Analyzing protein circular dichroism spectra for accurate secondary structures

Proteins: Structure, Function and Genetics

Volumn 35, Issue 3, 1999, Pages 307-312

  Johnson, W Curtis ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

Circular dichroism; Proteins; Secondary structure

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; CIRCULAR DICHROISM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

ALGORITHMS; CIRCULAR DICHROISM; PROTEIN STRUCTURE, SECONDARY; X-RAY DIFFRACTION;

EID: 0033562629     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990515)35:3<307::AID-PROT4>3.0.CO;2-3     Document Type: Article

References (33)

1. Greenfield N, Fasman GD. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 1969;8: 4108-4116.
2. Saxena VP, Wetlaufer DB. A new basis for interpreting the circular dichroism spectra of proteins. Proc Natl Acad Sci USA 1971;68:969-972.
3. Chen Y-H, Yang JT. A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular dichroism. Biochem Biophys Res Commun 1971;44:1285-1291.
4. Rosenkranz H, Scholten W. An improved method for the evaluation of helical protein conformation by means of circular dichroism. Hoppe-Seyler's Z Physiol Chem 1971;352:896-904.
5. Chen Y-H, Yang JT, Chan KH. Determination of the helix and β-form of proteins in aqueous solution by circular dichroism. Biochemistry 1974;13:3350-3359.
6. Bannister WH, Bannister JV. A study of three-component fitting of protein circular dichroism spectra. Int J Biochem 1974;5:679-686.
7. Chang CT, Wu C-SC, Yang JT. Circular dichroism analysis of protein conformation: inclusion of β-turns. Anal Biochem 1978;91: 13-31.
8. Brahms S, Brahms J. Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J Mol Biol 1980;138:149-178.
9. Bolotina IA, Chekhov VO, Lugauskas VYu, Finkel'shtein AV, Ptitsyn OB. Determination of the secondary structure of proteins from the circular dichroism spectra. 1. Protein reference spectra for α-, β-and irregular structures. Mol Biol (Eng. Transl.) 1980;14:701-709.
10. Provencher SW, Glöckner J. Estimation of protein secondary structure from circular dichroism. Biochemistry 1981;20:33-37.
11. Hennessey JP, Jr, Johnson WC, Jr. Information content in the circular dichroism of proteins. Biochemistry 1981;20:1085-1094.
12. Compton LA, Johnson WC, Jr. Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Anal Biochem 1986;155:155-167.
13. Manavalan P, Johnson WC, Jr. Variable selection method improves the prediction of protein secondary structure from circular dichroism. Anal Biochem 1987;167:76-85.
14. van Stokkum IHM, Spoelder HJW, Bloemendal M, van Grondelle R, Groen FCA. Estimation of protein secondary structure and error analysis from circular dichroism spectra. Anal Biochem 1990;191:110-118.
15. Pancoska P, Keiderling TA. Systematic comparison of statistical analysis of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins. Biochemistry 1991;30: 6885-6895.
16. Perczel A, Hollosi M, Tusnady G, Fasman GD. Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. Protein Eng 1991;4:669-679.
17. Böhm G, Muhr R, Jaenicke R. Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng 1992;5:191-195.
18. Perczel A, Park K, Fasman GD. Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide. Anal Biochem 1992;203:83-93.
19. Sreerama N, Woody RW. A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal Biochem 1993;209:32-44.
20. Sreerama N, Woody RW. Protein secondary structure from circular dichroism spectroscopy. Combining variable selection principle and cluster analysis with neural network, ridge regression and self-consistent methods. J Mol Biol 1994;242:497-507.
21. Dalmas B, Bannister WH. Prediction of protein secondary structure from circular dichroism spectra: an attempt to solve the problem of the best-fitting reference protein subsets. Anal Biochem 1995;225:39-48.
22. Rosenkranz H. Circular dichroism of globular proteins. A review of the limits of the CD methods for the calculation of secondary structure. Klin Chem Klin Biochem 1974;9:415-422.
23. Bannister WH, Bannister JV. Minireview: circular dichroism and protein structure. Int J Biochem 1974;5:673-677.
24. Woody RW. Circular dichroism of peptides. In: Hruby VJ, editors, The Peptides, Vol. 7. New York:Academic Press; 1985. p 15-114.
25. Yang JT, Wu C-SC, Martinez HM. Calculation of protein conformation from circular dichroism. Meth Enzymol 1986;130:208-269.
26. Johnson WC, Jr. Secondary structure of proteins through circular dichroism spectroscopy. Annu Rev Biophys Chem 1988;17:145-166.
27. Greenfield NJ. Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. Anal Biochem 1996;235:1-10.
28. Johnson WC, Jr. Analysis of circular dichroism spectra. Meth Enzymol 1992;210:426-447.
29. Manavalan P, Johnson WC, Jr. Protein secondary structure from circular dichroism spectra. Proc Int Symp Biomol Struct Interactions, Suppl J Biosci 1985;8:141-149.
30. Toumadje A, Alcorn SW, Johnson WC, Jr. Extending CD spectra of proteins to 168 nm improves the analysis of secondary structures. Anal Biochem 1992;200:321-331.
31. Mosteller F, Tukey JW. Data analysis and regression. Reading, MA: Addison-Wesley; 1977. 588 p.
32. Weisberg S. Applied linear regression. New York: John Wiley & Sons; 1980. 323 p.
33. King SM, Johnson WC. Assigning secondary structure from protein coordinate data. Proteins 1999;35:313-320.