Simulation of IR, Raman and VCD amide i band profiles of self-assembled peptides

Spectroscopy

Volumn 24, Issue 1-2, 2010, Pages 25-36

  Schweitzer Stenner, Reinhard ^a   Measey, Thomas J ^a  

^a DREXEL UNIVERSITY   (United States)

Author keywords

Amide I; Excitonic coupling; Hydrogel; Self assembly; VCD

Indexed keywords

AMIDES; ANISOTROPY; DICHROISM; HYDROGELS; PEPTIDES; THREE DIMENSIONAL COMPUTER GRAPHICS;

AMIDE I; AMIDE I BANDS; CIRCULAR DICHROISM SIGNALS; EXCITONIC COUPLING; IR BANDS; ISOTROPICS; STACKINGS; VIBRATIONAL CIRCULAR DICHROISM; VIBRATIONAL CIRCULAR DICHROISM SPECTRUM; Β-SHEET STRUCTURE;

SELF ASSEMBLY;

AMIDE;

ALGORITHM; ANISOTROPY; BETA SHEET; CIRCULAR DICHROISM; CONFERENCE PAPER; GELATION; HYDROGEL; INFRARED SPECTROSCOPY; PROTEIN ASSEMBLY; QUALITATIVE ANALYSIS; RAMAN SPECTROMETRY; SIGNAL DETECTION; THREE DIMENSIONAL IMAGING; VIBRATION;

EID: 77953754754     PISSN: 07124813     EISSN: None     Source Type: Journal    
DOI: 10.1155/2010/763610     Document Type: Conference Paper

References (31)

1. T.C. Holmes, Novel peptide-based biomaterial scaffolds for tissue engineering, Trends Biotechnol. 20 (2002), 16-21.
2. K. Rajagopal and J.P. Schneider, Self-assembling peptides and proteins for nanotechnological applications, Curr. Op. Struct. Biol. 14, 480.
3. V. Bellotti, P. Mangione andM. Stoppini, Biological activity and pathological implications of misfolded proteins, Cellular and Molecular Life Sciences 55 (1999), 977-991.
4. C.M. Dobson, Protein misfolding, evolution and disease, Trends in Biochemical Sciences 24 (1999), 329-332.
5. J. Bandekar, Amide modes and protein conformation, Biochim. Biophys. Acta 1120 (1992), 123-143.
6. X.G. Chen, R. Schweitzer-Stenner, S.A. Asher, N.G. Mirkin and S. Krimm, 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 (1995), 3074-3083.
7. X.G. Chen, R. Schweitzer-Stenner, N.G. Mirkin, S. Krimm and S.A. Asher, N-methylacetamide and its hydrogen-bonded water molecules are vibrationally coupled, J. Am. Chem. Soc. 116 (1994), 11141-11142.
8. G. Sieler and R. Schweitzer-Stenner, The amide I mode of peptides in aqueous solution involves vibrational coupling between the peptide group and water molecules of the hydration shell, J. Am. Chem. Soc. 119 (1997), 1720.
9. S. Krimm and J. Bandekar, Vibrational spectroscopy of peptides and proteins, Adv. Protein Chem. 38 (1986), 181.
10. R. Schweitzer-Stenner, Visible and UV-resonance Raman spectroscopy on model peptides, J. Raman Spectrosc. 32 (2001), 711.
11. J.W. Brauner, C. Dugan and R. Mendelsohn, 13C isotope labeling of hydrophobic peptides. Origin of the anomalous intensity distribution in the infrared amide I spectral region of β-sheet structures, J. Am. Chem. Soc. 122 (2000), 677-683.
12. H. Torii and M. Tasumi, Model calculations on the amide-I infrared bands of globular proteins, J. Chem. Phys. 96 (1992), 3379-3387.
13. H. Torii and M. Tasumi, Application of the three-dimensional doorway-state theory to analyses of the amide-I band of globular proteins, J. Chem. Phys. 97 (1992), 92-98.
14. R. Schweitzer-Stenner, Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure. A critical review, Vibr. Spectrosc. 42 (2006), 98-117.
15. J. Kubelka and T.A. Keiderling, 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 (2001), 12048-12058.
16. J. Kubelka, J. Kim, P. Bour and T.A. Keiderling, Contribution of transition dipole coupling to amide coupling in IR spectra of peptide secondary structures, Vibr. Spectrosc. 42 (2007), 63-73.
17. J. Kubelka and T.A. Keiderling, 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 (2001), 6142-6150.
18. R. Schweitzer-Stenner, T. Measey, A. Hagarman and I. Dragomir, The structure of unfolded peptides and proteins explored by Raman and IR spectroscopies, in: Vibrational Spectroscopy on Peptides and Proteins, S. Longhi and V.N. Uversky, eds, Wiley, Chichester, 2010, in press.
19. R. Schweitzer-Stenner, 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 (2009), 2922-2932.
20. C. Lee and M.H. Cho, Local amide I mode frequencies and coupling constants in multiple-stranded antiparallel beta-sheet polypeptides, J. Phys. Chem. B 108 (2004), 20397-20407.
21. R. Schweitzer-Stenner, Dihedral angles of tripeptides in solution determined by polarized Raman and FTIR spectroscopy, Biophys. J. 83 (2002), 523-1332
22. T. Measey and R. Schweitzer-Stenner, Aggregation of the amphipathic peptides (AAKA)n into antiparallel β-sheets, J. Am. Chem. Soc. 128 (2006), 13324-13325.
23. W. Jentzen, E. Unger, G. Karvounis, J.A. Shelnutt, W. Dreybrodt and R. Schweitzer-Stenner, Conformational properties of nickel(II) octaethylporphyrin in solution. 1. Resonance excitation profiles and temperature dependence of structuresensitive Raman lines, J. Phys. Chem. 100 (1995), 14184-14191.
24. T. Measey and R. Schweitzer-Stenner, Simulation of amide I-band profiles of trans polyproline based on an excitonic coupling model, Chem. Phys. Lett. 408 (2005), 123-127.
25. T. Measey, A. Hagarman, F. Eker, K. Griebenow and R. Schweitzer-Stenner, 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 (2005), 8195-8205.
26. R. Schweitzer-Stenner, F. Eker, K. Griebenow, X. Cao and L. Nafie, The conformation of tetraalanine in water determined by polarized Raman, FTIR and VCD spectroscopy, J. Am. Chem. Soc. 126 (2004), 2768-2776.
27. R. Schweitzer-Stenner, W. Gonzales, J.T. Bourne, J.A. Feng and G.A. Marshall, Conformational manifold of β-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 (2007), 13095-13109.
28. Y.Wang, R. Purello, S. Georgiou and T.G. Spiro, UVRR spectroscopy of the peptide bond. 2. Carbonyl H-bond effects on the ground- and excited-state structures of N-methylacetamide, J. Am. Chem. Soc. 113 (1991), 6359-6368.
29. H. Torii, T. Tatsumi, T. Kanazawa and M. Tasumi, Effects of intramolecular hydrogen-bonding interactions on the amide I mode of N-methylacetamide: matrix isolation infrared studies and ab initio molecular orbital calculations, J. Phys. Chem. B 102 (1998), 309-314.
30. A. Aggeli, I.A. Nyrkova, M. Bell, R. Harding, L. Carrick, T.C.B. McLeish, A.N. Semenov and N. Boden, Hierachical self-assembly of chiral rod-like molecules as a model for peptide β-shett tapes, ribbons, fibrils and fibers, Proc. Natl. Acad. Sci. USA 98 (2001), 11857-11862.
31. S. Jang, J.M. Yuan, J. Shin, T.J. Measey, R. Schweitzer-Stenner and F.Y. Li, Energy landscapes associated with the selfaggregation of an alanine-based oligopeptide (AAKA)4, J. Phys. Chem. B 113 (2009), 6054-6061.