wallace, B. A. (2003). Binding of the anticonvulsant drug lamotrigine and the neurotoxin batrachotoxin to voltage-gated sodium channels induces conformational changes associated with block and steady-state activation. Journal of Biological Chemistry 278, 10675–10682.CrossRefGoogle ScholarPubMed
Cronin, N. B., O'Reilly, A., Duclohier, H. & Wallace, B. A. (2005). Effects of deglycosylation of sodium channels on their structure and function. Biochemistry 44, 441–449.CrossRefGoogle ScholarPubMed
Dicko, C., Knight, D., Kenney, J. M. & Vollrath, F. (2004). Structural conformation of spidroin in solution: a synchrotron radiation circular dichroism study. Biomacromolecules 5, 758–767.CrossRefGoogle ScholarPubMed
Dicko, C., Hicks, M. R., Dafforn, T. R., Vollrath, F., Rodger, A. & Hoffmann, S. V. (2008). Breaking the 200 nm limit for routine flow linear dichroism measurements using UV synchrotron radiation. Biophysical Journal 95, 5974–5977.CrossRefGoogle ScholarPubMed
Edwards, Y. J., Lobley, A., Pentony, M. M. & Jones, D. T. (2009). Insights into the regulation of intrinsically disordered proteins in the human proteome by analysing sequence and gene expression data. Genome Biology 10, R50.CrossRefGoogle Scholar
Evans, P., Wyatt, K., Wistow, G. J., Bateman, O. A., Wallace, B. A. & Slingsby, C. (2004). The P23T cataract mutation causes loss of solubility of folded γD-crystallin. Journal of Molecular Biology 343, 435–444.CrossRefGoogle ScholarPubMed
Evans, P., Bateman, O. A., Slingsby, C. & Wallace, B. A. (2007). A reference dataset for circular dichroism spectroscopy tailored for the βγ-crystallin lens proteins. Experimental Eye Research 84, 1001–1008.CrossRefGoogle ScholarPubMed
France, L. L., Kieleczawa, J., Dunn, J. J., Hind, G. & Sutherland, J. C. (1992). Structural analysis of an outer surface protein from the lyme disease spirochete, Borrelia burgdorferi, using circular dichroism and fluorescence spectroscopy. Biochimica Biophysica Acta 1120, 59–68.CrossRefGoogle ScholarPubMed
Fukuyama, T., Matsuo, K. & Gekko, K. (2005). Vacuum-ultraviolet electronic circular dichroism of L-alanine in aqueous solution investigated by time-dependent density functional theory. Journal of Physical Chemistry A 109, 6928–6933.CrossRefGoogle ScholarPubMed
Garone, L., Albaugh, S. & Steiner, R. F. (1990). The secondary structure of turkey gizzard myosin light chain kinase and the nature of its interaction with calmodulin. Biopolymers 30, 1139–1149.CrossRefGoogle ScholarPubMed
Gilbert, A. T. B. & Hirst, J. D. (2004). Charge-transfer transitions in protein circular dichroism spectra. Journal of Molecular Structure (Theochem) 675, 53–60.CrossRefGoogle Scholar
Gitter-Amir, A., Rosenheck, K. & Schneider, A. S. (1976). Angular scattering analysis of the circular dichroism of biological cells. 1. The red blood cell membrane. Biochemistry 15, 3131–3137.CrossRefGoogle ScholarPubMed
Gray, D. M., Lang, D., Kuner, E., Vaughan, M. & Sutherland, J. (1984). A thin quartz cell suitable for vacuum ultraviolet-absorption and circular-dichroism measurements. Analytical Biochemistry 136, 247–250.CrossRefGoogle ScholarPubMed
Grossmann, J. G., Hall, J. F., Kanbi, L. D. & Hasnain, S. S. (2002). The N-terminal extension of rusticyanin is not responsible for its acid stability. Biochemistry 41, 3613–3619.CrossRefGoogle Scholar
Guerra-Giraldez, C., Moore, B., Neves, B., Wallace, B. A., Svergun, D. I., Brown, K. A. & Smith, D. F. (2005). Structural and functional analysis of the Leishmania infective stage-specific protein, SHERP. 3rd International Congress on Leishmania and Leishmaniasis Abstracts.Google Scholar
GUIDELINE Q6B (2001). International conference on harmonisation of technical requirements for registration of pharmaceuticals for human use.Google Scholar
Hoffmann, A., Kane, A., Nettels, D., Hertzog, D. E., Baumgärtel, P., Lengefeld, J., Reichardt, G., Horsley, D. A., Seckler, R., Bakajin, O. & Schuler, B. (2007). Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. Proceedings of the National Academy of Sciences USA 104, 105–110.CrossRefGoogle ScholarPubMed
Hoiberg-Nielsen, R., Shelton, A. P. T., Sorensen, K. K., Roessle, M., Svergun, D. I., Thulstrup, P. W., Jensen, K. J. & Arleth, L. (2008). 3- instead of 4-helix formation in a de novo designed protein in solution revealed by small angle X-ray scattering. Chembiochem 9, 2663–2572.CrossRefGoogle Scholar
Janes, R. W. (2005). Bioinformatics analyses of circular dichroism protein reference databases. Bioinformatics 21, 4230–4238.CrossRefGoogle ScholarPubMed
Janes, R. W. & Cuff, A. L. (2005). Overcoming protein denaturation caused by a high-flux synchrotron radiation circular dichroism beamline. Journal of Synchrotron Radiation 12, 524–529.CrossRefGoogle ScholarPubMed
Johnson, K. H., Gray, D. M. & Sutherland, J. C. (1991). Vacuum UV CD spectra of homopolymer duplexes and triplexes containing AT or AU base-pairs. Nucleic Acids Research 19, 2275–2280.CrossRefGoogle ScholarPubMed
Jones, C., Schiffmann, D., Knight, A. & Windsor, S. (2004). Val-CiD best practice guide: CD spectroscopy for the quality control of biopharmaceuticals. National Physical LAB report DQL-AS 008.Google Scholar
Kane, A. S., Hoffmann, A., Baumgartel, P., Seckler, R., Reichardt, G., Horsley, D. A., Schuler, B. & Bakajin, O. (2008). Microfluidic mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy. Analytical Chemistry 24, 9534–9541.CrossRefGoogle Scholar
Kelly, S. M. & Price, N. C. (2009). Sample preparation and good practice in circular dichroism spectroscopy. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 91–107. Amsterdam: IOS Press.Google Scholar
Kelly, S. M., Jess, T. J. & Price, N. C. (2005). How to study proteins by circular dichroism. Biochimica Biophysica. Acta 1751, 119–139.CrossRefGoogle ScholarPubMed
Laskowski, R. A., Macarthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK – a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26, 283–291.CrossRefGoogle Scholar
Lees, J. G. & Janes, R. W. (2008). Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations. BMC Bioinformatics 9, 24.CrossRefGoogle ScholarPubMed
Lees, J. & Wallace, B. A. (2002). Synchrotron radiation circular dichroism and conventional circular dichroism spectroscopy: a comparison. Spectroscopy 16, 121–125.CrossRefGoogle Scholar
Lees, J. G., Smith, B. R., Wien, F., Miles, A. J. & Wallace, B. A. (2004). CDtool – An integrated software package for circular dichroism spectroscopic data processing, analysis and archiving. Analytical Biochemistry 332, 285–289.CrossRefGoogle ScholarPubMed
Lees, J. G., Miles, A. J., Wien, F. & Wallace, B. A. (2006a). A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics 22, 1955–1962.CrossRefGoogle ScholarPubMed
Lees, J. G., Miles, A. J., Janes, R. W. & Wallace, B. A. (2006b). Optimisation and development of novel methodologies for secondary structure prediction from circular dichroism spectra. BMC Bioinformatics 7, 507–517.CrossRefGoogle Scholar
Liu, H. L., Peng, X. H., Zhao, F., Zhang, G. B., Tao, Y., Luo, Z. F., Li, Y., Teng, M. K., Li, X. & Wei, S. Q. (2009). N114S mutation causes loss of ATP-induced aggregation of human phosphoribosylpyrophosphate synthetase 1. Biochemical and Biophysical Research Communications 379, 1120–1125.CrossRefGoogle ScholarPubMed
Lobley, A., Whitmore, L. & Wallace, B. A. (2002). DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra. Bioinformatics 18, 211–212.CrossRefGoogle ScholarPubMed
Manolopoulos, S., Clarke, D., Derbyshire, G., Jones, G., Read, P. & Torbet, M. (2004). A new multichannel detector for proteomics studies and circular dichroism. Nuclear Instruments and Methods in Physics Research Section A – Accelerators Spectrometers Detectors and Associated Equipment 531, 302–306.Google Scholar
Mao, D. & Wallace, B. A. (1984). Differential light scattering and absorption flattening optical effects are minimal in the circular dichroism spectra of small unilamellar vesicles. Biochemistry 23, 2667–2673.CrossRefGoogle ScholarPubMed
Mao, D., Wachter, E. & Wallace, B. A. (1982). Folding of the H+-ATPase proteolipid in phospholipid vesicles. Biochemistry 21, 4960–4968.CrossRefGoogle ScholarPubMed
Matsuo, K. & Gekko, K. (2004). Vacuum-ultraviolet circular dichroism study of saccharides by synchrotron radiation spectrophotometry. Carbohydrate Research 339, 591–597.CrossRefGoogle ScholarPubMed
Matsuo, K., Sakai, K., Matsushima, Y., Fukuyama, T. & Gekko, K. (2003). Optical cell with a temperature-control unit for a vacuum-ultraviolet circular dichroism spectrophotometer. Analytical Sciences 19, 129–132.CrossRefGoogle ScholarPubMed
Matsuo, K., Yonehara, R. & Gekko, K. (2004). Secondary-structure analysis of proteins by vacuum-ultraviolet circular dichroism spectroscopy. Journal of Biochemistry 135, 405–411.CrossRefGoogle ScholarPubMed
Matsuo, K., Yonehara, R. & Gekko, K. (2005). Improved estimation of the secondary structures of proteins by vacuum-ultraviolet circular dichroism spectroscopy. Journal of Biochemistry 138, 79–88.CrossRefGoogle ScholarPubMed
Matsuo, K., Sakurada, Y., Yonehara, R., Kataoka, M. & Gekko, K. (2007). Secondary structure analysis of denatured proteins by vaccum ultraviolet circular dichroism spectroscopy. Biophysical Journal 92, 4088–4098.CrossRefGoogle Scholar
Matsuo, K., Watanabe, H. & Gekko, K. (2008). Improved sequence-based prediction of protein secondary structures by combining vacuum ultraviolet circular dichroism spectroscopy with neural network. Proteins: Structure Function and Bioinformatics 73, 104–112.CrossRefGoogle ScholarPubMed
Maytum, R. & Janes, R. W. (2007). Synchrotron radiation circular dichroism spectroscopy reveals a new structural transition in tropomyosin. Biophysical Journal 92, 362a.Google Scholar
Mckibbin, C., Farmer, N. A., Jeans, C., Reeves, P. J., Khorana, H. G., Wallace, B. A., Edwards, P. C., Villa, C. & Booth, P. J. (2007). Opsin stability and folding: modulation by phospholipid bicelles. Journal of Molecular Biology 374, 1319–1332.CrossRefGoogle ScholarPubMed
Miles, A. J. & Wallace, B. A. (2006). Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics. Chemical Society Reviews 35, 39–51.CrossRefGoogle Scholar
Miles, A. J. & Wallace, B. A. (2007). Synchrotron radiation circular dichroism (SRCD) spectroscopy: protein fold and supersecondary structure recognition. Biophysical Journal 92, 337a.Google Scholar
Miles, A. J. & Wallace, B. A. (2009a). Calibration techniques for circular dichroism and synchrotron radiation circular dichroism spectroscopy. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 73–90. Amsterdam: IOS Press.Google Scholar
Miles, A. J. & Wallace, B. A. (2009b). Sample preparation and good practice in synchrotron radiation circular dichroism spectroscopy. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 108–124. Amsterdam: IOS Press.Google Scholar
Miles, A. J., Wien, F., Lees, J. G., Rodger, A., Janes, R. W. & Wallace, B. A. (2003). Calibration and standardisation of synchrotron radiation circular dichroism and conventional circular dichroism spectrophotometers. Spectroscopy 17, 653–661.CrossRefGoogle Scholar
Miles, A. J., Wien, F. & Wallace, B. A. (2004). Redetermination of the extinction coefficient of camphor-β-sulfonic acid, a calibration standard for circular dichroism spectroscopy. Analytical Biochemistry 335, 338–339.CrossRefGoogle ScholarPubMed
Miles, A. J., Wien, F., Lees, J. G. & Wallace, B. A. (2005a). Calibration and standardisation of synchrotron radiation and conventional circular dichroism spectrometers. Part 2: Factors affecting magnitude and wavelength. Spectroscopy 19, 43–51.CrossRefGoogle Scholar
Miles, A. J., Whitmore, L. & Wallace, B. A. (2005b). Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data. Protein Science 14, 368–374.CrossRefGoogle ScholarPubMed
Miles, A. J., Hoffmann, S. V., Tao, Y., Janes, R. W. & Wallace, B. A. (2007). Synchrotron radiation circular dichroism (SRCD) spectroscopy: new beamlines and new applications in biology. Spectroscopy 21, 245–255.CrossRefGoogle Scholar
Miles, A. J., Janes, R. W., Brown, A., Clarke, D. T., Sutherland, J. C., Tao, Y., Wallace, B. A. & Hoffmann, S. V. (2008a). Light flux density threshold at which protein denaturation is induced by synchrotron radiation circular dichroism (SRCD) beamlines. Journal of Synchrotron Radiation 15, 420–422.CrossRefGoogle ScholarPubMed
Miles, A. J., Drechsler, A., Kristan, K., Anderluh, G., Norton, R. S., Wallace, B. A. & Separovic, F. (2008b). The effects of lipids on the structure of the eukaryotic cytolysin equinatoxin II: a synchrotron radiation circular dichroism spectroscopic study. Biochimica Biophysica Acta 1778, 2091–2096.CrossRefGoogle ScholarPubMed
Miron, S., Réfregiers, M., Gilles, A.-M. & Maurizot, J.-C. (2005). New synchrotron radiation circular dichroism end-station on DISCO beamline at SOLEIL synchrotron for biomolecular analysis. Biochimica Biophysica Acta 1725, 425–431.CrossRefGoogle Scholar
Nesgaard, L. W., Hoffmann, S. V., Andersen, C. B., Malmendal, A. & Otzen, D. E. (2008). Characterization of dry globular proteins and protein fibrils by synchrotron radiation circular vacuum UV circular dichroism. Biopolymers 89, 779–795.CrossRefGoogle ScholarPubMed
NIH NOTICE NOT-OD-03-032. (2003). Sharing research data.Google Scholar
Oakley, M. T. & Hirst, J. D. (2006). Charge-transfer transitions in protein circular dichroism calculations. Journal of the American Chemical Society 128, 12414–12415.CrossRefGoogle ScholarPubMed
Oberg, K. A., Ruysschaert, J. M. & Goormaghtigh, E. (2004). The optimization of protein secondary structure determination with infrared and circular dichroism spectra. European Journal of Biochemistry 271, 2937–2948.CrossRefGoogle ScholarPubMed
Ojima, N., Sakai, K., Fukazawa, T. & Gekko, K. (2000). Vacuum-ultraviolet circular dichroism spectrophotometer using synchrotron radiation: optical system and off-line performance. Chemistry Letters 7, 832–833.CrossRefGoogle Scholar
O'Reilly, A. O., Charalambous, K., Nurani, G., Powl, A. M. & Wallace, B. A. (2008). G219S mutagenesis as a means of stabilising conformational flexibility in the bacterial sodium channel NaChBac. Molecular Membrane Biology 25, 670–676.CrossRefGoogle ScholarPubMed
Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997). CATH – a hierarchic classification of protein domain structures. Structure 5, 1093–1108.CrossRefGoogle Scholar
Orry, A., Janes, R. W., Sarra, R., Hanlon, M. R. & Wallace, B. A. (2001). Synchrotron radiation circular dichroism spectroscopy: vacuum ultraviolet irradiation does not damage protein integrity. Journal of Synchrotron Radiation 8, 1027–1029.CrossRefGoogle Scholar
Park, K., Perczel, A. & Fasman, G. D. (1992). Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. Protein Science 1, 1032–1049.CrossRefGoogle ScholarPubMed
Provencher, S. W. & Glockner, J. (1981). Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20, 33–37.CrossRefGoogle ScholarPubMed
Qi, X. L., Holt, C., McNulty, D., Clarke, D. T., Brownlow, S. & Jones, G. R. (1997). Effect of temperature on the secondary structure of beta-lactoglobulin at pH 6.7, as determined by CD and IR spectroscopy: a test of the molten globule hypothesis. Biochemical Journal 324, 341–346.CrossRefGoogle ScholarPubMed
Qian, H. J., Yan, Y. L. & Tao, Y. (2003). Design and calibration of the monochromator in 3B1B beamline. High Energy Physics and Nuclear Physics – Chinese Edition 27, 125–128.Google Scholar
Ravi, J., Hills, A. E. & Knight, A. E. (2009). Reproducible circular dichroism measurements for biopharmaceutical applications. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 125–140. Amsterdam: IOS Press.Google Scholar
Richards, M. W., Hanlon, M. R., Berrow, N. S., Butcher, A., Dolphin, A. C. & Wallace, B. A. (2002). Synchrotron radiation circular dichroism (SRCD) and CD spectroscopic studies of the voltage-dependent calcium channel beta subunit and its domains. Biophysical Journal 82, 456a.Google Scholar
Rodger, A. (2009). Linear dichroism spectroscopy: techniques and applications. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 165–182. Amsterdam: IOS Press.Google Scholar
Scott, D. J., Grossmann, J. G., Tames, J. R. H., Byron, O., Wilson, K. S. & Otto, B. R. (2002). Low resolution solution structure of the apo form of Escherichia coli haemoglobin protease Hbp. Journal of Molecular Biology 315, 1179–1187.CrossRefGoogle ScholarPubMed
Serrano-Andres, L. & Fulscher, M. P. (2003). Theoretical study of the electronic spectroscopy of peptides. III. Charge-transfer transitions in polypeptides. Journal of the American Chemical Society 120, 10912–10920.CrossRefGoogle Scholar
Snyder, P. A. & Rowe, E. M. (1980). The first use of synchrotron radiation for vacuum ultraviolet circular dichroism measurements. Nuclear Instruments and Methods in Physics Research 172, 345–349.CrossRefGoogle Scholar
Sreerama, N. & Woody, R. W. (1994). Poly(Pro)II type structure in globular proteins – identification and CD analysis. Biochemistry 33, 10022–10025.CrossRefGoogle Scholar
Sreerama, N. & Woody, R. W. (2000). Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Analytical Biochemistry 287, 252–260.CrossRefGoogle ScholarPubMed
Sreerama, N. & Woody, R. W. (2003). Structural composition of beta(I)- and beta(II)-proteins. Protein Science 12, 384–388.CrossRefGoogle Scholar
Sreerama, N., Venyaminov, S. Y. & Woody, R. W. (2000). Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis. Analytical Biochemistry 287, 243–251.CrossRefGoogle ScholarPubMed
Stanley, W. A., Sokolova, A., Brown, A., Clarke, D. T., Wilmanns, M. & Svergun, D. I. (2004). Synergistic use of synchrotron radiation techniques for biological samples in solution: a case study on protein-ligand recognition by the peroxisomal import receptor Pex5p, Journal of Synchrotron Radiation 11, 490–496.CrossRefGoogle ScholarPubMed
Sutherland, J. C. (1996). Circular dichroism using synchrotron radiation. In Circular Dichroism and the Conformational Analysis of Biomolecules (ed. Fasman, G. D.), pp. 599–633. New York: Plenum Press.CrossRefGoogle Scholar
Sutherland, J. C. (2002). Simultaneous measurement of circular dichroism and fluorescence polarization anisotropy. Clinical Diagnostic Systems: Technologies and Instrumentation 4625, 126–136.Google Scholar
Sutherland, J. C. (2009). Measurement of circular dichroism and related spectroscopies with conventional and synchrotron light sources: theory and instrumentation. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 19–72. Amsterdam: IOS Press.Google Scholar
Sutherland, J. C., Desmond, E. J. & Takacs, P. Z. (1980). Versatile spectrometer for experiments using synchrotron radiation at wavelengths greater than 100 nm. Nuclear Instruments and Methods in Physics Research 172, 195–199.CrossRefGoogle Scholar
Sutherland, J. C., Emrick, A., France, L. L., Monteleone, D. C. & Trunk, J. (1992). Circular dichroism user facility at the National Synchrotron Light Source – estimation of protein secondary structure. Biotechniques 13, 588–590.Google ScholarPubMed
Symmons, M. F., Buchanan, S. G. S., Clarke, D. T., Jones, G. & Gay, N. J. (1997). X-ray diffraction and far-UV CD studies of filaments formed by a leucine-rich repeat peptide: structural similarity to the amyloid fibrils of prions and Alzheimer's disease beta-protein. FEBS Letters 412, 397–403.CrossRefGoogle Scholar
Tanaka, M., Yagi-Watanabe, K., Yamada, T., Kaneko, F. & Nakagawa, K. (2006). Development of vacuum-ultraviolet circular dichroism measurement system using a polarizing undulator. Chirality 18, 196–204.CrossRefGoogle ScholarPubMed
Tao, Y. & Wallace, B. A. (2009). SRCD2009. Synchtrotron Radiation News 22, 2–4.CrossRefGoogle Scholar
Teeters, C. L., Eccles, J. & Wallace, B. A. (1987). A theoretical analysis of the effects of sonication on differential absorption flattening in suspensions of membrane sheets. Biophysical Journal 51, 527–532.CrossRefGoogle ScholarPubMed
Thulstrup, P. W., Brask, J., Jensen, K. J. & Larsen, E. (2005). Synchrotron radiation circular dichroism spectroscopy applied to metmyoglobin and a 4-alpha-helix bundle carboprotein. Biopolymers 78, 46–52.CrossRefGoogle Scholar
Toumadje, A., Alcorn, S. W. & Johnson, W. C. Jr., (1992). Extending CD spectra of proteins to 168 nm improves the analysis for secondary structures. Analytical Biochemistry 200, 321–331.CrossRefGoogle ScholarPubMed
Van Stokkum, I. H. M., Spoelder, H. J. W., Bloemendal, M., Van Grondelle, R. & Groen, F. C. A. (1990). Estimation of protein secondary structure and error analysis from CD spectra. Analytical Biochemistry 191, 110–118.CrossRefGoogle Scholar
Vriend, G. (1990). WHATIF – a molecular modeling and drug design program. Journal of Molecular Graphics 8, 52–56.CrossRefGoogle Scholar
Wallace, B. A. (2000a). Conformational changes by synchrotron radiation circular dichroism spectroscopy. Nature Structural Biology 7, 708–709.CrossRefGoogle ScholarPubMed
Wallace, B. A. (2000b). Synchrotron radiation circular dichroism spectroscopy as a tool for investigating protein structures. Journal of Synchrotron Radiation 7, 289–295.CrossRefGoogle ScholarPubMed
Wallace, B. A. & Janes, R. W. (2001). Synchrotron radiation circular dichroism spectroscopy of proteins: secondary structure, fold recognition, and structural genomics. Current Opinions in Chemical Biology 5, 567–571.CrossRefGoogle ScholarPubMed
Wallace, B. A. & Janes, R. W. (2003). Circular dichroism and synchrotron radiation circular dichroism spectroscopy: tools for drug discovery. Biochemical Transactions 31, 631–633.CrossRefGoogle ScholarPubMed
Wallace, B. A. & Janes, R. W., eds. (2009). Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy. Amsterdam: IOS Press.Google Scholar
Wallace, B. A. & Janes, R. W. (2010). Synchrotron radiation circular dichroism (SRCD) spectroscopy – An enhanced method for examining protein conformations and protein interactions. Biochemical Society Transactions, in press.CrossRefGoogle Scholar
Wallace, B. A. & Mao, D. (1984). Circular dichroism analyses of membrane proteins: an examination of light scattering and absorption flattening in large membrane vesicles and membrane sheets. Analytical Biochemistry 142, 317–328.CrossRefGoogle ScholarPubMed
Wallace, B. A. & Teeters, C. L. (1987). Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments. Biochemistry 26, 65–70.CrossRefGoogle ScholarPubMed
Wallace, B. A., Lees, J., Orry, A. J. W., Lobley, A. & Janes, R. W. (2003). Analyses of circular dichroism spectra of membrane proteins. Protein Science 12, 875–884.CrossRefGoogle ScholarPubMed
Wallace, B. A., Wien, F., Miles, A. J., Lees, J. G., Hoffmann, S. V., Evans, P., Wistow, G. J. & Slingsby, C. (2004). Biomedical applications of synchrotron radiation circular dichroism spectroscopy: identification of mutant proteins associated with disease and development of a reference database for fold motifs. Faraday Discussions 17, 653–661.Google Scholar
Wallace, B. A., Whitmore, L. & Janes, R. W. (2006). The protein circular dichroism data bank (PCDDB): a bioinformatics and spectroscopic resource. Proteins: Structure, Function and Bioinformatics 62, 1–3.CrossRefGoogle ScholarPubMed
Warne, T., Serrano-Vega, M. J., Tate, C. G. & Schertler, G. F. X. (2009). Development and crystallization of a minimal thermostabilised G protein-coupled receptor. Protein Expression and Purification 65, 204–213.CrossRefGoogle ScholarPubMed
Wien, F. & Wallace, B. A. (2005). Calcium fluoride micro cells for synchrotron radiation circular dichroism spectroscopy. Applied Spectroscopy 59, 1109–1113.CrossRefGoogle ScholarPubMed
Wien, F., Miles, A. J., Lees, J. G., Hoffmann, S. V. & Wallace, B. A. (2005). VUV irradiation effects on proteins in high flux synchrotron radiation circular dichroism (SRCD) spectroscopy. Journal of Synchrotron Radiation 12, 517–523.CrossRefGoogle Scholar
Whitmore, L. & Wallace, B. A. (2004). DICHROWEB, An online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Research 32, W668–W673.CrossRefGoogle ScholarPubMed
Whitmore, L. & Wallace, B. A. (2008). Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers 89, 392–400.CrossRefGoogle ScholarPubMed
Whitmore, L. & Wallace, B. A. (2009). Methods of analysis for circular dichroism spectroscopy of proteins and the DichroWeb server. In Modern Techniques for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy (eds. Wallace, B. A. & Janes, R. W.), pp. 165–182. Amsterdam: IOS Press.Google Scholar
Whitmore, L., Janes, R. W. & Wallace, B. A. (2006). Protein circular dichroism data bank (PCDDB): data bank and website design. Chirality 18, 426–429.CrossRefGoogle ScholarPubMed
Woody, R. W. (1996). Theory of circular dichroism of proteins. In Circular Dichroism and the Conformational Analysis of Biomolecules (ed. Fasman, G. D.), pp. 25–67. New York: Plenum Press.CrossRefGoogle Scholar
Yagi-Watanabe, K., Tanaka, M., Yamada, T., Kaneko, F., Nakagawa, K. & Yuri, M. (2005). A vacuum ultraviolet polarimeter with quadruple-reflectors: polarization measurements at the TERAS BL-5 beamline. Nuclear Instruments and Methods in Physics Research Section A –Accelerators Spectrometers Detectors and Associated Equipment 553, 620–626.Google Scholar