Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

Nature Protocols

Volumn 10, Issue 3, 2015, Pages 382-396

  Yang, Huayan ^a   Yang, Shouning ^a   Kong, Jilie ^a   Dong, Aichun ^b   Yu, Shaoning ^a  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF NORTHERN COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM FLUORIDE; DEUTERIUM OXIDE; POTASSIUM BROMIDE; SODIUM CHLORIDE; WATER; ZINC SULFATE;

ALGORITHM; ANALYZER; AQUEOUS SOLUTION; ARTICLE; BETA SHEET; CHEMICAL BOND; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; DATA ANALYSIS SOFTWARE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INFRARED SPECTROSCOPY; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; QUANTITATIVE ANALYSIS; REFLECTOMETRY; SIGNAL NOISE RATIO; SPECTROMETER; WATER VAPOR; X RAY CRYSTALLOGRAPHY; ANALYSIS; CHEMICAL ANALYSIS; CHEMISTRY; GENETICS; PROCEDURES;

ANALYTIC SAMPLE PREPARATION METHODS; CALCIUM FLUORIDE; CHEMISTRY TECHNIQUES, ANALYTICAL; DEUTERIUM OXIDE; PROTEIN STRUCTURE, SECONDARY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; WATER;

EID: 84923818038     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2015.024     Document Type: Article

References (65)

1. Baker, M.J. et al. Using Fourier transform IR spectroscopy to analyze biological materials. Nat. Protoc. 9, 1771-1791 (2014
2. Arrondo, J.L., Muga, A., Castresana, J. & Goni, F.M. Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy. Prog. Biophys. Mol. Biol. 59, 23-56 (1993
3. Purcell, J.M. & Susi, H. Solvent denaturation of proteins as observed by resolution-enhanced Fourier transform infrared spectroscopy. J. Biochem. Biophys. Methods 9, 193-199 (1984
4. Susi, H. & Byler, D.M. Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol. 130, 290-311 (1986
5. Byler, D.M. & Susi, H. Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25, 469-487 (1986
6. Dong, A., Huang, P. & Caughey, W.S. Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29, 3303-3308 (1990
7. Lee, D.C., Haris, P.I., Chapman, D. & Mitchell, R.C. Determination of protein secondary structure using factor analysis of infrared spectra. Biochemistry 29, 9185-9193 (1990
8. Krimm, S. & Bandekar, J. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv. Protein Chem. 38, 181-364 (1986
9. Bandekar, J. Amide modes and protein conformation. Biochim. Biophys. Acta 1120, 123-143 (1992
10. Singh Bal, R. in Infrared Analysis of Peptides and Proteins Vol. 750 2-37 (American Chemical Society, 1999
11. Kong, J. & Yu, S. Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Biochim. Biophys. Sin. (Shanghai) 39, 549-559 (2007
12. Jiang, Y. et al. Qualification of FTIR spectroscopic method for protein secondary structural analysis. J. Pharm. Sci. 100, 4631-4641 (2011
13. Susi, H. & Michael Byler, D. Protein structure by Fourier transform infrared spectroscopy: second derivative spectra. Biochem. Biophys. Res. Commun. 115, 391-397 (1983
14. Lee, D.C., Hayward, J.A., Restall, C.J. & Chapman, D. Second-derivative infrared spectroscopic studies of the secondary structures of bacteriorhodopsin and Ca2+-ATPase. Biochemistry 24, 4364-4373 (1985
15. Yang, W.-J., Griffiths, P.R., Byler, D.M. & Susi, H. Protein conformation by infrared spectroscopy: resolution enhancement by Fourier self-deconvolution. Appl. Spectrosc. 39, 282-287 (1985
16. Olinger, J.M., Hill, D.M., Jakobsen, R.J. & Brody, R.S. Fourier transform infrared studies of ribonuclease in H2O and 2H2O solutions. Biochim. Biophys Acta 869, 89-98 (1986
17. Surewicz, W.K., Mantsch, H.H., Stahl, G.L. & Epand, R.M. Infrared spectroscopic evidence of conformational transitions of an atrial natriuretic peptide. Proc. Natl. Acad. Sci. USA 84, 7028-7030 (1987
18. Griebenow, K. & Klibanov, A.M. On protein denaturation in aqueousorganic mixtures but not in pure organic solvents. J. Am. Chem. Soc. 118, 11695-11700 (1996
19. Kauppinen, J.K., Moffatt, D.J., Mantsch, H.H. & Cameron, D.G. Fourier self-deconvolution: a method for resolving intrinsically overlapped bands. Appl. Spectrosc. 35, 271-276 (1981
20. Ruegg, M., Metzger, V. & Susi, H. Computer analyses of characteristic infrared bands of globular proteins. Biopolymers 14, 1465-1471 (1975
21. Fafarman, A.T. et al. Thiocyanate-capped nanocrystal colloids: vibrational reporter of surface chemistry and solution-based route to enhanced coupling in nanocrystal solids. J. Am. Chem. Soc. 133, 15753-15761 (2011
22. Lynch, I., Dawson, K.A. & Linse, S. Detecting cryptic epitopes created by nanoparticles. Sci. Signal. 2006, pe14 (2006
23. Van Stokkum, I.H., Spoelder, H.J., Bloemendal, M., Van Grondelle, R. & Groen, F.C. Estimation of protein secondary structure and error analysis from circular dichroism spectra. Anal. Biochem. 191, 110-118 (1990
24. Matsuo, K., Yonehara, R. & Gekko, K. Improved estimation of the secondary structures of proteins by vacuum-ultraviolet circular dichroism spectroscopy. J. Biochem. 138, 79-88 (2005
25. Greenfield, N.J. Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc. 1, 2876-2890 (2006
26. Arrondo, J.L.R. & Goñi, F.M. Structure and dynamics of membrane proteins as studied by infrared spectroscopy. Prog. Biophys. Mol. Biol. 72, 367-405 (1999
27. Goormaghtigh, E., Raussens, V. & Ruysschaert, J.M. Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim. Biophys. Acta 1422, 105-185 (1999
28. Barth, A. Infrared spectroscopy of proteins. Biochim. Biophys. Acta 1767, 1073-1101 (2007
29. Liu, K.Z., Shaw, R.A., Man, A., Dembinski, T.C. & Mantsch, H.H. Reagent-free, simultaneous determination of serum cholesterol in HDL and LDL by infrared spectroscopy. Clin. Chem. 48, 499-506 (2002
30. Lenk, T.J., Horbett, T.A., Ratner, B.D. & Chittur, K.K. Infrared spectroscopic studies of time-dependent changes in fibrinogen adsorbed to polyurethanes. Langmuir 7, 1755-1764 (1991
31. Goormaghtigh, E., Cabiaux, V. & Ruysschaert, J.M. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy. III. Secondary structures. Subcell. Biochem. 23, 405-450 (1994
32. Tamm, L.K. & Tatulian, S.A. Infrared spectroscopy of proteins and peptides in lipid bilayers. Q. Rev. Biophys. 30, 365-429 (1997
33. Arrondo, J.L. & Goni, F.M. Structure and dynamics of membrane proteins as studied by infrared spectroscopy. Prog. Biophys. Mol. Biol. 72, 367-405 (1999
34. Chapman, D., Jackson, M. & Haris, P.I. Investigation of membrane protein structure using Fourier transform infrared spectroscopy. Biochem. Soc. Trans. 17, 617-619 (1989
35. Angeletti, R.H. (ed.) Techniques in Protein Chemistry III. (Academic Press, 1992
36. Chittur, K.K. FTIR/ATR for protein adsorption to biomaterial surfaces. Biomaterials 19, 357-369 (1998
37. Yu, S. et al. Solution structure and structural dynamics of envelope protein domain III of mosquito-And tick-borne flaviviruses. Biochemistry 43, 9168-9176 (2004
38. Shen, X. et al. The secondary structure of calcineurin regulatory region and conformational change induced by calcium/calmodulin binding. J. Biol. Chem. 283, 11407-11413 (2008
39. Yu, S., Mei, F.C., Lee, J.C. & Cheng, X. Probing cAMP-dependent protein kinase holoenzyme complexes I? and II? by FT-IR and chemical protein footprinting. Biochemistry 43, 1908-1920 (2004
40. Dong, A., Huang, P. & Caughey, W.S. Redox-dependent changes in ?-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra. Biochemistry 31, 182-189 (1992
41. Dong, A et al. Infrared and circular dichroism spectroscopic characterization of structural differences between ?-lactoglobulin A and B. Biochemistry 35, 1450-1457 (1996
42. Dong, A., Matsuura, J., Manning, M.C. & Carpenter, J.F. Intermolecular ?-sheet results from trifluoroethanol-induced nonnative ?-helical structure in ?-sheet predominant proteins: Infrared and circular dichroism spectroscopic study. Arch. Biochem. Biophys. 355, 275-281 (1998
43. Dong, A., Malecki, J.M., Lee, L., Carpenter, J.F. & Lee, J.C. Ligand-induced conformational and structural dynamics changes in Escherichia coli cyclic AMP receptor protein. Biochemistry 41, 6660-6667 (2002
44. Dong, A. et al. Secondary structure of recombinant human cystathionine ?-synthase in aqueous solution: Effect of ligand binding and proteolytic truncation. Arch. Biochem. Biophys. 344, 125-132 (1997
45. Nasse, M.J., Ratti, S., Giordano, M. & Hirschmugl, C.J. Demountable liquid/flow cell for in vivo infrared microspectroscopy of biological specimens. Appl. Spectrosc. 63, 1181-1186 (2009
46. Surewicz, W.K. & Mantsch, H.H. New insight into protein secondary structure from resolution-enhanced infrared spectra. Biochim. Biophys. Acta 952, 115-130 (1988
47. Kalnin, N.N., Baikalov, I.A. & Venyaminov, S. Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. III. Estimation of the protein secondary structure. Biopolymers 30, 1273-1280 (1990
48. Venyaminov, S. & Kalnin, N.N. Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in ?-, ?-, and random coil conformations. Biopolymers 30, 1259-1271 (1990
49. Dong, A., Huang, P., Caughey, B. & Caughey, W.S. Infrared analysis of ligand- and oxidation-induced conformational changes in hemoglobins and myoglobins. Arch. Biochem. Biophys. 316, 893-898 (1995
50. Cameron, D.G. & Moffatt, D.J. A generalized approach to derivative spectroscopy. Appl. Spectrosc. 41, 539-544 (1987
51. Sarver, R.W. Jr & Krueger, W.C. Protein secondary structure from Fourier transform infrared spectroscopy: a database analysis. Anal. Biochem. 194, 89-100 (1991
52. Holloway, P.W. & Mantsch, H.H. Structure of cytochrome b5 in solution by Fourier-transform infrared spectroscopy. Biochemistry 28, 931-935 (1989
53. Chou, P.Y. & Fasman, G.D. β-turns in proteins. J. Mol. Biol. 115, 135-175 (1977
54. Venyaminov, S. & Kalnin, N.N. Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands. Biopolymers 30, 1243-1257 (1990
55. Dong, A., Randolph, T.W. & Carpenter, J.F. Entrapping intermediates of thermal aggregation in ?-helical proteins with low concentration of guanidine hydrochloride. J. Biol. Chem. 275, 27689-27693 (2000
56. Yu, S., Fan, F., Flores, S.C., Mei, F. & Cheng, X. Dissecting the mechanism of Epac activation via hydrogen-deuterium exchange FT-IR and structural modeling. Biochemistry 45, 15318-15326 (2006
57. Laemmli, U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685 (1970
58. Bassan, P. et al. Resonant Mie scattering in infrared spectroscopy of biological materials: understanding the 'dispersion artefact'. Analyst 134, 1586-1593 (2009
59. Kelly, J.G. et al. Biospectroscopy to metabolically profile biomolecular structure: a multistage approach linking computational analysis with biomarkers. J. Proteome Res. 10, 1437-1448 (2011
60. Prestrelski, S.J., Byler, D.M. & Liebman, M.N. Comparison of various molecular forms of bovine trypsin: correlation of infrared spectra with X-ray crystal structures. Biochemistry 30, 133-143 (1991
61. Savitzky, A. & Golay, M.J.E. Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem. 36, 1627-1639 (1964
62. Dong, A., Huang, P. & Caughey, W.S. Redox-dependent changes in ?-sheet and loop structures of Cu, Zn superoxide dismutase in solution observed by infrared spectroscopy. Arch. Biochem. Biophys. 320, 59-64 (1995
63. Sharma, H., Yu, S., Kong, J., Wang, J. & Steitz, T.A. Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding. Proc. Natl. Acad. Sci. USA 106, 16604-16609 (2009
64. Levitt, M. & Greer, J. Automatic identification of secondary structure in globular proteins. J. Mol. Biol. 114, 181-239 (1977
65. Pace, C.N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411-2423 (1995