A reference database for circular dichroism spectroscopy covering fold and secondary structure space

Bioinformatics

Volumn 22, Issue 16, 2006, Pages 1955-1962

  Lees, Jonathan G ^a,c   Miles, Andrew J ^a   Wien, Frank ^a,d   Wallace, B A ^a,b  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b DARESBURY LABORATORY   (United Kingdom)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^d SYNCHROTRON SOLEIL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; BIOPHYSICS; CIRCULAR DICHROISM; CLUSTER ANALYSIS; CONTROLLED STUDY; INFORMATION PROCESSING; MOLECULAR BIOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; RADIATION; REDUNDANCY ANALYSIS; REFERENCE DATABASE; SPECTRAL SENSITIVITY; STRUCTURAL BIOINFORMATICS; SYNCHROTRON;

EID: 33747855587     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl327     Document Type: Article

References (45)

1. Adzhubei,A.A. and Sternberg,M.J. (1993) Left-handed polyproline II helices commonly occur in globular proteins. J. Mol. Biol., 229, 472-493.
2. Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
3. Brunger,A.T. (1992) Free R Value: A novel statistical quantity for assessing the accurracy of crystal structures. Nature 355, 472-475.
4. Brahms,S. and Brahms,J. (1979) Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J. Mol. Biol., 138, 149-178.
5. Chen,Y.H. and Yang,J.T. (1971) A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular dichroism. Biochem. Biophys. Res. Commun., 44, 1285-1291.
6. Gilbert,A.T.B. and Hirst,J.D. (2004) Charge-transfer transitions in protein circular dichroism spectra. J. Mol. Struct. (THEOCHEM.), 675, 53-60.
7. Gill,S.C and von Hipple,P.H. (1989) Calculation of protein extinction coefficients from amino acid data. Anal. Biochem., 182, 319-326.
8. Hennessey,J.P.Jr and Johnson,W.C.Jr. (1981) Information content in the circular dichroism of proteins. Biochemistry, 20, 1085-1094.
9. Hobohm,U. et al. (1992) Selection of representative protein datasets. Protein Sci., 1, 409-417.
10. Janes,R.W. (2005) Bioinformatics analyses of circular dichroism protein reference databases. Bioinformatics, 21, 4230-4239.
11. Johnson,W.C.Jr. (1999) Analyzing protein circular dichroism spectra for accurate secondary structures. Proteins, 35, 307-312
12. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
13. Kelly,S.M. et al. (2005) How to study proteins by circular dichroism. Biochim. Biophys. Acta., 1751, 119-139.
14. Laskowski,R.A. et al. (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
15. Lees,J.G. et al. (2004) CDtool - an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving. Anal. Biochem., 332, 285-289.
16. Lobley,A. et al. (2002) DICHROWEB: An interactive website for the analysis of protein secondary structure from circular dichroism spectra. Bioinformatics, 18, 211-212.
17. MATLAB (2005). [7.0] MathWorks.
18. Matsuo,K. et al. (2004) Secondary-structure analysis of proteins by vacuum-ultraviolet circular dichroism spectroscopy. J. Biochem. (Tokyo), 135, 405-411.
19. Miles,A.J. and Wallace,B.A. (2006) Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics. Chem. Soc. Rev., 35, 39-51.
20. Miles,A.J. et al. (2003) Calibration and standardisation of synchrotron radiation circular dichroism (SRCD) amplitudes and conventional circular dichroism (CD) spectrophotometers. Spectroscopy, 17, 1-9.
21. Miles,A.J. et al. (2004) Redetermination of the extinction coefficient of camphor-10-sulfonic acid, a calibration standard for circular dichroism spectroscopy. Anal. Biochem., 335, 338-339.
22. Miles,A.J. et al. (2005) Calibration and standardisation of synchrotron radiation and conventional circular dichroism spectrometers. Part 2: factors affecting magnitude and wavelength. Spectroscopy, 19, 43-51.
23. Oberg,K.A. et al. (2003) Rationally selected basis proteins: A new approach to selecting proteins for spectroscopic secondary structure analysis. Protein Sci., 12, 2015-2031.
24. Oberg,K.A. et al. (2004) The optimization of protein secondary structure determination with infrared and circular dichroism spectra. Eur. J. Biochem., 271, 2937-2948.
25. Orengo,C.A. et al. (1994) Protein superfamilies and domain superfolds. Nature, 372, 631-634.
26. Orengo,C.A. et al. (2003) The CATH domain structure database. Methods Biochem. Anal., 44, 249-271.
27. Orry,A. et al. (2001) Synchrotron radiation circular dichroism spectroscopy: Vacuum ultraviolet irradiation does not damage protein integrity. J. Synchrotron Radiat., 8, 1027-1029.
28. Pancoska,P. and Keiderling,T.A. (1991) Systematic comparison of statistical analyses of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins. Biochemistry, 30, 6885-6895.
29. Pearl,F.M. et al. (2005) The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res., 33, 247-251.
30. Provencher,S.W. and Glockner,J. (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry, 20, 33-37.
31. Savitsky,A. and Golay,M.J.E. (1964) Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem., 36, 1627-1639.
32. Serrano-Andres,L. and Fulscher,M.P. (2003) Theoretical study of the electronic spectroscopy of peptides. III. Charge-transfer transitions in polypeptides. J. Am. Chem. Soc., 120, 10912-10920.
33. Sreerama,N. and 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. Anal. Biochem., 287, 252-260.
34. Sreerama,N. and Woody,R.W. (2003) Structural composition of beta(I)- and beta(II)-proteins. Protein Sci., 12, 384-388.
35. Sreerama,N. et al. (1999a) Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy. Protein Sci., 8, 370-380.
36. Sreerama,N. et al. (1999b) Tyrosine, phenylalanine, and disulfide contributions to the circular dichroism of proteins: Circular dichroism spectra of wild-type and mutant bovine pancreatic trypsin inhibitor. Biochemistry, 38, 10814-10822.
37. Toumadje,A. et al. (1992) Extending CD spectra of proteins to 168 nm improves the analysis for secondary structures. Anal. Biochem., 200, 321-331.
38. Wallace,B.A. (2000) Synchrotron radiation circular dichroism spectroscopy as a tool for investigating protein structures. J. Synchrotron Radiat., 7, 289-295.
39. Wallace,B.A. and Janes,R.W. (2001) Synchrotron radiation circular dichroism spectroscopy of proteins: Secondary structure, fold recognition and structural genomics. Curr. Opin. Chem. Biol., 5, 567-571.
40. Wallace,B.A. and Teeters,C.L. (1987) Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments. Biochemistry, 26, 65-70.
41. Wallace,B.A. et al. (2006) The Protein Circular Dichroism Data Bank (PCDDB): A bioinformatics and spectroscopic resource. Proteins, 62, 1-3.
42. Wallace,B.A. et al. (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 Discuss., 126, 237-243.
43. Whitmore,L. and Wallace,B.A. (2004) DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res., 32, 668-673.
44. Wien,F. and Wallace,B.A. (2005) Calcium fluoride micro cells for synchrotron radiation circular dichroism spectroscopy. Appl. Spectrosc., 59, 1109-1113.
45. Woody,R.W. (1996) Theory of circular dichroism of proteins. In Fasman,G.D. (ed), Circular Dichroism and the Conformational Analysis of Biomolecules. Plenum Press, New York. pp. 25-67.