Rationally selected basis proteins: A new approach to selecting proteins for spectroscopic secondary structure analysis

Protein Science

Volumn 12, Issue 9, 2003, Pages 2015-2031

  Oberg, Keith A ^a   Ruysschaert, Jean Marie ^a   Goormaghtigh, Erik ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Analysis; Basis sets, protein; Chemometrics; Circular dichroism; Crystallography; Data interpretation; Databases, protein; Infrared spectroscopy; Methods; Proteins; Secondary structure; Statistical analysis

Indexed keywords

ALPHA HELIX; ARTICLE; BETA SHEET; CHEMOMETRIC ANALYSIS; CIRCULAR DICHROISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DATA BASE; INFRARED SPECTROSCOPY; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; QUALITY CONTROL; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

CIRCULAR DICHROISM; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES; MASS SPECTROMETRY; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEOMICS; SOFTWARE; SPECTROPHOTOMETRY, INFRARED; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; STATISTICS;

EID: 0042510990     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0354703     Document Type: Article

References (57)

1. Bairoch, A. and Apweiler, R. 1997. The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res. 25: 31-36.
2. -. 1998. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 26: 38-42.
3. Bairoch, A. and Boeckmann, B. 1991. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 19 (Suppl.): 2247-2249.
4. Barth, A. 2000. The infrared absorption of amino acid side chains. Prog. Biophy. Mol. Biol. 74: 141-173.
5. Barton, G.J. 1994. SCOP: Structural classification of proteins. Trends Biochem. Sci. 19: 554-555.
6. 2O. J. Mol. Biol. 259: 774-791.
7. Brahms, S. and Brahms, J. 1980. Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J. Mol. Biol. 138: 149-178.
8. Chang, C.T., Wu, C.S., and Yang, J.T. 1978. Circular dichroic analysis of protein conformation: Inclusion of the β-turns. Anal. Biochem. 91: 13-31.
9. 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.
10. Chen, Y.H., Yang, J.T., and Martinez, H.M. 1972. Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. Biochemistry 11: 4120-4131.
11. Chen, Y.H., Yang, J.T., and Chau, K.H. 1974. Determination of the helix and β form of proteins in aqueous solution by circular dichroism. Biochemistry, 13: 3350-3359.
12. Dodge, C., Schneider, R., and Sander, C. 1998. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 26: 313-315.
13. Dousseau, F. and Pezolet, M. 1990. Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods. Biochemistry 29: 8771-8779.
14. Flores, T.P., Orengo, C.A., Moss, D.S., and Thornton, J.M. 1993. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2: 1811-1826.
15. Gill, S.C. and von Hippel, P.H. 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182: 319-326.
16. Goormaghtigh, E., Cabiaux, V., and Ruysschaert, J.M. 1994. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. III. Secondary structures. Subcell. Biochem. 23: 405-450.
17. Goormaghtigh, E., de Jongh, H.H., and Ruysschaert, J.M. 1996. Relevance of thin films prepared for attenuated total reflection Fourier transform infrared spectroscopy: Significance of the pH. Appl. Spectrosc. 50:1519-1527.
18. Greenfield, N. and Fasman, G.D. 1969. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8, 4108-4116.
19. Grishina, I.B. and Woody, R.W. 1994. Contributions of tryptophan side chains to the circular dichroism of globular proteins: Exciton couplets and coupled oscillators. Faraday Discuss. 99: 245-262.
20. Hennessey Jr., J.P. and Johnson Jr., W.C. 1981. Information content in the circular dichroism of proteins. Biochemistry 20: 1085-1094.
21. Hilbert, M., Bohm, G., and Jaenicke, R. 1993. Structural relationships of homologous proteins as a fundamental principle in homology modeling. Proteins 17: 138-151.
22. Hobohm, U. and Sander, C, 1994. Enlarged representative set of protein structures. Protein Sci. 3: 522-524.
23. Hobohm, U., Scharf, M., Schneider, R., and Sander, C. 1992. Selection of representative protein data sets. Protein Sci. 1: 409-417.
24. Hooft, R.W., Vriend, G., Sander, C., and Abola, E.E. 1996. Errors in protein structures. Nature 381: 272.
25. Hubbard, T.J.P., Murzin, A.G., Brenner, S.E., and Chothia, C. 1997. SCOP: A structural classification of proteins database. Nucleic Acids Res. 25: 236-239.
26. Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
27. 2O) solutions. III. Estimation of the protein secondary structure. Biopolymers 30: 1273-1280.
28. Keiderling, T.A., Wang, B., Urbanova, M., Pancoska, P., and Dukor, R.K. 1994. Empirical studies of protein secondary structure by vibrational circular dichroism and related techniques. α-lactalbumin and lysozyme as examples. Faraday Discuss. 99: 263-285.
29. Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946-950.
30. Lee, D.C., Haris, P.I., Chapman, D., and Mitchell, R.C. 1990. Determination of protein secondary structure using factor analysis of infrared spectra. Biochemistry 29: 9185-9193.
31. Levitt, M. and Greer, J. 1977. Automatic identification of secondary structure in globular proteins. J. Mol. Biol. 114: 181-239.
32. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
33. Nevskaya, N.A. and Chirgadze, Y.N. 1976. Infrared spectra and resonance interactions of amide-I and II vibration of α-helix. Biopolymers 15: 637-648.
34. Orengo, C.A., Jones, D.T., and Thornton, J.M. 1994. Protein superfamilies and domain superfolds. Nature 372: 631-634.
35. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
36. 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.
37. Pancoska, P., Yasui, S.C., and Keiderling, T.A. 1991. Statistical analyses of the vibrational circular dichroism of selected proteins and relationship to secondary structures. Biochemistry 30: 5089-5103.
38. Pancoska, P., Bitto, E., Janota, V., Urbanova, M., Gupta, V.P., and Keiderling, T.A. 1995. Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure. Protein Sci. 4: 1384-1401.
39. Pancoska, P., Fabian, H., Yoder, G., Baumruk, V., and Keiderling, T.A. 1996. Protein structural segments and their interconnections derived from optical spectra. Thermal unfolding of ribonuclease T1 as an example. Biochemistry 35: 13094-13106.
40. Perczel, A., Park, K., and Fasman, G.D. 1992. Deconvolution of the circular dichroism spectra of proteins: The circular dichroism spectra of the antiparallel β-sheet in proteins. Proteins 13: 57-69.
41. Powell, J.R., Wasacz, F.M., and Jakobsen, R.J. 1986. An algorithm for the reproducible spectral subtraction of water from the FTIR spectra of proteins in dilute solutions and adsorbed monolayers. Appl. Spectrosc. 40: 339-344.
42. 10-helices in globular proteins. Reexamination of Amide I infrared bands of α-lactalbumin and their assignment to secondary structures. Int. J. Pept. Protein Res. 37: 508-512.
43. Pribic, R., van Stokkum, I.H., Chapman, D., Haris, P.I., and Bloemendal, M. 1993. Protein secondary structure from Fourier transform infrared and/or circular dichroism spectra. Anal. Biochem. 214: 366-378.
44. Sander, C. and Schneider, R. 1993. The HSSP data base of protein structure-sequence alignments. Nucleic Acids Res. 21: 3105-3109.
45. Sarver, R.W.J. and Krueger, W.C. 1991a. Protein secondary structure from Fourier transform infrared spectroscopy: A data base analysis. Anal. Biochem. 194: 89-100.
46. -. 1991b. An infrared and circular dichroism combined approach to the analysis of protein secondary structure. Anal. Biochem. 199: 61-67.
47. Saxena, V.P. and Wetlaufer, D.B. 1971. A new basis for interpreting the circular dichroic spectra of proteins. Proc. Natl. Acad. Sci. 68: 969-972.
48. Scopes, R.K. 1987. Measurement of enzyme activity. In Protein purification: Principles and practice, pp. 278-283. Springer-Verlag, New York.
49. II-proteins. Protein Sci. 12: 384-388.
50. 2O) solutions. I. Spectral parameters of amino acid residue absorption bands. Biopolymers 30: 1243-1257.
51. Venyaminov, S.Y. and Vassilenko, K.S. 1994. Determination of protein tertiary structure class from circular dichroism spectra. Anal. Biochem. 222: 176-184.
52. Venyaminov, S.Y. and Yang, J.T. 1996. Determination of protein secondary structure. In Circular dichroism and the conformational analysis of biomolecules (ed. G.D. Fasman), pp. 69-107. Plenum Press, New York.
53. Venyaminov, S.Y., Baikalov, I.A., Shen, Z.M., Wu, C.S., and Yang, J.T. 1993. Circular dichroic analysis of denatured proteins: Inclusion of denatured proteins in the reference set. Anal. Biochem. 214: 17-24.
54. Wi, S., Pancoska, P., and Keiderling, T.A. 1998. Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: Effect of Fourier self-deconvolution of the amide I and amide II bands. Biospectroscopy 4: 93-106.
55. Woody, R.W. 1994. Contributions of tryptophan side chains to the far-ultraviolet circular dichroism of proteins. Eur. Biophys. J. 23: 253-262. -.
56. -. 1995. Circular dichroism. Methods Enzymol. 246: 34-71.
57. Woody, R.W. and Dunker, A.K. 1996. Aromatic and cysteine side-chain circular dichroism in proteins. In Circular dichroism and the conformational analysis of biomolecules (ed. G.D. Fasman), pp. 109-157. Plenum Press, New York.