Application of the local regression method interval partial least-squares to the elucidation of protein secondary structure

Analytical Biochemistry

Volumn 336, Issue 2, 2005, Pages 231-242

  Navea, Susana ^a   Tauler, Romà ^b   Juan, Anna De ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b DEPARTMENT OF ENVIRONMENTAL CHEMISTRY   (Spain)

Author keywords

Infrared amide bands; Infrared spectroscopy; Protein secondary structure; Regression methods

Indexed keywords

AMIDES; DECONVOLUTION; ENERGY DISPERSIVE X RAY ANALYSIS; INFRARED SPECTROSCOPY; PROTEINS; REGRESSION ANALYSIS; X RAY DIFFRACTION ANALYSIS;

DECONVOLUTION TECHNIQUES; INTERVAL PARTIAL LEAST SQUARES; INTERVAL PARTIAL LEAST-SQUARES (IPLS); MULTIVARIATE REGRESSION METHOD; POLYPEPTIDE BACKBONES; PROTEIN SECONDARY STRUCTURE; REGRESSION METHOD; SECONDARY STRUCTURE OF PROTEINS;

LEAST SQUARES APPROXIMATIONS;

ARTICLE; INFRARED SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; REGRESSION ANALYSIS; X RAY ANALYSIS;

EID: 11144304496     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ab.2004.10.016     Document Type: Article

References (25)

1. A. Elliot, and E.J. Ambrose Structure of synthetic polypeptides Nature 165 1950 921 922
2. S. Krimm, and J. Bandekar Vibrational Spectroscopy and conformation of peptides, polypeptides, and proteins Adv. Protein Chem. 38 1986 181 365
3. H. Susi, and D.M. Byler Examination of the secondary structure of proteins by deconvolved FTIR spectra Biopolymers 25 3 1986 469 487
4. W.K. Surewicz, and H.H. Mantsch New insight into protein secondary structure from resolution-enhanced infrared spectra Biochim. Biophys. Acta 952 2 1988 115 130
5. A. Dong, P. Huang, and W.S. Caughey Protein secondary structures in water from second-derivative amide I infrared spectra Biochemistry 29 13 1990 3303 3308
6. K. Eckert, R. Grosse, J. Malur, and K.R.H. Repke Calculation and use of protein-derived conformation-related spectra for the estimate of the secondary structure of proteins from their infrared spectra Biopolymers 16 1977 2549 2563
7. D.C. Lee, P.I. Haris, D. Chapman, and R.C. Mitchell Determination of protein secondary structure using factor analysis of infrared spectra Biochemistry 29 1990 9185 9193
8. F. Dousseau, and M. Pezolet 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 1990 8771 8779
9. K. Rahmelow, and W. Hübner Secondary structure determination of proteins in aqueous solution by infrared spectroscopy: a comparison of multivariate data analysis methods Anal. Biochem. 241 1996 5 13
10. L. Norgaard, A. Saudland, J. Wagner, J.P. Nielsen, L. Munck, and S.B. Engelsen Interval Partial Least-Squares regression (iPLS): comparative chemometric study with an example from near-infrared spectroscopy Appl. Spectrosc. 54 3 2000 413 419
11. http://www.biochem.ucl.ac.uk/bsm/pdbsum/
12. http://lamar.colostate.edu/~sreeram/CDPro/
13. A.E. Boardman, B.S. Hui, and H. Wold The Partial Least-Squares fix point method of estimating interdependent systems with latent-variables Commun. Stat. A-Theory Methods 10 7 1981 613 639
14. S. Wold, H. Martens, and H. Wold The multivariate calibration-problem in chemistry solved by the PLS method Lecture Notes Math. 973 1983 286 293
15. The UNSCRAMBLER, Camo ASA, Inc., Nedre Vollgate 8, N-0158 Oslo, Norway. Available from: 〈http://www.camo.com〉
16. PLS_toolboxfor Matlab, Eigenvector Research, Inc., 830 Wapato Lake Road, Manson, WA 98831. Available from: 〈http://www.eigenvector.com〉
17. Pirouette, Infometrix, Inc., 10634 E. Riverside Dr., Suite 250, Bothell, WA 98011. Available from: 〈http://www.infometrix.com〉
18. http://www.models.kvl.dk/source/clipls/index.asp
19. S. Cai, and B.R. Singh A distinct utility of the Amide III infrared band for secondary structure estimation of aqueous protein solution using Partial Least Squares methods Biochemistry 43 2004 2541 2549
20. R.W. Sarver Jr., and W.C. Krueger Protein secondary structure from fourier transform infrared spectroscopy: a data base analysis Anal. Biochem. 194 1991 89 100
21. R.W. Sarver Jr., and W.C. Krueger An infrared and circular dichroism combined approach to the analysis of protein secondary structure Anal. Biochem. 199 1991 61 67
22. J.L.R. Arrondo, A. Muga, and F.M. Goñi Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy Prog. Biophys. Molec. Biol. 59 1993 23 56
23. L.K. Tamm, and S.A. Tatulian Infrared spectroscopy of proteins and peptides in lipid bilayers Q. Rev. Biophys. 30 1997 365 429
24. T.F. Kumosinki, and J.J. Unruh Quantitation of the global secondary structure of globular proteins by FTIR spectroscopy: comparison with X-ray crystallographic structure Talanta 43 1996 199 219
25. J.T. Pelton, and L.R. McLean Spectroscopic methods for analysis of protein secondary structure Anal. Biochem. 277 2000 167 176