Skip to main content
SpringerLink
Log in

Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

We report density functional theory (DFT) calculations of the Raman spectra for hexapepetides of glutamic acid and lysine in three different conformations (α, β and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1a–c
Fig. 2a–e
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  1. Stefani M (2004) Biochim Biophys Acta 1739:5–25

    CAS  Google Scholar 

  2. Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM (1999) Proc Natl Acad Sci USA 96:3590–3594

    Article  CAS  Google Scholar 

  3. Dobson CM (2001) Philos Trans R Soc Lond B 356:133–145

    Article  CAS  Google Scholar 

  4. Fandrich M, Fletcher MA, Dobson CM (2001) Nature 410:165–166

    Article  CAS  Google Scholar 

  5. Jas GS, Eaton WA, Hofrichter J (2001) J Phys Chem B 105:261–272

    Article  CAS  Google Scholar 

  6. Manas ES, Getahun Z, Wright WW, DeGrado WF, Vanderkooi JM (2000) J Am Chem Soc 122:9883–9890

    Article  CAS  Google Scholar 

  7. Maji SK, Amsden JJ, Rothschild KJ, Condron MM, Teplow DB (2005) Biochemistry 44:13365–13376

    Article  CAS  Google Scholar 

  8. Fasman GD (1996) Circular dichroism and the conformational analaysis of biomolecules. Plenum, New York

    Google Scholar 

  9. Ozdemir A, Lednev IK, Asher SA (2002) Biochemistry 41:1893–1896

    Article  CAS  Google Scholar 

  10. McColl IH, Blanch EW, Hecht L, Barron LD (2004) J Am Chem Soc 126:8181–8188

    Article  CAS  Google Scholar 

  11. Barron LD, Hecht L, Ford SJ, Bell AF, Wilson G (1995) J Mol Struct 349:397–400

    Article  CAS  Google Scholar 

  12. McColl IH, Blanch EW, Hecht L, Kallenbach NR, Barron LD (2004) J Am Chem Soc 126:5076–5077

    Article  CAS  Google Scholar 

  13. Zhu FJ, Isaacs NW, Hecht L, Barron LD (2005) Structure 13:1409–1419

    Article  CAS  Google Scholar 

  14. Spiro T (1987) Biological application of Raman spectroscopy, Vol 1. Raman spectra and the conformation of biological macromolecules. Wiley, New York

    Google Scholar 

  15. Chi ZH, Asher SA (1998) J Phys Chem B 102:9595–9602

    Article  CAS  Google Scholar 

  16. Asher SA, Mikhonin AV, Bykov S (2004) J Am Chem Soc 126:8433–8440

    Article  CAS  Google Scholar 

  17. Lednev IK, Karnoup AS, Sparrow MC, Asher SA (1999) J Am Chem Soc 121:8074–8086

    Article  CAS  Google Scholar 

  18. Scheiner S, Kern CW (1977) J Am Chem Soc 99:7042–7050

    Article  CAS  Google Scholar 

  19. Creighton TE (1993) Proteins: structures and molecular properties. Freeman, New York

    Google Scholar 

  20. Baker EN, Hubbard RE (1984) Prog Biophys Mol Biol 44:97–179

    Article  CAS  Google Scholar 

  21. Bochicchio B, Tamburro AM (2002) Chirality 14:782–792

    Article  CAS  Google Scholar 

  22. Martino M, Bavoso A, Guantieri V, Coviello A, Tamburro AM (2000) J Mol Struct 519:173–189

    Article  CAS  Google Scholar 

  23. Mezei M, Fleming PJ, Srinivasan R, Rose GD (2004) Proteins 55:502–507

    Article  CAS  Google Scholar 

  24. Gnanakaran S, Hochstrasser RM, Garcia AE (2004) Proc Natl Acad Sci USA 101:9229–9234

    Article  CAS  Google Scholar 

  25. Thanki N, Thornton JM, Goodfellow JM (1988) J Mol Biol 202:637–657

    Article  CAS  Google Scholar 

  26. Daggett V, Levitt M (1992) J Mol Biol 223:1121–1138

    Article  CAS  Google Scholar 

  27. Stapley BJ, Creamer TP (1999) Protein Sci 8:587–595

    CAS  Google Scholar 

  28. Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG, Miller AF, Creamer TP (2001) Biochemistry 40:14376–14383

    Article  CAS  Google Scholar 

  29. Adzhubei AA, Sternberg MJE (1993) J Mol Biol 229:472–493

    Article  CAS  Google Scholar 

  30. Makarov AA, Lobachov VM, Adzhubei IA, Esipova NG (1992) FEBS Lett 306:63–65

    Article  CAS  Google Scholar 

  31. Makarov AA, Esipova NG, Lobachov VM, Grishkovsky BA, Pankov YA (1984) Biopolymers 23:5–22

    Article  CAS  Google Scholar 

  32. Hodes ZI, Nemethy G, Scheraga HA (1979) Biopolymers 18:1565–1610

    Article  CAS  Google Scholar 

  33. Eisenhaber F, Adjhubei AA, Eisenmenger F, Esipova NG (1992) Biofizika 37:62–67

    CAS  Google Scholar 

  34. Schweitzer-Stenner R (2006) Vib Spectrosc 42:98–117

    Article  CAS  Google Scholar 

  35. Nielsen OF (2005) In: Jiskoot WCDJA (ed) Methods for structural analysis of protein pharmaceuticals. AAPS, Arlington, pp 167–199

    Google Scholar 

  36. Chi ZH, Chen XG, Holtz JSW, Asher SA (1998) Biochemistry 37:2854–2864

    Article  CAS  Google Scholar 

  37. Diem M (1993) Introduction to modern vibrational spectroscopy. Wiley, New York

    Google Scholar 

  38. Herrmann C, Reiher M (2007) First-principles approach to vibrational spectroscopy of biomolecules. In: Reiher M (ed) Atomistic approaches in modern biology: from quantum chemistry to molecular simulations. Springer, Berlin, pp 85–132

    Google Scholar 

  39. Deng Z, Polavarapu PL, Ford SJ, Hecht L, Barron LD, Ewig CS, Jalkanen K (1996) J Phys Chem 100:2025–2034

    Article  CAS  Google Scholar 

  40. Han WG, Jalkanen KJ, Elstner M, Suhai S (1998) J Phys Chem B 102:2587–2602

    Article  CAS  Google Scholar 

  41. Vaden TD, Gowers SAN, de Boer T, Steill JD, Oomens J, Snoek LC (2008) J Am Chem Soc 130:14640–14650

    Article  CAS  Google Scholar 

  42. Song SH, Asher SA (1989) J Am Chem Soc 111:4295–4305

    Article  CAS  Google Scholar 

  43. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, Rev E.01. Gaussian Inc, Wallingford CT

    Google Scholar 

  44. Noordik GSJH (2000) J Comput Aided Mol Des 14:123–134

    Article  Google Scholar 

  45. Scheiner S (2009) J Phys Chem B 113:10421–10427

    Article  CAS  Google Scholar 

  46. Wieczorek R, Dannenberg JJ (2004) J Am Chem Soc 126:14198–14205

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by the National Science Foundation (CCF/CHE 0832622). The authors are thankful to University of Central Florida (UCF) Institute for Simulations and Training (IST) HPC Stokes facility, UCF I2Lab, and the US Department of Energy National Energy Research Scientific Computing Center (DOE NERSC) for the generous donation of computer time. The authors would like to thank Prof. Alfonse Schulte for fruitful discussions.

Author information

Authors and Affiliations

  1. NanoScience Technology Center and Department of Chemistry, University of Central Florida, Orlando, FL, 32826, USA

    Workalemahu Mikre Berhanu

  2. NanoScience Technology Center, University of Central Florida, Orlando, FL, 32826, USA

    Ivan A. Mikhailov

  3. NanoScience Technology Center, Department of Chemistry, and Department of Physics, University of Central Florida, Orlando, FL, 32826, USA

    Artëm E. Masunov

Authors
  1. Workalemahu Mikre Berhanu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivan A. Mikhailov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Artëm E. Masunov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Artëm E. Masunov.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Berhanu, W.M., Mikhailov, I.A. & Masunov, A.E. Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?. J Mol Model 16, 1093–1101 (2010). https://doi.org/10.1007/s00894-009-0610-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-009-0610-2

Keywords

Search

Navigation