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Optical Spectroscopic Methods for the Analysis of Biological Macromolecules

  • Linda O. NarhiEmail author
  • Cynthia H. Li
  • Ranjini Ramachander
  • Juraj Svitel
  • Yijia Jiang
Chapter
Part of the Biophysics for the Life Sciences book series (BIOPHYS, volume 6)

Abstract

The interaction of light with macromolecules is used in multiple different ways in the life sciences. These interactions can be exploited to learn about the structure, stability, and function of proteins and nucleic acids. In this chapter we cover analysis of macromolecules, primarily at equilibrium, by UV absorbance, circular dichroism, fluorescence, Fourier transform infrared, and Raman spectroscopies, and light scattering. A brief description of the underlying theory and some examples of applications are provided for each technique.

Keywords

UV absorbance Fluorescence spectroscopy Fourier transform infrared (FTIR) spectroscopy Raman spectroscopy Circular dichroism Light scattering Spectroscopy 

References

  1. 1.
    Atkins P, de Paula J (2009) Atkin’s Physical chemistry, 9th edn. Oxford University Press, OxfordGoogle Scholar
  2. 2.
    Berg JM, Tymoczko JL, Stryer L (2006) Biochemistry, 6th edn. W H Freeman and Company, New York, NYGoogle Scholar
  3. 3.
    Nelson DL, Cox MM (2008) Lehninger’s Principles of biochemistry, 5th edn. W H Freeman and Company, New York, NYGoogle Scholar
  4. 4.
    Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walker P (2007) Molecular biology of the cell, 5th edn. Garland Science, Taylor and Francis Group, New York, NYGoogle Scholar
  5. 5.
    McQuarrie DA, Smith JD (1997) Physical chemistry: a molecular approach. University Science, Sausalito, CAGoogle Scholar
  6. 6.
    Atkins P, De Paula J (2005) Physical chemistry for the life sciences. W H Freeman and Company, New York, NYGoogle Scholar
  7. 7.
    Larsen D (2011) Electronic spectroscopy. http://chemwiki.ucdavis.edu
  8. 8.
    Wetlaufer DB (1962) Ultraviolet spectra of proteins and amino acids. Adv Protein Chem 17:303–390Google Scholar
  9. 9.
    Schmid F-X (2001) Biological macromolecules: UV-visible spectrophotometry in encyclopedia of life sciences. Macmillan, London, pp 1–4. http://www.els.net
  10. 10.
    Kerekr M (1969) The scattering of light and other electromagnetic radiation. Academic, New York, NYGoogle Scholar
  11. 11.
    van Holde KE, Johnson WC, Ho PS (2006) Chapter 7: Scattering from solutions of macromolecules. In: van Holde KE, Johnson WC, Ho PS (eds) Principles of physical biochemistry, 2nd edn. Pearson Prentice Hall, Upper Saddle River, NJGoogle Scholar
  12. 12.
    Demeester J, De Smedt S, Sanders NN, Haustraete J (2005) Chapter 7: Light scattering, In: Jiskoot W, Crommelin D (eds) Methods for structural analysis of protein pharmaceutics. AAPS, Arlington, VAGoogle Scholar
  13. 13.
    Kueltzo LA, Middaugh CR (2005) Ultraviolet absorption spectroscopy in methods for structural analysis of protein pharmaceuticals. AAPS, Arlington, VAGoogle Scholar
  14. 14.
    Mach H, Middaugh RC (2010) Ultraviolet spectroscopy as a tool in therapeutic protein development. J Pharm Sci 100:1214–1227Google Scholar
  15. 15.
    Omura T, Sato R (1964) The carbon monoxide-binding pigment of liver microsomes: I. Evidence for its hemoprotein nature. J Biol Chem 239:2370–2378PubMedGoogle Scholar
  16. 16.
    Pace CN, Vajdos F, Fee L, Grimsley G, Gray T (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci 4:2411–2423PubMedGoogle Scholar
  17. 17.
    Burke CJ, Sanyal G, Bruner MW, Ryan JA, LaFemina RL, Robins HL, Zeft AS, Middaugh CR, Cordingly MG (1992) Structural implications of spectroscopic characterization of a putative zinc finger peptide from HIV-1 integrase. J Biol Chem 267(14):9639–9644PubMedGoogle Scholar
  18. 18.
    Narhi LO, Fulco AJ (1987) Identification and characterization of two functional domains in cytochrome P-450 BM-3, a catalytically self-sufficient monooxygenase induced by barbiturates in Bacillus megaterium. J Biol Chem 262:6683–6690PubMedGoogle Scholar
  19. 19.
    Warburg O, Christian W (1941) Isolierung und krystallisation des garungsferments enolase. Biochem Z 310:384–421Google Scholar
  20. 20.
    Mach H, Thomson JA, Middaugh CR (1989) Quantitative analysis of protein mixtures by second derivative absorption spectroscopy. Anal Biochem 181:79–85PubMedGoogle Scholar
  21. 21.
    Mach H, Middaugh R (1994) Simultaneous monitoring of the environment of tryptophan, tyrosine and phenylalanine residues in protein by near-ultraviolet second derivative spectroscopy. Anal Biochem 222:323–331PubMedGoogle Scholar
  22. 22.
    Bray MR, Carrierre AD, Clarke AJ (1994) Quantitation of tryptophan and tyrosine residues in proteins by fourth derivative spectroscopy. Anal Biochem 221:278–284PubMedGoogle Scholar
  23. 23.
    Kelly SM, Jess TJ, Price NC (2005) How to study proteins by circular dichroism. Biochim Biophys Acta 1751:119–139PubMedGoogle Scholar
  24. 24.
    Sreerama N, Woody RW (2004) Computation and analysis of protein circular dichroism spectra. Methods Enzymol 383:318–351PubMedGoogle Scholar
  25. 25.
    Sreerama N, Woody RW (2004) On the analysis of membrane protein circular dichroism spectra. Protein Sci 13:100–112PubMedGoogle Scholar
  26. 26.
    Sreerama N, Woody RW (1993) A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal Biochem 209:32–44PubMedGoogle Scholar
  27. 27.
    Manavalan P, Johnson WC Jr (1987) Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal Biochem 167:76–85PubMedGoogle Scholar
  28. 28.
    Johnson WC (1999) Analyzing protein circular dichroism spectra for accurate secondary structures. Proteins 35:307–312PubMedGoogle Scholar
  29. 29.
    Andrade MA, Chacón P, Merelo JJ, Morán F (1993) Evaluation of secondary structure of proteins from UV circular dichroism using an unsupervised neural network. Protein Eng 6:383–390PubMedGoogle Scholar
  30. 30.
    Provencher SW, Glöckner J (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20:33–37PubMedGoogle Scholar
  31. 31.
    Lobley L, Whitmore BAW (2002) DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra. Bioinformatics 18:211–212PubMedGoogle Scholar
  32. 32.
    Whitmore L, Wallace BA (2004) DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res 32:W668–W673PubMedGoogle Scholar
  33. 33.
    Hardin Strickland E (1974) Aromatic contributions to circular dichroism spectra of proteins. CRC Crit Rev Biochem 2:113–175Google Scholar
  34. 34.
    Krell T, Horsburgh MJ, Cooper A, Kelly SM, Coggins JR (1996) Localization of the active site of type II dehydroquinases. Identification of a common arginine-containing motif in the two classes of dehydroquinases. J Biol Chem 271:24492–24497PubMedGoogle Scholar
  35. 35.
    Pain R (2005) Determining the CD spectrum of a protein. Curr Protoc Protein Sci Chapter 7:Unit 7.6Google Scholar
  36. 36.
    Venyaminov SY, Vassilenko KS (1994) Determination of protein tertiary structure class from circular dichroism spectra. Anal Biochem 222:176–184PubMedGoogle Scholar
  37. 37.
    Kypr J, Kejnovska I, Renciuk D, Vorlickova M (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 37(6):1713–1725PubMedGoogle Scholar
  38. 38.
    Marty R, N’soukpoé-Kossi CN, Charbonneau DM, Kreplak L, Tajmir-Riahi H (2009) Structural characterization of cationic lipid-tRNA complexes. Nucleic Acids Res 37(15):5197–5520PubMedGoogle Scholar
  39. 39.
    Greenfield NJ (1996) Methods to estimate conformation of proteins and polypeptides from CD data. Anal Biochem 235(1):1–10PubMedGoogle Scholar
  40. 40.
    Perczel A, Hollosi M, Tusnady G, Fasman GD (1991) Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. Protein Eng 4:669–679PubMedGoogle Scholar
  41. 41.
    Perczel A, Fasman GD (1993) Effect of spectral window size on circular dichroism spectra deconvolution of proteins. Biophys Chem 48:19–29Google Scholar
  42. 42.
    Venyaminov SW, Baikalov I, Chuen-Shang C, Yang JT (1991) Some problems of CD analysis of protein conformation. Anal Biochem 198:250–255PubMedGoogle Scholar
  43. 43.
    Cover TM, Hart PE (1967) Nearest neighbor pattern classification. IEEE Trans Inf Theory 13(1):21–27Google Scholar
  44. 44.
    Thermo OMNIC software manual (TQ Analyst Algorithm) (1998) QC compare method for classifying materialsGoogle Scholar
  45. 45.
    Li C, Nguyen X, Narhi LO, Chemmalil L, Towers E, Muzammil S, Gabrielson JP, Jiang Y (2011) Applications of circular dichroism for structural analysis of proteins: qualification of near- and far-UV CD for protein higher order structural analysis. J Pharm Sci 100(11):4642–4654PubMedGoogle Scholar
  46. 46.
    D’Antonio J, Murphy B, Manning M, Al-Azzam W (2012) Comparability of protein therapeutics: quantitative comparison of second-derivative amide I infrared spectra. J Pharm Sci 101(6):2025–2033PubMedGoogle Scholar
  47. 47.
    Teska B, Li C, Winn B, Arthur K, Jiang Y, Gabrielson J (2013) Comparison of quantitative spectral similarity analysis methods for protein higher order structure confirmation. Anal Biochem 434:153–165PubMedGoogle Scholar
  48. 48.
    Klewpatinond M, Viles JH (2007) Fragment length influences affinity for Cu2+ and Ni2+ binding to His96 or His111 of the prion protein and spectroscopic evidence for a multiple histidine binding only at low pH. Biochem J 404:393–402PubMedGoogle Scholar
  49. 49.
    Jemth P, Gianni S, Day R, Li B, Johnson CM, Daggett V, Fersht AR (2004) Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proc Natl Acad Sci U S A 101:6450–6455PubMedGoogle Scholar
  50. 50.
    Zitzewitz JA, Bilsel O, Luo J, Jones BE, Matthews CR (1995) Probing the folding mechanism of a leucine zipper peptide by stopped-flow circular dichroism spectroscopy. Biochemistry 34:12812–12819PubMedGoogle Scholar
  51. 51.
    Andersson LA, Peterson JA (1995) Active-site analysis of ferric P450 enzymes: hydrogen bonding effects on the circular dichroism spectra. Biochem Biophys Res Commun 211:389–395PubMedGoogle Scholar
  52. 52.
    Wallace BA (2005) Shining new light on protein structure and function thru synchrotron radiation circular dichroism (SRCD) spectroscopy. Aust Biochem 36:47–50Google Scholar
  53. 53.
    Wallace BA, Janes RW (2010) Synchrotron radiation circular dichroism (SRCD) spectroscopy—an enhanced method for examining protein conformations and protein interactions. Biochem Soc Trans 38:861–873PubMedGoogle Scholar
  54. 54.
    Keiderling TA, Yasui SC, Narayanan U, Annamalai A, Malon P, Kobrinskaya R, Yang L (1988) Vibrational circular dichroism of biopolymers. In: Schmid ED, Schneider FW, Siebert F (eds) Spectroscopy of biological molecules new advances. Wiley, New York, NY, pp 73–76Google Scholar
  55. 55.
    Yasui SC, Keiderling TA (1988) Vibrational circular dichroism of polypeptides and proteins. Mikrochim Acta 95:325–327Google Scholar
  56. 56.
    Keiderling TA (1993) Vibrational circular dichroism of proteins polysaccharides and nucleic acids. In: Baianu I, Pessen H, Kumosinski T (eds) Physical chemistry of food processes, vol 2 advanced techniques, structures and applications. Van Nostrand Reinhold, New York, NY, pp 307–337Google Scholar
  57. 57.
    Keiderling TA, Qi X (2002) Spectroscopic characterization of unfolded peptides and proteins studied with infrared absorption and vibrational circular dichroism spectra. Adv Protein Chem 62:111–161PubMedGoogle Scholar
  58. 58.
    Keiderling TA (2002) Protein and peptide secondary structure and conformational determination with vibrational circular dichroism. Curr Opin Chem Biol 6(5):682–688PubMedGoogle Scholar
  59. 59.
    Malon P, Kobrinskaya R, Keiderling TA (1988) Vibrational circular dichroism of polypeptides XII. Re-evaluation of the Fourier transform vibrational circular dichroism of poly-gamma-benzyl-L-glutamate. Biopolymers 27(5):733–746PubMedGoogle Scholar
  60. 60.
    Mao D, Wallace BA (1984) Differential light scattering and absorption flattening optical effects are minimal in the circular dichroism spectra of small unilamellar vesicles. Biochemistry 23:2667–2673PubMedGoogle Scholar
  61. 61.
    Lakowicz JR (1996) Principles of fluorescence spectroscopy, 2nd edn. Kluwer Academic/Plenum, New York, NYGoogle Scholar
  62. 62.
    Szabo AG, Stephanik TM, Wayner DM, Young NM (1983) Conformational heterogeneity of the copper binding site in azurin. Biophys J 41:233–244PubMedGoogle Scholar
  63. 63.
    Latypov RF, Liu D, Gunasekaran K, Harvey TS, Razinkov VI, Raibekas AA (2008) Structural and thermodynamic effects of ANS binding to human interleukin-1 receptor antagonist. Protein Sci 17(4):652–663PubMedGoogle Scholar
  64. 64.
    Eftink M (2000) Intrinsic fluorescence in proteins. In: Lakowicz JR (ed) Topics in fluorescence spectroscopy: protein fluorescence, vol 6. Springer, New York, NY, pp 1–16Google Scholar
  65. 65.
    Narhi LO, Kenney WC, Arakawa T (1991) Conformational changes of recombinant human granulocyte-colony stimulating factor induced by pH and guanidine hydrochloride. J Protein Chem 10(4):359–367PubMedGoogle Scholar
  66. 66.
    Kolvenbach CG, Elliott S, Sachdev R, Arakawa T, Narhi LO (1993) Characterization of two fluorescent tryptophans in recombinant human granulocyte-colony stimulating factor: comparison of native sequence protein and tryptophan-deficient mutants. J Protein Chem 12(2):229–236PubMedGoogle Scholar
  67. 67.
    Brems DN (2002) The kinetics of G-CSF folding. Protein Sci 11(10):2504–2511PubMedGoogle Scholar
  68. 68.
    Calhoun DB, Vanderkooi JM, Holtorn GR, Englander SW (1986) Protein fluorescence quenching by small molecules: protein penetration versus solvent exposure. Proteins 1:109–115PubMedGoogle Scholar
  69. 69.
    Thakkar SV, Kim JH, Samra HS, Sathish HA, Bishop SM, Joshi SB, Volkin DB, Middaugh CR (2012) Local dynamics and their alteration by excipients modulate the global conformational stability of an lgG1 monoclonal antibody. J Pharm Sci 101(12):4444–4457PubMedGoogle Scholar
  70. 70.
    Lukas TJ, Burgess WH, Prendergast FG, Lau W, Watterson DM (1986) Calmodulin binding domains: characterization of a phosphorylation and calmodulin binding site from myosin light chain kinase. Biochemistry 25:1458–1464PubMedGoogle Scholar
  71. 71.
    Cogen U, Shinitzky M, Weber G, Nishida T (1973) Micro-viscosity and order in the hydrocarbon region of phospholipid and phospholipid-cholesterol dispersions determined with fluorescent probes. Biochemistry 12:521–528Google Scholar
  72. 72.
    Daniel E, Weber G (1966) Cooperative effects in binding by bovine serum albumin I. The binding of 1-anilino-8-naphthalene-sulfonate. Fluorimetric titrations. Biochemistry 5:1893–1900PubMedGoogle Scholar
  73. 73.
    He F, Phan DH, Hogan S, Bailey R, Becker GW, Narhi LO, Razinkov VI (2010) Detection of IgG aggregation by a high throughput method based on extrinsic fluorescence. J Pharm Sci 99:2598–2608PubMedGoogle Scholar
  74. 74.
    Lakowicz JR, Keating-Nakamoto S (1984) Red-edge excitation of fluorescence and dynamic properties of proteins and membranes. Biochemistry 23(13):3013–3021PubMedGoogle Scholar
  75. 75.
    Chattopadhyay A, Mukherjee S (1993) Fluorophore environments in membrane-bound probes: a red edge excitation shift study. Biochemistry 32(14):3804–3811PubMedGoogle Scholar
  76. 76.
    Shih WM, Gryczynski Z, Lakowicz JR, Spudich JA (2000) A FRET-based sensor reveals large ATP hydrolysis-induced conformational changes and three distinct states of the molecular motor myosin. Cell 102(5):683–694PubMedGoogle Scholar
  77. 77.
    Rajan RS, Illing ME, Bence NF, Kopito RR (2001) Specificity in intracellular protein aggregation and inclusion body formation. Proc Natl Acad Sci U S A 98(23):13060–13065PubMedGoogle Scholar
  78. 78.
    Miyawaki A, Llopis J, Heim R, McCaffery JM, Adams JA, Ikura M, Tsien RY (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388:882–887PubMedGoogle Scholar
  79. 79.
    Aoki V, Fukumori LMI, Freitas EL, Sousa JX Jr, Perigo AM, Oliveira ZNP (2010) Direct and indirect immunofluorescence. An Bras Dermatol 85(4):490–500PubMedGoogle Scholar
  80. 80.
    Johnston JA, Ward CL, Kopito RR (1998) Aggresomes: a cellular response to misfolded proteins. J Cell Biol 143(7):1883–1898PubMedGoogle Scholar
  81. 81.
    Tsou MF, Wang WJ, George KA, Uryu K, Stearns T, Jallepalli PV (2009) Polo kinase and separase regulate the mitotic licensing of centriole duplication in human cells. Dev Cell 17(3):344–354PubMedGoogle Scholar
  82. 82.
    Kim J, Lee J, Kwon D, Lee H, Grailhe R (2011) A comparative analysis of resonance energy transfer methods for Alzheimer related protein-protein interactions in living cells. Mol Biosyst 7:2991–2996PubMedGoogle Scholar
  83. 83.
    Prestrelski SJ, Arakawa T, Carpenter JF (1993) Separation of freezing- and drying-induced denaturation of lyophilized proteins using stress specific stabilization: II. Structural studies using infrared spectroscopy. Arch Biochem Biophys 303:465–473PubMedGoogle Scholar
  84. 84.
    Sharma VK, Kalonia DS (2003) Steady-state tryptophan fluorescence spectroscopy study to probe tertiary structure of proteins in solid powders. J Pharm Sci 92(4):890–899PubMedGoogle Scholar
  85. 85.
    Ramachander R, Jiang Y, Li C, Eris T, Young M, Dimitrova M, Narhi L (2008) Solid state fluorescence of lyophilized proteins. Anal Biochem 376(2):173–182PubMedGoogle Scholar
  86. 86.
    Araki A, Sako Y (1987) Determination of free and total homocysteine in human plasma by high-performance liquid chromatography with fluorescence detection. J Chromatogr 422:43–52PubMedGoogle Scholar
  87. 87.
    Koivisto P, Peltonen K (2010) Analytical methods in DNA and protein adduct analysis. Anal Bioanal Chem 398:2563–2572PubMedGoogle Scholar
  88. 88.
    Nishikida K, Nishio E, Hannah RW (1995) Selected applications of modern FTIR techniques. Gordon and Breach/Kodansha Ltd., TokyoGoogle Scholar
  89. 89.
    Dong A, Huang P, Caughey WS (1990) Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29(13):3303–3308PubMedGoogle Scholar
  90. 90.
    Surewicz WK, Mantsch HH, Chapman D (1993) Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment. Biochemistry 32(2):389–394PubMedGoogle Scholar
  91. 91.
    Vedantham G, Sparks HG, Sane SU, Tzannis S, Przybycien TM (2000) A holistic approach for protein secondary structure estimation from infrared spectra in H2O solutions. Anal Biochem 285(1):33–49PubMedGoogle Scholar
  92. 92.
    Prestrelski SJ, Tedeschi N, Arakawa T, Carpenter JF (1993) Dehydration-induced conformational transitions in proteins and their inhibition by stabilizers. Biophys J 65:661–671PubMedGoogle Scholar
  93. 93.
    Prestrelski SJ, Pikal KA, Arakawa T (1995) Optimization of lyophilization conditions for recombinant human interleukin-2 by dried state conformational analysis using Fourier transform infrared spectroscopy. Pharm Res 12(9):1250–1259PubMedGoogle Scholar
  94. 94.
    Costantino HR, Carrasquillo KG, Cordero RA, Mumenthaler M, Hsu CC, Griebenow K (1998) Effect of excipients on the stability and structure of lyophilized recombinant human growth hormone. J Pharm Sci 87(11):1412–1420PubMedGoogle Scholar
  95. 95.
    Van Straaten J, Peppas NA (1991) ATR-FTIR analysis of protein adsorption on polymeric surfaces. J Biomater Sci 2(2):113–121Google Scholar
  96. 96.
    Tunc S, Maitz MF, Steiner G, Vazquez L, Pham MT, Salzer R (2005) In situ conformational analysis of fibrinogen absorbed on Si surfaces. Colloids Surf B Biointerfaces 42:219–225PubMedGoogle Scholar
  97. 97.
    Byler DM, Susi H (1986) Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25:469–487PubMedGoogle Scholar
  98. 98.
    Dong A, Hyslop RM, Pringle DL (1996) Differences in conformational dynamics of RNase A and S as observed by infrared spectroscopy and hydrogen-deuterium exchange. Arch Biochem Biophys 333:275–281PubMedGoogle Scholar
  99. 99.
    Zhang Y, Lewis RAH, Hodges RS, McElhaney RN (1992) FTIR spectroscopic studies of the conformation and amide hydrogen exchange of a peptide model of the hydrophobic transmembrane alpha-helixes of membrane. Biochemistry 31(46):11572–11578PubMedGoogle Scholar
  100. 100.
    Dong A, Matsuura J, Allison SD, Chrisman E, Manning MC, Carpenter JF (1996) Infrared and circular dichroism spectroscopic characterization of structural differences in beta-lactoglobulin A and B. Biochemistry 35:1450–1457PubMedGoogle Scholar
  101. 101.
    Kaiden K, Matsui T, Tanaka S (1987) A study of the amide III band by FT-IR spectrometry of the secondary structure of albumin, myoglobin, and γ-globulin. Appl Spectrosc 41(2):180–184Google Scholar
  102. 102.
    Lewandowska K, Balachander N, Sukenik CN, Culp LA (1989) Modulation of fibronectin adhesive functions for fibroblasts and neural cells by chemically derivatized substrata. J Cell Physiol 141(2):334–345PubMedGoogle Scholar
  103. 103.
    Sukenik CN, Balachander N, Culp LA, Lewandowska K, Merritt K (1990) Modulation of cell adhesion by modification of titanium surfaces with covalently attached self-assembled monolayers. J Biomed Mater Res 24(10):1307–1323PubMedGoogle Scholar
  104. 104.
    Eikje NS, Aizawa K, Ozaki Y (2005) Vibrational spectroscopy for molecular characterisation and diagnosis of benign, premalignant and malignant skin tumours. Biotechnol Annu Rev 11:191–225PubMedGoogle Scholar
  105. 105.
    Mackanos MA, Contag CH (2010) Fiber-optic probes enable cancer detection with FTIR spectroscopy. Trends Biotechnol 28(6):317–323PubMedGoogle Scholar
  106. 106.
    Baker MJ, Gazi E, Brown MD, Shanks JH, Clarke NW, Gardner P (2009) Investigating FTIR based histopathology for the diagnosis of prostate cancer. J Biophotonics 2(1–2):104–113PubMedGoogle Scholar
  107. 107.
    Ostrowska KM, Garcia A, Meade AD, Malkin A, Okewumi I, O’Leary JJ, Martin C, Byrne HJ, Lyng FM (2011) Correlation of p16INK4A expression and HPV copy number with cellular FTIR spectroscopic signatures of cervical cancer cells. Analyst 136:1365–1373PubMedGoogle Scholar
  108. 108.
    Fu K, Griebenow K, Hsieh L, Klibanov AM, Langer R (1999) FTIR characterization of the secondary structure of proteins encapsulated with PLGA microspheres. J Control Release 58:357–366PubMedGoogle Scholar
  109. 109.
    Dong A, Jones LS, Kerwin BA, Krishnan S, Carpenter JF (2006) Secondary structures of proteins adsorbed onto aluminum hydroxide adjuvant: infrared spectroscopic analysis of proteins from low solution concentrations. Anal Biochem 351:282–289PubMedGoogle Scholar
  110. 110.
    Hoehne M, Samuel F, Dong A, Wurth C, Mahler HC, Carpenter JF, Randolph T (2010) Adsorption of monoclonal antibodies to glass microparticles. J Pharm Sci 100:123–132PubMedGoogle Scholar
  111. 111.
    Goormaghtigh E, Ruysschaert JM, Raussens V (2006) Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys J 90(8):2946–2957PubMedGoogle Scholar
  112. 112.
    Griebenow K, Klibanov AM (1995) Lyophilization induced reversible changes in the secondary structure of proteins. Proc Natl Acad Sci U S A 92:10969–10976PubMedGoogle Scholar
  113. 113.
    Chittur KK (1998) FTIR/ATR for protein adsorption to biomaterial surfaces. Biomaterials 19(4–5):357–369PubMedGoogle Scholar
  114. 114.
    Goldberg ME, Chaffotte AF (2005) Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy. Protein Sci 14(11):2781–2792PubMedGoogle Scholar
  115. 115.
    Service RJ, Hillier W, Debus RJ (2010) Evidence from FTIR difference spectroscopy of an extensive network of hydrogen bonds near the oxygen-evolving Mn[4]Ca cluster of photosystem II involving D1–Glu, 65, D2–Glu312, and D1–Glu329. Biochemistry 49(31):6655–6669Google Scholar
  116. 116.
    Hastings G, Bandaranayake KM, Carrion E (2008) Time-resolved FTIR difference spectroscopy in combination with specific isotope labeling for the study of A1, the secondary electron acceptor in photosystem I. Biophys J 94(11):4383–4392PubMedGoogle Scholar
  117. 117.
    Barth A (2000) Review, the infrared absorption of amino acid side chains. Prog Biophys Mol Biol 74:141–173PubMedGoogle Scholar
  118. 118.
    Mäntele W (1993) Reaction-induced infrared difference spectroscopy for the study of protein function and reaction mechanisms. Trends Biochem Sci 18(6):197–202PubMedGoogle Scholar
  119. 119.
    Zscherp C, Barth A (2001) Reaction-induced infrared difference spectroscopy for the study of protein reaction mechanisms. Biochemistry 40(7):1875–1883PubMedGoogle Scholar
  120. 120.
    Barth A (2007) Infrared spectroscopy of proteins. Biochim Biophys Acta 1767(9):1073–1101PubMedGoogle Scholar
  121. 121.
    Lacob RE, Engen JR (2012) Hydrogen exchange mass spectrometry, are we out of the quicksand? J Am Soc Mass Spectrom 23:1003–1010Google Scholar
  122. 122.
    Norris AL et al (2009) NMR detected hydrogen–deuterium exchange reveals differential dynamics of antibiotic- and nucleotide-bound aminoglycoside phosphotransferase 3′-IIIa. J Am Chem Soc 131(24):8587–8594PubMedGoogle Scholar
  123. 123.
    Houde D, Berkowitz SA, Engen JR (2011) The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J Pharm Sci 100:2071–2086PubMedGoogle Scholar
  124. 124.
    Narhi LO, Wood SJ, Steavenson S, Jiang Y, Wu GM, Anafi D, Kaufman SA, Martin F, Sitney K, Denis P, Louis JC, Wypych J, Biere AL, Citron M (1999) Both familial Parkinson’s disease mutations accelerate alpha-synuclein aggregation. J Biol Chem 274:9843–9846PubMedGoogle Scholar
  125. 125.
    Baenziger JE, Méthot N (1995) Fourier transform infrared and hydrogen/deuterium exchange reveal an exchange-resistant core of α-helical peptide hydrogens in the nicotinic acetylcholine receptor. J Biol Chem 270:29129–29137PubMedGoogle Scholar
  126. 126.
    Rath P, DeGrip WJ, Rothschild KJ (1998) Photoactivation of rhodopsin causes an increased hydrogen-deuterium exchange of buried peptide groups. Biophys J 74(1):192–198PubMedGoogle Scholar
  127. 127.
    French DL, Arakawa T, Li T (2004) Fourier transform infrared spectroscopy investigation of protein conformation in spray-dried protein/trehalose powders. Biopolymers 73(4):524–531PubMedGoogle Scholar
  128. 128.
    Yu S, Fan F, Flores SC, Mei F, Cheng X (2006) Dissecting the mechanism of Epac activation via hydrogen-deuterium exchange FT-IR and structural modeling. Biochemistry 45(51):15318–15326PubMedGoogle Scholar
  129. 129.
    Kamerzell TJ, Middaugh CR (2007) Two-dimensional correlation spectroscopy reveals coupled immunoglobulin regions of differential flexibility that influence stability. Biochemistry 46:9762–9776PubMedGoogle Scholar
  130. 130.
    Fabian H, Naumann D (2006) Methods to study protein folding by stopped-flow FT-IR. Methods 34(1):28–40Google Scholar
  131. 131.
    Reinstädler D, Fabian H, Backmann J, Naumann D (1996) Refolding of thermally and urea-denatured ribonuclease A monitored by time-resolved FTIR spectroscopy. Biochemistry 35(49):15822–15830PubMedGoogle Scholar
  132. 132.
    Panick G, Winter R (2000) Pressure-induced unfolding/refolding of ribonuclease A, static and kinetic Fourier transform infrared spectroscopy study. Biochemistry 39(7):1862–1869PubMedGoogle Scholar
  133. 133.
    Sethuraman A, Belfort G (2005) Protein structural perturbation and aggregation on homogeneous surfaces. Biophys J 88(2):1322–1333PubMedGoogle Scholar
  134. 134.
    Sharma S, Berne BJ, Kumar SK (2010) Thermal and structural stability of adsorbed proteins. Biophys J 99(4):1157–1165PubMedGoogle Scholar
  135. 135.
    Noda I (1986) Two-dimensional infrared (2D-IR) spectroscopy of synthetic and biopolymers. Bull Am Phys Soc 31:520–524Google Scholar
  136. 136.
    Noda I (1989) Two-dimensional infrared spectroscopy. J Am Chem Soc 111:8116–8118Google Scholar
  137. 137.
    Noda I (1990) Two-dimensional infrared (2D IR) spectroscopy, theory and applications. Appl Spectrosc 44:550–561Google Scholar
  138. 138.
    Sosa LDV et al (2011) The structure, molecular dynamics, and energetics of centrin–melittin complex. Proteins 79:3132–3143Google Scholar
  139. 139.
    Jiang Y et al (2011) Qualification of FTIR spectroscopic method for protein secondary structural analysis. J Pharm Sci 100(11):4631–4641PubMedGoogle Scholar
  140. 140.
    Kendrick BS et al (1996) Quantitation of the area of overlap between second-derivative amide I infrared spectra to determine the structural similarity of a protein in different states. J Pharm Sci 85(2):155–158PubMedGoogle Scholar
  141. 141.
    Keiderling TA, Silva RAGD (2002) Review: conformational studies of peptides with infrared techniques. In: Goodman M, Herrman G (eds) Houben-Weyl synthesis of peptides and peptidomimetics, vol 22Eb. Georg Thiem, New York, NY, pp 715–738Google Scholar
  142. 142.
    Chou KC (1983) Identification of low-frequency modes in protein molecules. Biochem J 215:465–469PubMedGoogle Scholar
  143. 143.
    Chou KC (1984) Low-frequency vibration of DNA molecules. Biochem J 221:27–31PubMedGoogle Scholar
  144. 144.
    Ellis DI, Goodacre R (2006) Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy. Analyst 131(8):875–885PubMedGoogle Scholar
  145. 145.
    Callender R, Deng H (1994) Nonresonance Raman difference spectroscopy: a general probe of protein structure, ligand binding, enzymatic catalysis, and the structures of other biomacromolecules. Ann Rev Biophy Biomol Struct 23:215–245Google Scholar
  146. 146.
    Spiro TG, Gaber BP (1977) Laser Raman scattering as a probe of protein structure. Annu Rev Biochem 46:553–570PubMedGoogle Scholar
  147. 147.
    Tuma R (2005) Raman spectroscopy of proteins: from peptides to large assemblies. J Raman Spectrosc 36:307–319Google Scholar
  148. 148.
    Benevides, JM, Overman, SA, Thomas GJ (2004) Raman spectroscopy of proteins. Curr Protoc Protein Sci Chapter 17:Unit 17.8Google Scholar
  149. 149.
    Lednev IK, Karnoup AS, Sparrow MC, Asher SA (1999) Alpha-helix peptide folding and unfolding activation barriers: a nanosecond UV resonance Raman study. J Am Chem Soc 121:8074–8086Google Scholar
  150. 150.
    Siamwiza MN, Lord RC, Chen MC, Takamatsu T, Harada I, Matsuura H, Shimanouchi T (1975) Interpretation of the doublet at 850 and 830 cm−1 in the Raman spectra of tyrosyl residues in proteins and certain model compounds. Biochemistry 14:4870–4876PubMedGoogle Scholar
  151. 151.
    Arp Z, Autrey D, Laane J, Overman SA, Thomas GJ Jr (2001) Tyrosine Raman signatures of the filamentous virus Ff are diagnostic of non-hydrogen-bonded phenoxyls: demonstration by Raman and infrared spectroscopy of p-cresol vapor. Biochemistry 40:2522–2529PubMedGoogle Scholar
  152. 152.
    Takeuchi H, Harada I (1986) Normal coordinate analysis of the indole ring. Spectrochim Acta 42A:1069–1078Google Scholar
  153. 153.
    Takeuchi H, Matsuno M, Overman SA, Thomas GJ Jr (1996) Raman linear intensity difference of flow-oriented macromolecules: orientation of the indole ring of tryptophan-26 in filamentous virus fd. J Am Chem Soc 118:3498–3507Google Scholar
  154. 154.
    Miura T, Takeuchi H, Harada I (1989) Tryptophan Raman bands sensitive to hydrogen bonding and side-chain conformation. J Raman Spectrosc 20:667–671Google Scholar
  155. 155.
    Miura T, Takeuchi H, Harada I (1991) Raman spectroscopic characterization of tryptophan side chains in lysozyme bound to inhibitors: role of the hydrophobic box in the enzymatic function. Biochemistry 30:6074–6080PubMedGoogle Scholar
  156. 156.
    Kitagawa T, Azuma T, Hamaguchi K (1979) The Raman spectra of Bence-Jones proteins. Disulfide stretching frequencies and dependence of Raman intensity of tryptophan residues on their environments. Biopolymers 18:451–465Google Scholar
  157. 157.
    Li H, Thomas GJ Jr (1991) Cysteine conformation and sulfhydryl interactions in proteins and viruses. I. Correlation of the Raman S-H band with hydrogen bonding and intramolecular geometry in model compounds. J Am Chem Soc 113:456–462Google Scholar
  158. 158.
    Li H, Wurrey CJ, Thomas GJ Jr (1992) Cysteine conformation and sulfhydryl interactions in proteins and viruses. 2. Normal coordinate analysis of the cysteine side chain in model compounds. J Am Chem Soc 114:7463–7469Google Scholar
  159. 159.
    Li H, Hanson C, Fuchs JA, Woodward C, Thomas GJ Jr (1993) Determination of the pKa values of active-center cysteines, cysteines-32 and -35, in Escherichia coli thioredoxin by Raman spectroscopy. Biochemistry 32:5800–5808PubMedGoogle Scholar
  160. 160.
    Takeuchi H, Kimura Y, Koitabashi I, Harada I (1991) Raman bands of N-deuterated histidinium as markers of conformation and hydrogen bonding. J Raman Spectrosc 22:233–236Google Scholar
  161. 161.
    Tasumi M, Harada I, Takamatsu T, Takahashi S (1982) Raman studies of L-histidine and related compounds in aqueous solutions. J Raman Spectrosc 12:149–151Google Scholar
  162. 162.
    Harada I, Takeuchi H (1986) Raman and ultraviolet resonance Raman of proteins and related compounds. In: Clark RJH, Hester RE (eds) Advances in spectroscopy. John Wiley & Sons, New York, NY, pp 113–175Google Scholar
  163. 163.
    Russell MP, Vohník S, Thomas GJ Jr (1995) Design and performance of an ultraviolet resonance Raman spectrometer for proteins and nucleic acids. Biophys J 68:1607–1612PubMedGoogle Scholar
  164. 164.
    Arzhantsev S, Vilker V, Kauffman J (2012) Deep-ultraviolet (UV) resonance Raman spectroscopy as a tool for quality control of formulated therapeutic proteins. Appl Spectrosc 66(11):1262–1268PubMedGoogle Scholar
  165. 165.
    Bai Y, Sosnick TR, Mayne L, Englander SW (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269:192–197PubMedGoogle Scholar
  166. 166.
    Barron LD, Hecht L, Blanch EW, Bell AF (2000) Solution structure and dynamics of biomolecules from Raman optical activity. Prog Biophys Mol Biol 73:1–49PubMedGoogle Scholar
  167. 167.
    Benevides JM, Li T, Lu XJ, Srinivasan AR, Olson WK, Weiss MA, Thomas GJ Jr (2000) Protein-directed DNA structure. II. Raman spectroscopy of a leucine zipper bZIP complex. Biochemistry 39:548–556PubMedGoogle Scholar
  168. 168.
    Thomas GJ Jr, Benevides JM, Overman SA, Ueda T, Ushizawa K, Saitoh M, Tsuboi M (1995) Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations. Biophys J 68:1073–1088PubMedGoogle Scholar
  169. 169.
    Thomas GJ Jr (1999) Raman spectroscopy of protein and nucleic acid assemblies. Annu Rev Biophys Biomol Struct 28:1–27PubMedGoogle Scholar
  170. 170.
    Benevides JM, Thomas GJ Jr (1983) Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA. Nucleic Acids Res 11:5747–5761PubMedGoogle Scholar
  171. 171.
    Thomas GJ Jr, Agard DA (1984) Quantitative analysis of nucleic acids, proteins and viruses by Raman band deconvolution. Biophys J 46:763–768PubMedGoogle Scholar
  172. 172.
    Wen Z, Cao X, Phillips J (2010) Application of Raman spectroscopy in biopharmaceutical manufacturing. Am Pharm Rev 13:46–53Google Scholar
  173. 173.
    Cao X, Wen Z, Vance A, Torraca G (2009) Raman microscopic applications in the biopharmaceutical industry: in situ identification of foreign particulates inside glass containers with aqueous formulated solutions. Appl Spectrosc 63(7):830–834PubMedGoogle Scholar
  174. 174.
    Zhu F, Isaacs NW, Hecht N, Barron LD (2005) Raman optical activity: a tool for protein structure analysis. Structure 13(10):1409–1419PubMedGoogle Scholar
  175. 175.
    Wyatt PJ (1993) Light scattering and the absolute characterization of macromolecules. Anal Chim Acta 272:1–40Google Scholar
  176. 176.
    Goldberg DS, Bishop SM, Shah AU, Sathish HA (2011) Formulation development of therapeutic monoclonal antibodies using high-throughput fluorescence and static light scattering techniques: role of conformational and colloidal stability. J Pharm Sci 100(4):1306–1315Google Scholar
  177. 177.
    Wen J, Arakawa T, Philo JS (1996) Size exclusion chromatography with on-line light scattering, absorbance, and refractive index detectors for studying protein and their interactions. Anal Biochem 240:155–166PubMedGoogle Scholar
  178. 178.
    Mandel M (1993) Applications of dynamic light scattering to polyelectrolytes in solution. In: Brown W (ed) Dynamic light scattering: the method and some applications. Oxford, New York, NY, pp 319–371Google Scholar
  179. 179.
    Philo JS (2009) A critical review of methods for size characterization of non-particulate protein aggregates. Curr Pharm Biotechnol 10:359–372PubMedGoogle Scholar
  180. 180.
    Narhi LO (ed) (2013) Biophysics of protein therapeutic development. Springer, NYGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Linda O. Narhi
    • 1
    Email author
  • Cynthia H. Li
    • 1
  • Ranjini Ramachander
    • 1
  • Juraj Svitel
    • 1
  • Yijia Jiang
    • 1
  1. 1.Research and Development, Amgen, Inc.Thousand OaksUSA

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