Protein structural class identification directly from NMR spectra using averaged chemical shifts

Bioinformatics

Volumn 19, Issue 16, 2003, Pages 2054-2064

  Mielke, S P ^a,b   Krishnan, V V ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTON;

ARTICLE; BIOINFORMATICS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; INFORMATION SYSTEM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0242661071     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg280     Document Type: Article

References (65)

1. Ando,I., Kuroki,S., Kurosu,H. and Yamanobe,T. (2001) NMR chemical shift calculations and structural characterizations of polymers. Prog. Nucl. Mag. Reson. Spectrosc., 39, 79-133.
2. Atkinson,R.A. and Saudek,V. (2002) The direct determination of protein structure by NMR without assignment. FEBS Lett., 510, 1-4.
3. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
4. Boberg,J., Salakoski,T. and Vihinen,M. (1995) Accurate prediction of protein secondary structural class with fuzzy structural vectors. Protein Eng., 8, 505-512.
5. Bussian,B.M. and Sander,C. (1989) How to determine protein secondary structure in solution by Raman spectroscopy: practical guide and test case DNase I. Biochemistry, 28, 4271-4277.
6. Cai,Y.D., Liu,X.J., Xu Xb,X. and Zhou,G.P. (2001) Support Vector Machines for predicting protein structural class. BMC Bioinformatics, 2, 3.
7. Carlacci,L. and Englander,S.W. (1993) The loop problem in proteins: a Monte Carlo simulated annealing approach. Biopolymers, 33, 1271-1286.
8. Case,D.A. (2000) Interpretation of chemical shifts and coupling constants in macromolecules. Curr. Opin. Struct. Biol., 10, 197-203.
9. Chi,Z., Chen,X.G., Holtz,J.S. and Asher,S.A. (1998) UV resonance Raman-selective amide vibrational enhancement: quantitative methodology for determining protein secondary structure. Biochemistry, 37, 2854-2864.
10. Chou,K.C. and Zhang,C.T. (1995) Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol., 30, 275-349.
11. Chou,P.Y. (1989) Prediction of protein structural class from amino acid composition. In Fasman,G.D. (ed.), Prediction of Protein Structure and Principles of Protein Conformation, Plenum Press, New York, pp. 549-586.
12. Cid,H., Bunster,M., Canales,M. and Gazitua,F. (1992) Hydrophobicity and structural classes in proteins. Protein Eng., 5, 373-375.
13. Cohen,F.E. and Kuntz,I.D. (1987) Origins of structural diversity within sequentially identical hexapeptides. Proteins, 2, 162-166.
14. Cohen,B.I., Presnell,S.R. and Cohen,F.E. (1993) Prediction of the three-dimensional structure of human growth hormone. Protein Sci., 2, 2134-2145.
15. Cornilescu,G., Delaglio,F. and Bax,A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR, 13, 289-302.
16. Deleage,G. and Dixon,J.S. (1989) Use of class prediction to improve protein secondary structure prediction. In Fasman,G.D. (ed.), Prediction of Protein Structure and Principles of Protein Conformation, Plenum Press, New York, pp. 587-597.
17. Deleage,G. and Roux,B. (1987) An algorithm for protein secondary structure prediction based on class prediction. Protein Eng., 1, 289-294.
18. Deleage,G., Tinland,B. and Roux,B. (1987) A computerized version of the Chou and Fasman method for predicting the secondary structure of proteins. Anal. Biochem., 163, 292-297.
19. Dietmann,S. and Holm,L. (2001) Identification of homology in protein structure classification. Nat. Struct. Biol., 8, 953-957.
20. Eisenhaber,F., Imperiale,F., Argos,P. and Frommel,C. (1996) Prediction of Secondary Structural Content of Proteins From Their Amino Acid Composition Alone. 1. New Analytic Vector Decomposition Methods. Proteins-Structure Function and Genetics, 25, 157-168.
21. Ernst,R.R., Bodenhausen,G. and Wokaun,A. (1990) Principles of Nuclear Magnetic Resonance in One and Two Dimensions, The International series of monographs on chemistry; 14, Clarendon Press, Oxford.
22. Grishaev,A. and Llinas,M. (2002) Protein structure elucidation from NMR proton densities. Proc. Natl Acad. Sci. USA, 99, 6713-6718.
23. Gutowsky,H.S., Saika,A., Takeda,M. and Woessner,D.E. (1957) Proton magnetic resonance studies on natural rubber. II. Line shape and T1 measurements. J. Chem. Phys., 27, 534-542.
24. Havlin,R.H., Laws,D.D., Bitter,H.M. L., Sanders,L.K., Sun,H. H., Grimley,J.S., Wemmer,D.E., Pines,A. and Oldfield,E. (2001) An experimental and theoretical investigation of the chemical shielding tensors of C-13(alpha) of alanine, valine, and leucine residues in solid peptides and in proteins in solution. J. Am. Chem. Soc., 123, 10362-10369.
25. Ikegami,T., Okada,T., Ohki,I., Hirayama,J., Mizuno,T. and Shirakawa,M. (2001) Solution structure and dynamic character of the histidine-containing phosphotransfer domain of anaerobic sensor kinase ArcB from Escherichia coli. Biochemistry, 40, 375-386.
26. Johnson,W.C., Jr. (1990) Protein secondary structure and circular dichroism: a practical guide. Proteins, 7, 205-214.
27. Klein,P. and Delisi,C. (1986) Prediction of protein structural class by discriminant analysis. Biopolymers, 25, 1659-1672.
28. Klein,P. (1986) Prediction of protein structural class from the amino acid sequence. Biochim. Biophys. Acta., 874, 205-215.
29. Kneller,D.G., Cohen,F.E. and Langridge,R. (1990) Improvements in protein secondary structure prediction by an enhanced neural network. J. Mol. Biol., 214, 171-182.
30. Koradi,R., Billeter,M., Engeli,M., Guntert,P. and Wuthrich,K. (1998) Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J. Mag. Reson., 135, 288-297.
31. Lee,M.S. and Cao,B. (1996) Nuclear magnetic resonance chemical shift: comparison of estimated secondary structures in peptides by nuclear magnetic resonance and circular dichroism. Protein Eng., 9, 15-25.
32. Levitt,M. and Chothia,C. (1976) Structural patterns in globular proteins. Nature, 261, 552-558.
33. Li,Q.Z. and Lu,Z.Q. (2001) The prediction of the structural class of protein: application of the measure of diversity. J. Theor. Biol., 213, 493-502.
34. Lo Conte,L., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.
35. Luo,R.Y., Feng,Z.P. and Liu,J.K. (2002) Prediction of protein structural class by amino acid and polypeptide composition. Eur. J. Biochem., 269, 4219-4225.
36. Metfessel,B.A., Saurugger,P.N., Connelly,D.P. and Rich,S.S. (1993) Cross-validation of protein structural class prediction using statistical clustering and neural networks. Protein Sci., 2, 1171-1182.
37. Moseley,H.N.B. and Montelione,G.T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol., 9, 635-642.
38. Muggleton,S., King,R.D. and Sternberg,M.J. (1992) Protein secondary structure prediction using logic-based machine learning. Protein Eng., 5, 647-657.
39. Nakashima,H., Nishikawa,K. and Ooi,T. (1986) The folding type of a protein is relevant to the amino acid composition. J. Biochem. (Tokyo), 99, 153-162.
40. Nishikawa,K. and Ooi,T. (1982) Correlation of the amino acid composition of a protein to its structural and biological characters. J. Biochem. (Tokyo), 91, 1821-1824.
41. Nishikawa,K. and Ooi,T. (1986a) Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods. Biochim. Biophys. Acta., 871, 45-54.
42. Nishikawa,K. and Ooi,T. (1986b) Radial locations of amino acid residues in a globular protein: correlation with the sequence. J. Biochem. (Tokyo), 100, 1043-1047.
43. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells ,M.B. and Thornton,J. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
44. Perczel,A., Hollosi,M., Tusnady,G. and Fasman,G.D. (1991) Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. Protein Eng., 4, 669-679.
45. Pervushin,K., Riek,R., Wider,G. and Wuthrich,K. (1997) Attenuated T-2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl Acad. Sci. USA, 94, 12366-12371.
46. Press,W.H. (1988) Numerical Recipes in C: The Art of Scientific Computing, Cambridge University Press, Cambridge, New York.
47. Sanders,J.C., Haris,P.I., Chapman,D., Otto,C. and Hemminga,M.A. (1993) Secondary structure of M13 coat protein in phospholipids studied by circular dichroism, Raman, and Fourier transform infrared spectroscopy. Biochemistry, 32, 12446-12454.
48. Seavey,B.R., Farr,E.A., Westler,W.M. and Markley,J.L. (1991) A relational database for sequence-specific protein NMR data. J. Biomol. NMR, 1, 217-236.
49. Sharman,G.J., Griffiths-Jones,S.R., Jourdan,M. and Searle,M.S. (2001) Effects of amino acid phi,psi propensities and secondary structure interactions in modulating H alpha chemical shifts in peptide and protein beta-sheet. J Am. Chem. Soc., 123, 12318-12324.
50. Sibley,A.B., Cosman,M. and Krishnan, V.V. (2003) An empirical correlation between secondary structure content and averaged chemical shifts in proteins. Biophys. J. 84, 1223-1227.
51. Sreerama,N. and Woody,R.W. (1994) 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., 242, 497-507.
52. Szilagyi,L. (1995) Chemical shifts in proteins come of age. Prog. Nucl. Magn. Reson. Spectrosc., 27, 325-443.
53. Taylor,W.R. (2002) A 'periodic table' for protein structures. Nature, 416, 657-660.
54. Wang,H., He,Y., Hsu,K.T., Magliocca,J.F., Storch,J. and Stark,R.E. (1998) 1H, 15N and 13C resonance assignments and secondary structure of apo liver fatty acid-binding protein. J. Biomol. NMR, 12, 197-199.
55. Wang,Z.X. (2001) The prediction accuracy for protein structural class by the component- coupled method is around 60%. Proteins, 43, 339-340.
56. Wang,Z.X. and Yuan,Z. (2000) How good is prediction of protein structural class by the component- coupled method? Proteins, 38, 165-175.
57. Williams,R.W., McIntyre,J.O., Gaber,B.P. and Fleischer,S. (1986) The secondary structure of calcium pump protein in light sarcoplasmic reticulum and reconstituted in a single lipid component as determined by Raman spectroscopy. J. Biol. Chem., 261, 14520-14524.
58. Wishart,D.S., Bigam,C.G., Yao,J., Abildgaard,F., Dyson,H.J., Oldfield,E., Markley,J.L. and Sykes,B.D. (1995) H-1, C-13 and N-15 Chemical Shift Referencing in Biomolecular NMR. J. Biomol. NMR, 6, 135-140.
59. Wishart,D.S. and Case,D.A. (2001) Use of chemical shifts in macromolecular structure determination. Methods Enzymol., 338, 3-34.
60. Wishart,D.S. and Sykes,B.D. (1994) The C-13 chemical-shift index - a simple method for the identification of protein secondary structure using C-13 chemical-shift data. J. Biomol. NMR, 4, 171-180.
61. Wüthrich,K. (1986) NMR of Proteins and Nucleic Acids. The George Fisher Baker non-resident lectureship in chemistry at Cornell University, Wiley, New York.
62. Zhang,C.T. and Chou,K.C. (1992) An optimization approach to predicting protein structural class from amino acid composition. Protein Sci., 1, 401-408.
63. Zhang,C.T. and Zhang,R. (1998) A new criterion to classify globular proteins based on their secondary structure contents. Bioinformatics, 14, 857-865.
64. Zhou,G., Xu,X. and Zhang,C.T. (1992) A weighting method for predicting protein structural class from amino acid composition. Eur. J. Biochem., 210, 747-749.
65. Zhou,G.P. (1998) An intriguing controversy over protein structural class prediction. J. Protein Chem., 17, 729-738.