Protein secondary structure content in solution, films and tissues: Redundancy and complementarity of the information content in circular dichroism, transmission and ATR FTIR spectra

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1794, Issue 9, 2009, Pages 1332-1343

  Goormaghtigh, Erik ^a   Gasper, Régis ^a   Bénard, Audrey ^a   Goldsztein, Andréa ^a   Raussens, Vincent ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Circular dichroism; FTIR imaging; FTIR sensors; IR spectroscopy; Protein film; Secondary structure

Indexed keywords

ATR PROTEIN;

ALPHA HELIX; ARTICLE; CIRCULAR DICHROISM; INFRARED SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN PROCESSING; PROTEIN STRUCTURE;

BIOPSY; BIOSENSING TECHNIQUES; BREAST NEOPLASMS; CELL LINE, TUMOR; CIRCULAR DICHROISM; FEMALE; HUMANS; MALE; PROSTATIC NEOPLASMS; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 69249222742     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.06.007     Document Type: Article

References (95)

1. Barth A., and Zscherp C. What vibrations tell us about proteins. Quaterly Rev. Biophys. 35 (2002) 369-430
2. 2+-ATPase: an FTIR study. Biophys. J. 89 (2005) 4352-4363
3. Stolz M., Lewitzki E., Thoenges D., Mantele W., Barth A., and Grell E. FTIR difference spectroscopy of Na, K-ATPase. J. Gen. Physiol. 126 (2005) 32A
4. Thoenges D., and Barth A. Direct measurement of enzyme activity with infrared spectroscopy. J. Biomol. Screen. 7 (2002) 353-357
5. Zscherp C., and Barth A. Reaction-induced infrared difference spectroscopy for the study of protein reaction mechanisms. Biochemistry 40 (2001) 1875-1883
6. Hakizimana P., Masureel M., Gbaguidi B., Ruysschaert J.M., and Govaerts C. Interactions between phosphatidylethanolamine headgroup and LmrP, a multidrug transporter. J. Biol. Chem. 283 (2008) 9369-9376
7. Gbaguidi B., Ruysschaert J.M., and Vigano C. Requirement of phosphatidylethanolamine for the normal structure and activity of the multidrug transporter LmrP. FEBS J. 272 (2005) 232
8. Gbaguidi B., Hakizimana P., Vandenbussche G., and Ruysschaert J.M. Conformational changes in a bacterial multidrug transporter are phosphatidylethanolamine-dependent. Cell. Mol. Life Sci. 64 (2007) 1571-1582
9. 2O. J. Mol. Biol. 259 (1996) 774-791
10. Chen Y.H., Yang J.T., and Martinez H.M. Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. Biochemistry 11 (1972) 4120-4131
11. Fasman G.D. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. In: Fasman G.D. (Ed). Circular Dichroism and The Conformation of Biomolecules (1996), Plenum, New York and London 381-412
12. McPhie P. Circular dichroism studies on proteins in films and in solution: estimation of secondary structure by g-factor analysis. Anal. Biochem. 293 (2001) 109-119
13. Park K., Perczel A., and Fasman G.D. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. Prot. Sci. 1 (1992) 1032-1049
14. Sarver Jr. R.W., and Krueger W.C. An infrared and circular dichroism combined approach to the analysis of protein secondary structure. Anal. Biochem. 199 (1991) 61-67
15. Sreerama N., and Woody R.W. A self-consistent method for the analysis of protein secondary structure from circular-dichroism. Anal. Biochem. 209 (1993) 32-44
16. Sreerama N., Venyaminov S.Y., and Woody R.W. Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis. Anal. Biochem. 287 (2000) 243-251
17. Sreerama N., and Woody R.W. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem. 287 (2000) 252-260
18. Wallace B.A., Lees J.G., Orry A.J.W., Lobley A., and Janes R.W. Analyses of circular dichroism spectra of membrane proteins. Prot. Sci. 12 (2003) 875-884
19. Raussens V., Ruysschaert J.M., and Goormaghtigh E. Protein concentration is not an absolute prerequisite for the determination of secondary structure from circular dichroism spectra: a new scaling method. Anal. Biochem. 319 (2003) 114-121
20. Arrondo J.L., Etxabe I., Dornberger U., and Goni F.M. Probing protein conformation by infrared spectroscopy. Biochem. Soc. Trans. 22 (1994) 380S
21. Baello B.I., Pancoska P., and Keiderling T.A. Enhanced prediction accuracy of protein secondary structure using hydrogen exchange Fourier transform infrared spectroscopy. Anal. Biochem. 280 (2000) 46-57
22. Byler D.M., and Susi H. Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25 (1986) 469-487
23. Dousseau F., and Pezolet M. 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
24. Haris P.I., Chapman D., and Benga G. A Fourier-transform infrared spectroscopic investigation of the hydrogen-deuterium exchange and secondary structure of the 28-kDa channel-forming integral membrane protein (CHIP28). Eur. J. Biochem. 233 (1995) 659-664
25. Hering J.A., Innocent P.R., and Haris P.I. An alternative method for rapid quantification of protein secondary structure from FTIR spectra using neural networks. Spectroscopy-An Int. J. 16 (2002) 53-69
26. Jackson M., and Mantsch H.H. The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit. Rev. Biochem. Mol. Biol. 30 (1995) 95-120
27. Lee D.C., Haris P.I., Chapman D., and Mitchell R.C. Determination of protein secondary structure using factor analysis of infrared spectra. Biochemistry 29 (1990) 9185-9193
28. Navea S., Tauler R., and de Juan A. Application of the local regression method interval partial least-squares to the elucidation of protein secondary structure. Anal. Biochem. 336 (2005) 231-242
29. Rahmelow K., and Hubner W. Secondary structure determination of proteins in aqueous solution by infrared spectroscopy: a comparison of multivariate data analysis methods. Anal. Biochem 241 (1996) 5-13
30. Surewicz W.K., and Mantsch H.H. New insight into protein secondary structure from resolution-enhanced infrared spectra. Biochim. Biophys. Acta 952 (1988) 115-130
31. Vedantham G., Sparks H.G., Sane S.U., Tzannis S., and Przybycien T.M. A holistic approach for protein secondary structure estimation from infrared spectra in H(2)O solutions. Anal. Biochem. 285 (2000) 33-49
32. Navea S., Tauler R., Goormaghtigh E., and de Juan A. Chemometric tools for classification and elucidation of protein secondary structure from infrared and circular dichroism spectroscopic measurements. Proteins-Struct. Funct. Bioinformatics 63 (2006) 527-541
33. Cabiaux V., Brasseur R., Wattiez R., Falmagne P., Ruysschaert J.M., and Goormaghtigh E. Secondary structure of diphtheria toxin and its fragments interacting with acidic liposomes studied by polarized infrared spectroscopy. J. Biol. Chem. 264 (1989) 4928-4938
34. Goormaghtigh E., Cabiaux V., and Ruysschaert J.M. Secondary structure and dosage of soluble and membrane proteins by attenuated total reflection Fourier-transform infrared spectroscopy on hydrated films. Eur. J. Biochem. 193 (1990) 409-420
35. Goormaghtigh E., Ruysschaert J.M., and Raussens V. Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys. J. 90 (2006) 2946-2957
36. Jansen T.L.C., and Knoester J. Two-dimensional infrared population transfer spectroscopy for enhancing structural markers of proteins. Biophys. J. 94 (2008) 1818-1825
37. Barth A. Infrared spectroscopy of proteins. Biochim. Biophys. Acta 1767 (2007) 1073-1101
38. Goormaghtigh E., Raussens V., and Ruysschaert J.M. Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim. Biophys. Acta 1422 (1999) 105-185
39. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., and Thornton J.M. CATH - a hierarchic classification of protein domain structures. Structure 5 (1997) 1093-1108
40. Oberg K.A., Ruysschaert J.M., and Goormaghtigh E. Rationally selected basis proteins: a new approach to selecting proteins for spectroscopic secondary structure analysis. Prot. Sci. 12 (2003) 2015-2031
41. Oberg K.A., Ruysschaert J.M., and Goormaghtigh E. The optimization of protein secondary structure determination with infrared and CD spectra. Eur. J. Biochem. 271 (2004) 2937-2948
42. de-Jongh H.H., Goormaghtigh E., and Killian J.A. Analysis of circular dichroism spectra of oriented protein-lipid complexes: toward a general application. Biochemistry 33 (1994) 14521-14528
43. S. Devouge, J. Conti, A. Goldsztein, E. Gosselin, A. Brans, M. Voué, J. De Coninck, F. Homblé, E. Goormaghtigh, J. Marchand-Brynaert, Surface functionalization of germanium ATR devices for use in FTIR-biosensors, J. Colloid Interface Sci. in press (2008).
44. A. Goldzstein, A. Aamouche, F. Homblé, M. Voué, J. Conti, J. De Coninck, S. Devouge, J. Marchand-Brynaert, E. Goormaghtigh, Ligand-receptor interactions in complex media: a new type of biosensors for the detection of coagulation factor VIII, Biosens Bioelectron (2008) in press.
45. Vigano C., Ruyssehaert J.M., and Goormaghtigh E. Sensor applications of attenuated total reflection infrared spectroscopy. Talanta 65 (2005) 1132-1142
46. Voue M., Goormaghtigh E., Homble F., Marchand-Brynaert J., Conti J., Devouge S., and De Coninck J. Biochemical interaction analysis on ATR devices: a wet chemistry approach for surface functionalization. Langmuir 23 (2007) 949-955
47. Baenziger J.E., and Chew J.P. Desensitization of the nicotinic acetylcholine receptor mainly involves a structural change in solvent-accessible regions of the polypeptide backbone. Biochemistry 36 (1997) 3617-3624
48. Baenziger J.E., Miller K.W., and Rothschild K.J. Incorporation of the nicotinic acetylcholine receptor into planar multilamellar films: characterization by fluorescence and Fourier transform infrared difference spectroscopy. Biophys. J. 61 (1992) 983-992
49. Methot N., Demers C.N., and Baenziger J.E. Structure of both the ligand- and lipid-dependent channel-inactive states of the nicotinic acetylcholine receptor probed by FTIR spectroscopy and hydrogen exchange. Biochemistry 34 (1995) 15142-15149
50. Ryan S.E., Demers C.N., Chew J.P., and Baenziger J.E. Structural effects of neutral and anionic lipids on the nicotinic acetylcholine receptor. An infrared difference spectroscopy study. J. Biol. Chem. 271 (1996) 24590-24597
51. Scheirlinckx F., Raussens V., Ruysschaert J.M., and Goormaghtigh E. Conformational changes in gastric H+/K+-ATPase monitored by difference Fourier-transform infrared spectroscopy and hydrogen/deuterium exchange. Biochem. J. 382 (2004) 121-129
52. Scheirlinckx F., Buchet R., Ruysschaert J.M., and Goormaghtigh E. Monitoring of secondary and tertiary structure changes in the gastric H+/K+-ATPase by infrared spectroscopy. Eur. J. Biochem. 268 (2001) 3644-3653
53. Harrison A., Pearl F., Sillitoe I., Slidel T., Mott R., Thornton J., and Orengo C. Recognizing the fold of a protein structure. Bioinformatics 19 (2003) 1748-1759
54. Orengo C.A., Martin A.M., Hutchinson G., Jones S., Jones D.T., Michie A.D., Swindells M.B., and Thornton J.M. Classifying a protein in the CATH database of domain structures. Acta Crystallogr., D Biol. Crystallogr. 54 (1998) 1155-1167
55. Kabsch W., and Sander S. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
56. Goormaghtigh E., and Ruysschaert J.M. Subtraction of atmospheric water contribution in Fourier transform infrared spectroscopy of biological membranes and proteins. Spectrochim. Acta 50A (1994) 2137-2144
57. Bruun S.W., Kohler A., Adt I., Sockalingum G.D., Manfait M., and Martens H. Correcting attenuated total reflection-Fourier transform infrared spectra for water vapor and carbon dioxide. Appl. Spectrosc. 60 (2006) 1029-1039
58. E. Goormaghtigh, 2009. FTIR Data Processing and Analysis Tools. In Advances in Biomedical Spectroscopy. A. Barth, editor. in press
59. Powell J.R., Wasacz F.M., and Jakobsen R.J. An algorithm for the reproducible spectral subtraction of water from the FTIR spectra of proteins in dilute solutions and adsorbed monolayers. Appl. Spectrosc. 40 (1986) 339-344
60. de-Jongh H.H., Goormaghtigh E., and Ruysschaert J.M. The different molar absorptivities of the secondary structure types in the amide I region: an attenuated total reflection infrared study on globular proteins. Anal. Biochem. 242 (1996) 95-103
61. Chapman D., Gomez Fernandez J.C., Goni F.M., and Barnard M. Difference infrared spectroscopy of aqueous model and biological membranes using an infrared data station. Can J. Biochem. 2 (1980) 315-323
62. Vincent S.S., Star C., and Levin I.W. Infrared spectroscopic study of the pH-dependent secondary structure of brain clathrin. Biochemistry 23 (1984) 625-631
63. Dong A., Huang P., and Caughey W.S. Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29 (1990) 3303-3308
64. Haris P.I., Lee D.C., and Chapman D. A Fourier transform infrared investigation of the structural differences between ribonuclease A and ribonuclease S. Biochim. Biophys. Acta 874 (1986) 255-265
65. Dousseau F., Therrien M., and Pezolet M. Appl. Spectrosc. 40 (1989) 538-542
66. Vasilescu V., and Katona E. Deuteration as a tool in investigating the role of water in the structure and function of excitable membranes. Methods Enzymol. 127 (1986) 662-678
67. Barth A., and Mantele W. ATP-induced phosphorylation of the sarcoplasmic reticulum Ca2+ ATPase: molecular interpretation of infrared difference spectra. Biophys. J. 75 (1998) 538-544
68. Heimburg T., and Marsh D. Investigation of secondary and tertiary structural changes of cytochrome c in complexes with anionic lipids using amide hydrogen exchange measurements: an FTIR study. Biophys. J. 65 (1993) 2408-2417
69. Raussens V., Narayanaswami V., Goormaghtigh E., Ryan R.O., and Ruysschaert J.M. Hydrogen/deuterium exchange kinetics of apolipophorin-III in lipid-free and phospholipid-bound states. An analysis by Fourier transform infrared spectroscopy. J. Biol. Chem. 271 (1996) 23089-23095
70. Meskers S., Ruysschaert J.M., and Goormaghtigh E. Hydrogen-deuterium exchange of streptavidin and its complex with biotin studied by 2D-Attenuated total reflection Fourier transform infrared spectroscopy. J. Am. Chem. Soc. 121 (1999) 5115-5122
71. Bryson E.A., Rankin S.E., Goormaghtigh E., Ruysschaert J.M., Watts A., and Pinheiro T.J. Structure and dynamics of lipid-associated states of apocytochrome c. Eur. J. Biochem. 267 (2000) 1390-1396
72. Grimard V., Vigano C., Margolles A., Wattiez R., van-Veen H.W., Konings W.N., Ruysschaert J.M., and Goormaghtigh E. Structure and dynamics of the membrane-embedded domain of LmrA investigated by coupling polarized ATR-FTIR spectroscopy and (1)H/(2)H exchange. Biochemistry 40 (2001) 11876-11886
73. Vigano C., Goormaghtigh E., and Ruysschaert J.M. Detection of structural and functional asymmetries in P-glycoprotein by combining mutagenesis and H/D exchange measurements. Chem. Phys. Lipids 122 (2003) 121-135
74. Raussens V., Ruysschaert J.M., and Goormaghtigh E. Analysis of H-1/H-2 exchange kinetics using model infrared spectra. Appl. Spectrosc. 58 (2004) 68-82
75. Vigano C., Smeyers M., Raussens V., Scheirlinckx F., Ruysschaert J.M., and Goormaghtigh E. Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: a new tool to resolve protein structure and dynamics. Biopolymers 74 (2004) 19-26
76. Alegre-Cebollada J., del Pozo A.M., Gavilanes J.G., and Goormaghtigh E. Infrared spectroscopy study on the conformational changes leading to pore formation of the toxin sticholysin II. Biophts. J. 93 (2007) 3191-3201
77. Krisko A., Stjepanovic G., Pifat G., Ruysschaert J.M., and Goormaghtigh E. Detection of apolipoprotein B100 early conformational changes during oxidation. Biochim. Biophys. Acta (Biomembranes) 1768 (2007) 2923-2930
78. Fringeli U.P. In situ infrared attenuated total reflection (IR ATR) spectroscopy: a complementary analytical tool for drug design and drug delivery. Chimia 46 (1992) 200-214
79. Citra M.J., and Axelsen P.H. Determination of molecular order in supported lipid membranes by internal reflection Fourier transform infrared spectroscopy. Biophys. J. 71 (1996) 1796-1805
80. Hansen W.H.J. Opt. Soc. Am. 58 (1968) 380-390
81. Hansen W.H. Adv. Electrochem. Electrochem. Eng. 9 (1973) 1-60
82. Cabiaux V., Agerberth B., Johansson J., Homble F., Goormaghtigh E., and Ruysschaert J.M. Secondary structure and membrane interaction of PR-39, a Pro+Arg-rich antibacterial peptide. Eur. J. Biochem. 224 (1994) 1019-1027
83. Goormaghtigh E., Cabiaux V., and Ruysschaert J.M. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. II. Experimental aspects, side chain structure, and H/D exchange. Subcell. Biochem. 23 (1994) 363-403
84. Chen Y.-H., Yang J.T., and Chau K.H. Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry 13 (1974) 3350-3359
85. Goormaghtigh E., Cabiaux V., and Ruysschaert J.M. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. III. Secondary structures. Subcell. Biochem. 23 (1994) 405-450
86. Goormaghtigh E., Cabiaux V., and Ruysschaert J.M. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. I. Assignments and model compounds. Subcell. Biochem. 23 (1994) 329-362
87. Diem M., Boydston-White S., and Chiriboga L. Infrared spectroscopy of cells and tissues: shining light onto a novel subject. Appl. Spectrosc. 53 (1999) 148A-161A
88. Pacifico A., Chiriboga L.A., Lasch P., and Diem M. Infrared spectroscopy of cultured cells - II. Spectra of exponentially growing, serum-deprived and confluent cells. Vibr. Spectrosc. 32 (2003) 107-115
89. Wehbe K., Pinneau R., Moenner M., Deleris G., and Petibois C. FT-IR spectral imaging of blood vessels reveals protein secondary structure deviations induced by tumor growth. Anal. Bioanal. Chem. 392 (2008) 129-135
90. Petibois C., Gouspillou G., Wehbe K., Delage J.P., and Deleris G. Analysis of type I and IV collagens by FT-IR spectroscopy and imaging for a molecular investigation of skeletal muscle connective tissue. Anal. Bioanal. Chem. 386 (2006) 1961-1966
91. Petibois C., and Deleris G. Chemical mapping of tumor progression by FT-IR imaging: towards molecular histopathology. Trends Biotech. 24 (2006) 455-462
92. Petibois C., Drogat B., Bikfalvi A., Deleris G., and Moenner M. Histological mapping of biochemical changes in solid tumors by FT-IR spectral imaging. FEBS Lett. 581 (2007) 5469-5474
93. Pribic R., van Stokkum I.H., Chapman D., Haris P.I., and Bloemendal M. Protein secondary structure from Fourier transform infrared and/or circular dichroism spectra. Anal. Biochem. 214 (1993) 366-378
94. Baenziger J.E., Miller K.W., McCarthy M.P., and Rothschild K.J. Probing conformational changes in the nicotinic acetylcholine receptor by Fourier transform infrared difference spectroscopy. Biophys. J. 62 (1992) 64-66
95. Baenziger J.E., Miller K.W., and Rothschild K.J. Fourier transform infrared difference spectroscopy of the nicotinic acetylcholine receptor: evidence for specific protein structural changes upon desensitization. Biochemistry 32 (1993) 5448-5454