Abstract
Vibrational circular dichroism (VCD) spectroscopy is an invaluable spectroscopic techniques utilized to exploit the optical strength of vibrational transitions for structure analysis. In this chapter, we describe the protocol for measuring and self-consistently analyzing VCD and the corresponding FT-IR spectra of short peptides. This process involves the decomposition of the IR spectrum as well as simulations of the amide I band profiles in both spectra based on structural models of the peptides investigated. This type of spectral analysis should be complemented with similar investigations of Raman spectra, which are described in the subsequent chapter. The structural analysis of short, unfolded peptides described in this chapter can easily be extended for the analysis of longer unfolded peptides or even proteins. This is particularly important in view of the demonstrated biological relevance of intrinsically disordered peptides and proteins (IDPs).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Keiderling TA (1996) Vibrational circular dichroism: application to conformational analysis of biomolecules. In: Fasman GD (ed) Circular dichroism and the conformational analysis of biomolecules. Plenumn, New York, p 555
Keiderling TA, Xu Q (2002) Unfolded proteins studied with IR and VCD spectra. Adv Protein Chem 62:111–161
Sutherland JC (2009) Measurement of circular dichroism and related spectroscopies with conventional and synchotron light sources: theory and instrumentation. In: Wallace BA, Janes RW (eds) Modern techniques for circular dichroism spectroscopy. IOS, Amsterdam, pp 19–73
Nafie LA (1997) Infrared and Raman vibrational optical activity. Annu Rev Phys Chem 48:357
Nafie LA, Dukor RK, Freedman TB (2002) Dichroism and optical activity in optical spectroscopy. In: Chalmers J, Griffiths P (eds) Handbook of vibrational spectroscopy. Wiley, New York, pp 731–744
Chen XG, Schweitzer-Stenner R, Asher SA, Mirkin NG, Krimm S (1995) Vibrational assignments of trans-N-methylacetamide and some of its deuterated isotopomers from band decomposition of IR, visible, and resonance Raman spectra. J Phys Chem 99:3074–3083
Han W-G, Jakanen KJ, Elstner M, Suhai S (1998) Theoretical study of aqueous N-Acetyl-L-alanine N-methylamide: structures and Raman, VCD, and ROA spectra. J Phys Chem B 102:2587–2602
Schweitzer-Stenner R, Gonzales W, Bourne JT, Feng JA, Marshall GA (2007) Conformational manifold of α-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations. J Am Chem Soc 129:13095–13109
Bouŕ P, Keiderling TA (2005) Vibrational spectral simulation for peptides of mixed secondary structure: method comparisons with the Trpzip model hairpin. J Phys Chem B 123:23687–23697
Tanaka S, Scheraga HA (1976) Statistical mechanical treatment of protein conformation. II. A three-state model for specific-sequence copolymers of amino acids. Macromolecules 9:150–167
Schweitzer-Stenner R (2006) Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure. A critical review. Vib Spectrosc 42:98–117
Schweitzer-Stenner R (2009) Distribution of conformations sampled by the central amino acid residue in Tripeptides inferred from amide I band profiles and NMR scalar coupling constants. J Phys Chem B 113:2922–2932
Hagarman A, Measey TJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R (2010) Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I band profiles and NMR scalar coupling constants. J Am Chem Soc 132:542
Chicz RM, Regnier FE (1990) High-performance liquid chromatography: effective protein purification by various chromatographic modes. Methods Enzymol 182:392–421
Ingle JD, Crouch SR (1988) Infrared spectrometry. In: Spectrochemical analysis. Prentice Hall, Upper Saddle River, NJ, p 404–437
Skoog DA, Holler FJ, Nieman TA (1998) An introduction to infrared spectrometry. In: Principles of Instrumental Analysis, 5th ed. Harcourt Brace and Company, Philadelphia, USA, p 380–428
(2000) Model SR810 DSP lock-in amplifier, 1.6 ed. Stanford Research Systems, Sunnyvale, CA
(1999) Series SR640 Dual-channel filters, 2.6 ed. Stanford Research Systems, Inc, Sunnyvale, CA
Graf J, Nguyen PH, Stock G, Schwalbe H (2007) Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/nmr study. J Am Chem Soc 129:1179–1189
Jentzen W, Unger E, Karvounis G, Shelnutt JA, Dreybrodt W, Schweitzer-Stenner R (1995) Conformational properties of nickel(II) octaethylporphyrin in solution. 1. Resonance excitation profiles and temperature dependence of structure-sensitive Raman lines. J Phys Chem 100:14184–14191
Woutersen S, Hamm P (2000) Structure determination of trialanine in water using polarized sensitive two-dimensional vibrational spectroscopy. J Phys Chem B 104:11316–11320
Eker F, Cao X, Nafie L, Schweitzer-Stenner R (2002) Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR and VCD spectroscopy study. J Am Chem Soc 124:14330–14341
Schweitzer-Stenner R (2002) Dihedral angles of tripeptides in solution determined by polarized Raman and FTIR spectroscopy. Biophys J 83:523–532
Torii H, Tasumi M (1998) Ab initio molecular orbital study of the amide i vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix. J Raman Spectrosc 29:81–86
Krimm S, Bandekar J (1986) Vibrational spectroscopy of peptides and proteins. Adv Protein Chem 38:181
Woutersen S, Hamm P (2001) Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution. J Chem Phys 114:2727–2737
Gorbunov RD, Kosov DS, Stock G (2005) Ab initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence and transferability. J Chem Phys 122:224904–224915
Ham S, Cha S, Choi J-H, Cho M (2003) Amide I modes of tripeptides: Hessian matrix reconstruction and isotope effects. J Chem Phys 119:1452–1461
Ham S, Cho M (2003) Amide I modes in the N-methylacetamide dimer and glycine dipeptide analog: diagonal force constants. J Chem Phys 118:6915–6922
Gorbunov RD, Nguyen PH, Kobus M, Stock G (2007) Quantum-classical description of the amide I vibrational spectrum of trialanine. J Chem Phys 126:054509
Measey T, Hagarman A, Eker F, Griebenow K, Schweitzer-Stenner R (2005) Side chain dependence of intensity and wavenumber position of amide I′ in IR and visible Raman spectra of XA and AX dipeptides. J Phys Chem B 109:8195–8205
Eker F, Cao X, Nafie L, Griebenow K, Schweitzer-Stenner R (2003) The structure of alanine based tripeptides in water and dimethyl sulfoxide probed by vibrational spectroscopy. J Phys Chem B 107:358–365
Eker F, Griebenow K, Schweitzer-Stenner R (2004) A β1–28 fragment of the amyloid peptide predominantly adopts a polyproline II conformation in an acidic solution. Biochemistry 43:6893–6898
Schweitzer-Stenner R, Measey T, Hagarman A, Eker F, Griebenow K (2006) Salmon calcitonin an amyloid β: two peptides with amyloidogenic capacity adopt different conformational manifolds in their unfolded states. Biochemistry 45:2810–2819
Schweitzer-Stenner R, Measey T, Kakalis L, Jordan F, Pizzanelli S, Forte C, Griebenow K (2007) Conformations of alanine-based peptides in water probed by FTIR, Raman, vibrational circular dichroism, electronic circular dichroism, and NMR spectroscopy. Biochemistry 46:1587–1596
Schweitzer-Stenner R, Eker F, Perez A, Griebenow K, Cao X, Nafie LA (2003) The structure of tri-proline in water probed probed by polarized Raman, Fourier transform infrared, vibrational circular dichroism and electronic ultraviolet circular dichroism spectroscopy. Biopolymers 71:558–568
Holzwarth G, Chabay I (1972) Optical activity of vibrational transitions: a coupled oscillator model. J Chem Phys 57:1632–1638
Huang Q, Schweitzer-Stenner R (2004) Conformational analysis of tetrapeptides by exploiting the excitonic coupling between amide I modes. J Raman Spectrosc 53:586–591
Lee C, Cho MH (2004) Local amide I mode frequencies and coupling constants in multiple-stranded antiparallel beta-sheet polypeptides. J Phys Chem B 108:20397–20407
Kubelka J, Keiderling TA (2001) Differentiation of β-sheet-forming structures: Ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein β-sheets. J Am Chem Soc 123:12048–12058
Kubelka J, Keiderling TA (2001) The anomalous infrared amide I intensity distribution in 13C isotopically labeled peptide β-sheets comes from extended, multiple –stranded structures. An ab initio study. J Am Chem Soc 123:6142–6150
Schweitzer-Stenner R, Measey TJ (2010) Simulation of IR, Raman and VCD amide I band profiles of self-assembled peptides. Spectroscopy 24:25–36
Schweitzer-Stenner R (2004) Secondary structure analysis of polypeptides based on an excitonic coupling model to describe the band profile of amide I of IR, Raman and vibrational circular dichroism spectra. J Phys Chem B 108:16965–16975
Verbaro D, Ghosh I, Nau WM, Schweitzer-Stenner R (2010) Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I′ band profiles. J Phys Chem B 114:17201–17208
Schweitzer-Stenner R, Measey TJ, Hagarman A, Dragomir I (2010) The structure of unfolded peptides and proteins explored by Raman and IR spectroscopies. In: Assessing Structures and Conformation of Intrinsically Disordered Proteins”, Editors: S. Longhi and V.N. Uversky. Wiley & Sons, 171–224:2012
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Schweitzer-Stenner, R., Soffer, J.B., Verbaro, D. (2012). Structure Analysis of Unfolded Peptides I: Vibrational Circular Dichroism Spectroscopy. In: Uversky, V., Dunker, A. (eds) Intrinsically Disordered Protein Analysis. Methods in Molecular Biology, vol 895. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-927-3_18
Download citation
DOI: https://doi.org/10.1007/978-1-61779-927-3_18
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-926-6
Online ISBN: 978-1-61779-927-3
eBook Packages: Springer Protocols