European Biophysics Journal

, Volume 32, Issue 8, pp 661–670 | Cite as

Circular dichroism spectra of β-peptides: sensitivity to molecular structure and effects of motional averaging

  • Xavier Daura
  • Dirk Bakowies
  • Dieter Seebach
  • Jörg Fleischhauer
  • Wilfred F. van Gunsteren
  • Peter Krüger


Circular dichroism spectra of two β-peptides, i.e. peptides composed of β-amino acids, calculated using ensembles of configurations obtained by molecular dynamics simulation are presented. The calculations were based on 200 ns simulations of a β-heptapeptide in methanol at 298 K and 340 K and a 50 ns simulation of a β-hexapeptide in methanol at 340 K. In the simulations the peptides sampled both folded (helical) and unfolded structures. Trajectory structures with common backbone conformations were identified and grouped into clusters. The CD spectra were calculated for individual structures, based on peptide-group dipole transition moments obtained from semi-empirical molecular orbital theory and using the so-called matrix method. The single-structure spectra were then averaged over entire trajectories and over clusters of structures. Although certain features of the experimental CD spectra of the β-peptides are reproduced by the trajectory-average spectra, there exist clear differences between the two sets of spectra in both wavelength and peak intensities. The analysis of individual contributions to the average spectra shows that, in general, the interpretation of a CD signal in terms of a single structure is not possible. Moreover, there is a large variation in the CD spectra calculated for a set of individual structures that belong to the same cluster, even when a structurally tight clustering criterion is used. This indicates that the CD spectra of these peptides are very sensitive to small local structural differences.


Circular dichroism Cluster analysis Computer simulation Molecular dynamics Peptide folding 


  1. Abele S, Guichard G, Seebach D (1998) (S)-β3-Homolysine- and (S)-β3-homoserine-containing β-peptides: CD spectra in aqueous solution. Helv Chim Acta 81:2141–2156CrossRefGoogle Scholar
  2. Appella DH, Christianson LA, Karle IL, Powell DR, Gellman SH (1996) β-Peptide foldamers: robust helix formation in a new family of β-amino acid oligomers. J Am Chem Soc 118:13071–13072CrossRefGoogle Scholar
  3. Appella DH, Christianson LA, Klein DA, Powell DR, Huang X, Barchi JJ, Gellman SH (1997) Residue-based control of helix shape in β-peptide oligomers. Nature 387:381–384PubMedGoogle Scholar
  4. Appella DH, Barchi JJ Jr, Durell SR, Gellman SH (1999) Formation of short, stable helices in aqueous solution by β-amino acid hexamers. J Am Chem Soc 121:2309–2310CrossRefGoogle Scholar
  5. Applequist J (1973) Polarizability theory of optical rotation. J Chem Phys 58:4251–4259Google Scholar
  6. Applequist J, Bode KA (2000) Fully extended poly(β-amino acid) chains: translational helices with unusual theoretical π-π* absorption and circular dichroic spectra. J Phys Chem A 104:7129–7132CrossRefGoogle Scholar
  7. Applequist J, Bode KA, Appella DH, Christianson LA, Gellman SH (1998) Theoretical and experimental circular dichroic spectra of the novel helical foldamer poly[(1R,2R)-trans-2-aminocyclopentanecarboxylic acid]. J Am Chem Soc 120:4891–4892CrossRefGoogle Scholar
  8. Bayley PM, Nielsen EB, Schellman JA (1969) The rotatory properties of molecules containing 2 peptide groups: theory. J Phys Chem 73:228–243PubMedGoogle Scholar
  9. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690Google Scholar
  10. Berova N, Nakanishi K, Woody RW (2000) Circular dichroism: principles and application. Wiley-VCH, New YorkGoogle Scholar
  11. Besley NA, Hirst JD (1999) Theoretical studies toward quantitative protein circular dichroism calculations. J Am Chem Soc 121:9636–9644CrossRefGoogle Scholar
  12. Bode KA, Applequist J (1997) Poly(β-amino acid) helices. Theoretical π-π* absorption and circular dichroic spectra. Macromolecules 30:2144–2150CrossRefGoogle Scholar
  13. Bode KA, Applequist J (1998) Globular protein ultraviolet circular dichroic spectra. Calculation from crystal structures via the dipole interaction model. J Am Chem Soc 120:10938–10946CrossRefGoogle Scholar
  14. Borman S (1997) β-Peptides: nature improved? Chem Eng News 75:32–35Google Scholar
  15. Bringmann G, Mühlbacher J, Repges C, Fleischhauer J (2001) MD-based CD calculations for the assignment of the absolute axial configuration of the naphthylisoquinoline alkaloid dioncophylline A. J Comput Chem 22:1273–1278CrossRefGoogle Scholar
  16. Burgi R, Pitera J, van Gunsteren WF (2001) Assessing the effect of conformational averaging on the measured values of observables. J Biomol NMR 19:305–320CrossRefPubMedGoogle Scholar
  17. Chandrasekhar J, Saunders M, Jorgensen WL (2001) Efficient exploration of conformational space using the stochastic search method: application to β-peptide oligomers. J Comput Chem 22:1646–1654CrossRefGoogle Scholar
  18. Chung YJ, Christianson LA, Stanger HE, Powell DR, Gellman SH (1998) A β-peptide reverse turn that promotes hairpin formation. J Am Chem Soc 120:10555–10556CrossRefGoogle Scholar
  19. Clark LB (1995) Polarization assignments in the vacuum UV spectra of the primary amide, carboxyl, and peptide groups. J Am Chem Soc 117:7974–7986Google Scholar
  20. Daura X, van Gunsteren WF, Rigo D, Jaun B, Seebach D (1997) Studying the stability of a helical β-heptapeptide by molecular dynamics simulations. Chem Eur J 3:1410–1417Google Scholar
  21. Daura X, Jaun B, Seebach D, van Gunsteren WF, Mark AE (1998) Reversible peptide folding in solution by molecular dynamics simulation. J Mol Biol 280:925–932CrossRefPubMedGoogle Scholar
  22. Daura X, Antes I, van Gunsteren WF, Thiel W, Mark AE (1999a) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins Struct Funct Genet 36:542–555CrossRefPubMedGoogle Scholar
  23. Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE (1999b) Peptide folding: when simulation meets experiment. Angew Chem Int Ed 38:236–240CrossRefGoogle Scholar
  24. Daura X, van Gunsteren WF, Mark AE (1999c) Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins Struct Funct Genet 34:269–280CrossRefPubMedGoogle Scholar
  25. Daura X, Gademann K, Schäfer H, Jaun B, Seebach D, van Gunsteren WF (2001) The β-peptide hairpin in solution: conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation. J Am Chem Soc 123:2393–2404CrossRefPubMedGoogle Scholar
  26. Del Bene J, Jaffe HH (1968a) Use of CNDO method in spectroscopy. 2. 5-membered rings. J Chem Phys 48:4050Google Scholar
  27. Del Bene J, Jaffe HH (1968b) Use of CNDO method in spectroscopy. 1. Benzene, pyridine and diazines. J Chem Phys 48:1807Google Scholar
  28. DeVoe H (1964) Optical properties of molecular aggregates. 1. Classical model of electronic absorption+refraction. J Chem Phys 41:393–400Google Scholar
  29. DeVoe H (1965) Optical properties of molecular aggregates. 2. Classical theory of refraction absorption and optical activity of solutions and crystals. J Chem Phys 43:3199–3208Google Scholar
  30. Eliel EL, Wilen SH (1994) Stereochemistry of organic compounds. Wiley, New YorkGoogle Scholar
  31. Fleischhauer J, Kramer B, Zobel E, Koslowski A (1991) MATMAC: matrix and Tinoco method Aachen. Aachen, GermanyGoogle Scholar
  32. Fleischhauer J, Grotzinger J, Kramer B, Krüger P, Wollmer A, Woody RW, Zobel E (1994) Calculation of the circular-dichroism spectrum of cyclo(L-Tyr- L-Tyr) based on a molecular-dynamics simulation. Biophys Chem 49:141–152CrossRefPubMedGoogle Scholar
  33. Foresman JB, Head-Gordon M, Pople JA, Frisch MJ (1992) Toward a systematic molecular-orbital theory for excited-states. J Phys Chem 96:135–149Google Scholar
  34. Gademann K, Ernst M, Hoyer D, Seebach D (1999a) Synthesis and biological evaluation of a cyclo-β-tetrapeptide as a somatostatin analogue. Angew Chem Int Ed 38:1223–1226CrossRefGoogle Scholar
  35. Gademann K, Hintermann T, Schreiber JV (1999b) β-Peptides: twisting and turning. Curr Med Chem 6:905–925Google Scholar
  36. Gademann K, Jaun B, Seebach D, Perozzo R, Scapozza L, Folkers G (1999c) Temperature-dependent NMR and CD spectra of β-peptides: on the thermal stability of β-peptide helices – is the folding process of β-peptides non-cooperative? Helv Chim Acta 82:1–11Google Scholar
  37. Gademann K, Ernst M, Seebach D, Hoyer D (2000) The cyclo-β-tetrapeptide (β-HPhe-β-HThr-β-HLys-β-HTrp): synthesis, NMR structure in methanol solution, and affinity for human somatostatin receptors. Helv Chim Acta 83:16–33Google Scholar
  38. Gellman SH (1998) Foldamers: a manifesto. Acc Chem Res 31:173–180CrossRefGoogle Scholar
  39. Glättli A, Daura X, Seebach D, Van Gunsteren WF (2002) Can one derive the conformational preference of a β-peptide from its CD spectrum? J Am Chem Soc 124:12972–12978Google Scholar
  40. Goldmann E, Sanford AA, Mukamel S (2001) Electronic excitations of polyalanine; test of the independent chromophore approximation. Phys Chem Chem Phys 3:2893–2903CrossRefGoogle Scholar
  41. Gung BW, Zou D, Stalcup AM, Cottrell CE (1999) Characterization of a water-soluble, helical β-peptide. J Org Chem 64:2176–2177CrossRefGoogle Scholar
  42. Hamuro Y, Schneider JP, DeGrado WF (1999) De novo design of antibacterial β-peptides. J Am Chem Soc 121:12200–12201CrossRefGoogle Scholar
  43. Hintermann T, Seebach D (1997) The biological stability of β-peptides: no interactions between α- and β-peptidic structures? Chimia 51:244–247Google Scholar
  44. Hirst JD (1998a) Improving protein circular dichroism calculations through better ab initio models of the amide chromophore. Enantiomer 3:215–220Google Scholar
  45. Hirst JD (1998b) Improving protein circular dichroism calculations in the far-ultraviolet through reparametrizing the amide chromophore. J Chem Phys 109:782–788CrossRefGoogle Scholar
  46. Iverson BL (1997) Betas are brought into the fold. Nature 385:113–115PubMedGoogle Scholar
  47. Krauthäuser S, Christianson LA, Powell DR, Gellman SH (1997) Antiparallel sheet formation in β-peptide foldamers: effects of β-amino acid substitution on conformational preference. J Am Chem Soc 119:11719–11720CrossRefGoogle Scholar
  48. Kurapkat G, Krüger P, Wollmer A, Fleischhauer J, Kramer B, Zobel E, Koslowski A, Botterweck H, Woody RW (1997) Calculations of the CD spectrum of bovine pancreatic ribonuclease. Biopolymers 41:267–287CrossRefPubMedGoogle Scholar
  49. Möhle K, Günther R, Thormann M, Sewald N, Hofmann HJ (1999) Basic conformers in β-peptides. Biopolymers 50:167–184CrossRefPubMedGoogle Scholar
  50. Peter C, Daura X, van Gunsteren WF (2001) Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. J Biomol NMR 20:297–310CrossRefPubMedGoogle Scholar
  51. Porter EA, Wang X, Lee H-S, Weisblum B, Gellman SH (2000a) Non-haemolytic β-amino-acid oligomers. Nature 405:298PubMedGoogle Scholar
  52. Porter EA, Wang X, Lee H-S, Weisblum B, Gellman SH (2000b) Antibiotics – non-haemolytic β-amino-acid oligomers. Nature 404:565–565CrossRefPubMedGoogle Scholar
  53. Rueping M, Schreiber JV, Lelais G, Jaun B, Seebach D (2002) Mixed β23-hexapeptides and β23-nonapeptides folding to (P)-helices with alternating twelve- and ten-membered hydrogen-bonded rings. Helv Chim Acta 85:2577–2593CrossRefGoogle Scholar
  54. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341Google Scholar
  55. Scott WRP, Hünenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Krüger P, van Gunsteren WF (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596–3607Google Scholar
  56. Seebach D, Ciceri PE, Overhand M, Jaun B, Rigo D, Oberer L, Hommel U, Amstutz R, Widmer H (1996a) Probing the helical secondary structure of short-chain β-peptides. Helv Chim Acta 79:2043–2066Google Scholar
  57. Seebach D, Overhand M, Kühnle FNM, Martinoni B, Oberer L, Hommel U, Widmer H (1996b) β-Peptides: synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexpeptide in solution and its stability towards pepsin. Helv Chim Acta 79:913–941Google Scholar
  58. Seebach D, Gademann K, Schreiber JV, Matthews JL, Hintermann T, Jaun B, Oberer L, Hommel U, Widmer H (1997) 'Mixed' β-peptides: a unique helical secondary structure in solution. Helv Chim Acta 80:2033–2038Google Scholar
  59. Seebach D, Abele S, Gademann K, Guichard G, Hintermann T, Jaun B, Matthews JL, Schreiber JV (1998a) β2- and β3-peptides with proteinaceous side chains: synthesis and solution structures of constitutional isomers, a novel helical secondary structure and the influence of solvation and hydrophobic interactions on folding. Helv Chim Acta 81:932–982Google Scholar
  60. Seebach D, Abele S, Schreiber JV, Martinoni B, Nussbaum AK, Schild H, Schulz H, Hennecke H, Woessner R, Bitsch F (1998b) Biological and pharmacokinetic studies with β-peptides. Chimia 52:734–739Google Scholar
  61. Seebach D, Abele S, Sifferlen T, Hänggi M, Gruner S, Seiler P (1998c) Preparation and structure of β-peptides consisting of geminally disubstituted β2,2- and β3,3-amino acids: a turn motif for β-peptides. Helv Chim Acta 81:2218–2243CrossRefGoogle Scholar
  62. Seebach D, Abele S, Gademann K, Jaun B (1999) Pleated sheets and turns of β-peptides with proteinogenic side chains. Angew Chem Int Ed 38:1595–1597CrossRefGoogle Scholar
  63. Seebach D, Schreiber JV, Abele S, Daura X, van Gunsteren WF (2000a) Structure and conformation of β-oligopeptide derivatives with simple proteinogenic side chains: circular dichroism and molecular dynamics investigations. Helv Chim Acta 83:34–57CrossRefGoogle Scholar
  64. Seebach D, Sifferlen T, Mathieu PA, Häne AM, Krell CM, Bierbaum DJ, Abele S (2000b) CD spectra in methanol of β-oligopeptides consisting of β-amino acids with functionalized side chains, with alternating configuration, and with geminal backbone substituents – fingerprints of new secondary structures? Helv Chim Acta 83:2849–2864Google Scholar
  65. Tinoco I (1960) Optical and other electronic properties of polymers. J Chem Phys 33:1332–1338Google Scholar
  66. Tinoco I (1962) Theoretical aspects of optical activity. 2. Polymers. Adv Chem Phys 4:113–160Google Scholar
  67. van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG (1996) Biomolecular simulation: the GROMOS96 manual and user guide. Hochschulverlag, ETH Zürich/BIOMOS, Zürich/GroningenGoogle Scholar
  68. Werder M, Hauser H, Abele S, Seebach D (1999) β-Peptides as inhibitors of small-intestinal cholesterol and fat absorption. Helv Chim Acta 82:1774–1783CrossRefGoogle Scholar
  69. Woody RW (1995) Absorption and circular dichroism. In: Sauer K (ed) Biochemical spectroscopy, vol 246. Academic Press, San Diego, pp 34–71Google Scholar
  70. Woody RW (1996) Theory of circular dichroism of proteins. In: Fasman DG (ed) Circular dichroism and the conformational analysis of biomolecules. Plenum Press, New York, pp 25–67Google Scholar
  71. Woody RW, Sreerama N (1999) Comment on "improving protein circular dichroism calculations in the far-ultraviolet through reparametrizing the amide chromophore", J Chem Phys 109:782 (1998). J Chem Phys 111:2844–2845CrossRefGoogle Scholar
  72. Woody RW, Tinoco I (1967) Optical rotation of oriented helices. 3. Calculation of rotatory dispersion and circular dichroism of α- and 310-helix. J Chem Phys 46:4927–Google Scholar
  73. Wu YD, Wang DP (1998) Theoretical studies of β-peptide models. J Am Chem Soc 120:13485–13493CrossRefGoogle Scholar
  74. Wu YD, Wang DP (1999) Theoretical study on side-chain control of the 14-helix and the 10/12-helix of β-peptides. J Am Chem Soc 121:9352–9362CrossRefGoogle Scholar

Copyright information

© EBSA 2003

Authors and Affiliations

  • Xavier Daura
    • 1
    • 4
  • Dirk Bakowies
    • 1
  • Dieter Seebach
    • 2
  • Jörg Fleischhauer
    • 3
  • Wilfred F. van Gunsteren
    • 1
  • Peter Krüger
    • 1
    • 3
  1. 1.Laboratory of Physical ChemistrySwiss Federal Institute of Technology ZurichZurichSwitzerland
  2. 2.Laboratory of Organic ChemistrySwiss Federal Institute of Technology ZurichZurichSwitzerland
  3. 3.Institut für Organische ChemieRWTH AachenAachenGermany
  4. 4.Institució Catalana de Recerca i Estudis Avançats (ICREA) and Institute of Biotechnology and BiomedicineUniversitat Autònoma de BarcelonaBellaterraSpain

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