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. 2002 Jul;83(1):523–532. doi: 10.1016/S0006-3495(02)75188-6

Dihedral angles of tripeptides in solution directly determined by polarized Raman and FTIR spectroscopy.

Reinhard Schweitzer-Stenner 1
PMCID: PMC1302166  PMID: 12080139

Abstract

The amide I mode of the peptide linkage is highly delocalized in peptides and protein segments due to through-bond and through-space vibrationally coupling between adjacent peptide groups. J. Phys. Chem. B. 104:11316-11320) used coherent femtosecond infrared (IR) spectroscopy to determine the excitonic coupling energy and the orientational angle between the transition dipole moments of the interacting amide I modes of cationic tri-alanine in D(2)O. Recently, the same parameters were determined for all protonation states of tri-alanine by analyzing the amide I bands in the respective IR and isotropic Raman spectra (. J. Am. Chem. Soc. 119:1720-1726.). In both studies, the dihedral angles phi and psi were then obtained by utilizing the orientational dependence of the coupling energy obtained from ab initio calculations on tri-glycine in vacuo (. J. Raman Spectrosc. 29:81-86) to obtain an extended 3(1) helix-like structure for the tripeptide. In the present paper, a novel algorithm for the analysis of excitonic coupling between amide I modes is presented, which is based on the approach by Schweitzer-Stenner et al. but avoids the problematic use of results from ab initio calculations. Instead, the dihedral angles are directly determined from infrared and visible polarized Raman spectra. First, the interaction energy and the corresponding degree of wave-function mixing were obtained from the amide I profile in the isotropic Raman spectrum. Second, the depolarization ratios and the amide I profiles in the anisotropic Raman and IR-absorption spectra were used to determine the orientational angle between the peptide planes and the transition dipole moments, respectively. Finally, these two geometric parameters were utilized to determine the dihedral angles phi and psi between the interacting peptide groups. Stable extended conformations with dihedral angles in the beta-sheet region were obtained for all protonation states of tri-alanine, namely phi(+) = -126 degrees, psi(+) = 178 degrees; phi(+/-) = -110 degrees, psi(+/-) = 155 degrees; and phi(-) = -127 degrees, psi(-) = 165 degrees for the cationic, zwitterionic, and anionic state, respectively. These values reflect an extended beta-helix structure. Tri-glycine was found to be much more heterogeneous in that different extended conformers coexist in the cationic and zwitterionic state, which yield a noncoincidence between isotropic and anisotropic Raman scattering. Our study introduces vibrational spectroscopy as a suitable tool for the structure analysis of peptides in solution and tripeptides as suitable model systems for investigating the role of local interactions in determining the propensity of peptide segments for distinct secondary structure motifs.

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Selected References

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  1. Arnott S., Dover S. D. Refinement of bond angles of an alpha-helix. J Mol Biol. 1967 Nov 28;30(1):209–212. doi: 10.1016/0022-2836(67)90253-7. [DOI] [PubMed] [Google Scholar]
  2. Bandekar J. Amide modes and protein conformation. Biochim Biophys Acta. 1992 Apr 8;1120(2):123–143. doi: 10.1016/0167-4838(92)90261-b. [DOI] [PubMed] [Google Scholar]
  3. Barron L. D., Hecht L., Blanch E. W., Bell A. F. Solution structure and dynamics of biomolecules from Raman optical activity. Prog Biophys Mol Biol. 2000;73(1):1–49. doi: 10.1016/s0079-6107(99)00017-6. [DOI] [PubMed] [Google Scholar]
  4. Chi Z., Asher S. A. UV resonance Raman determination of protein acid denaturation: selective unfolding of helical segments of horse myoglobin. Biochemistry. 1998 Mar 3;37(9):2865–2872. doi: 10.1021/bi971161r. [DOI] [PubMed] [Google Scholar]
  5. Chi Z., Chen X. G., Holtz J. S., Asher S. A. UV resonance Raman-selective amide vibrational enhancement: quantitative methodology for determining protein secondary structure. Biochemistry. 1998 Mar 3;37(9):2854–2864. doi: 10.1021/bi971160z. [DOI] [PubMed] [Google Scholar]
  6. Dong J., Wan Z. L., Chu Y. C., Nakagawa S. N., Katsoyannis P. G., Weiss M. A., Carey P. R. Isotope-edited Raman spectroscopy of proteins: a general strategy to probe individual peptide bonds with application to insulin. J Am Chem Soc. 2001 Aug 15;123(32):7919–7920. doi: 10.1021/ja011101f. [DOI] [PubMed] [Google Scholar]
  7. Dyson H. J., Lerner R. A., Wright P. E. The physical basis for induction of protein-reactive antipeptide antibodies. Annu Rev Biophys Biophys Chem. 1988;17:305–324. doi: 10.1146/annurev.bb.17.060188.001513. [DOI] [PubMed] [Google Scholar]
  8. Gnanakaran S., Hochstrasser R. M. Conformational preferences and vibrational frequency distributions of short peptides in relation to multidimensional infrared spectroscopy. J Am Chem Soc. 2001 Dec 26;123(51):12886–12898. doi: 10.1021/ja011088z. [DOI] [PubMed] [Google Scholar]
  9. Goodman M., Zhu Q., Kent D. R., Amino Y., Iacovino R., Benedetti E., Santini A. Conformational analysis of the dipeptide taste ligand L-aspartyl-D-2-aminobutyric acid-(S)-alpha-ethylbenzylamide and its analogues by NMR spectroscopy, computer simulations and X-ray diffraction studies. J Pept Sci. 1997 May-Jun;3(3):231–241. doi: 10.1002/(sici)1099-1387(199705)3:3<231::aid-psc105>3.0.co;2-3. [DOI] [PubMed] [Google Scholar]
  10. Hamm P., Lim M., DeGrado W. F., Hochstrasser R. M. The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure. Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2036–2041. doi: 10.1073/pnas.96.5.2036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hu X., Dick L. A., Spiro T. G. Fourier transform infrared evidence against Asp beta 99 protonation in hemoglobin: nature of the Tyr alpha 42-Asp beta 99 quaternary H-bond. Biochemistry. 1998 Jun 30;37(26):9445–9448. doi: 10.1021/bi9805644. [DOI] [PubMed] [Google Scholar]
  12. Kiso Y., Matsumoto H., Mizumoto S., Kimura T., Fujiwara Y., Akaji K. Small dipeptide-based HIV protease inhibitors containing the hydroxymethylcarbonyl isostere as an ideal transition-state mimic. Biopolymers. 1999;51(1):59–68. doi: 10.1002/(SICI)1097-0282(1999)51:1<59::AID-BIP7>3.0.CO;2-3. [DOI] [PubMed] [Google Scholar]
  13. Krimm S., Bandekar J. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv Protein Chem. 1986;38:181–364. doi: 10.1016/s0065-3233(08)60528-8. [DOI] [PubMed] [Google Scholar]
  14. Lee O., Roberts G. M., Diem M. IR vibrational CD in alanyl tripeptide: indication of a stable solution conformer. Biopolymers. 1989 Oct;28(10):1759–1770. doi: 10.1002/bip.360281009. [DOI] [PubMed] [Google Scholar]
  15. Lyu P. C., Liff M. I., Marky L. A., Kallenbach N. R. Side chain contributions to the stability of alpha-helical structure in peptides. Science. 1990 Nov 2;250(4981):669–673. doi: 10.1126/science.2237416. [DOI] [PubMed] [Google Scholar]
  16. Marqusee S., Baldwin R. L. Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design. Proc Natl Acad Sci U S A. 1987 Dec;84(24):8898–8902. doi: 10.1073/pnas.84.24.8898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Schmidt U., Langner J. Cyclotetrapeptides and cyclopentapeptides: occurrence and synthesis. J Pept Res. 1997 Jan;49(1):67–73. doi: 10.1111/j.1399-3011.1997.tb01122.x. [DOI] [PubMed] [Google Scholar]
  18. Schweitzer-Stenner R., Eker F., Huang Q., Griebenow K. Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy. J Am Chem Soc. 2001 Oct 3;123(39):9628–9633. doi: 10.1021/ja016202s. [DOI] [PubMed] [Google Scholar]
  19. Tanaka S., Scheraga H. A. Statistical mechanical treatment of protein conformation. 5. A multistate model for specific-sequence copolymers of amino acids. Macromolecules. 1977 Jan-Feb;10(1):9–20. doi: 10.1021/ma60055a002. [DOI] [PubMed] [Google Scholar]
  20. Tobias D. J., Brooks C. L., 3rd Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry. 1991 Jun 18;30(24):6059–6070. doi: 10.1021/bi00238a033. [DOI] [PubMed] [Google Scholar]
  21. Torreggiani A., Tamba M., Fini G. Binding of copper(II) to carnosine: Raman and IR spectroscopic study. Biopolymers. 2000;57(3):149–159. doi: 10.1002/(SICI)1097-0282(2000)57:3<149::AID-BIP3>3.0.CO;2-G. [DOI] [PubMed] [Google Scholar]
  22. Wright P. E., Dyson H. J., Lerner R. A. Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry. 1988 Sep 20;27(19):7167–7175. doi: 10.1021/bi00419a001. [DOI] [PubMed] [Google Scholar]
  23. Wüthrich K., Grathwohl C. A novel approach for studies of the molecular conformations in flexible polypeptides. FEBS Lett. 1974 Aug 1;43(3):337–340. doi: 10.1016/0014-5793(74)80674-5. [DOI] [PubMed] [Google Scholar]
  24. Zimmerman S. S., Scheraga H. A. Local interactions in bends of proteins. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4126–4129. doi: 10.1073/pnas.74.10.4126. [DOI] [PMC free article] [PubMed] [Google Scholar]

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