Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy

Abstract

X-ray crystallography and nuclear magnetic resonance measurements provide us with atomically resolved structures of an ever-growing number of biomolecules. These static structural snapshots are important to our understanding of biomolecular function, but real biomolecules are dynamic entities that often exploit conformational changes and transient molecular interactions to perform their tasks. Nuclear magnetic resonance methods can follow such structural changes, but only on millisecond timescales under non-equilibrium conditions. Time-resolved X-ray crystallography has recently been used to monitor the photodissociation of CO from myoglobin on a subnanosecond timescale1, yet remains challenging to apply more widely. In contrast, two-dimensional infrared spectroscopy, which maps vibrational coupling between molecular groups and hence their relative positions and orientations2,3,4,5,6,7,8,9,10,11, is now routinely used to study equilibrium processes on picosecond timescales. Here we show that the extension of this method into the non-equilibrium regime12,13 allows us to observe in real time in a short peptide the weakening of an intramolecular hydrogen bond and concomitant opening of a β-turn. We find that the rate of this process is two orders of magnitude faster than the ‘folding speed limit’ established for contact formation between protein side chains14.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Absorption and transient 1D spectra.
Figure 2: Equilibrium 2D-IR spectra.
Figure 3: Transient 2D-IR spectra.
Figure 4: Molecular dynamics results.

References

  1. Schotte, F. et al. Watching a protein as it functions with 150-ps time-resolved X-ray crystallography. Science 300, 1944–1947 (2003)

    ADS  CAS  Article  Google Scholar 

  2. Fang, C. & Hochstrasser, R. M. Two-dimensional infrared spectra of the 13C:18O isotopomers of alanine residues in an α-helix. J. Phys. Chem. B 109, 18652–18663 (2005)

    CAS  Article  Google Scholar 

  3. Wang, J., Chen, J. & Hochstrasser, R. M. Local structure of β-hairpin isotopomers by FTIR, 2D IR, and ab initio theory. J. Phys. Chem. B 110, 7545–7555 (2006)

    CAS  Article  Google Scholar 

  4. Asbury, J. B. et al. Hydrogen bond dynamics probed with ultrafast infrared heterodyne-detected multidimensional vibrational stimulated echoes. Phys. Rev. Lett. 91, 237402 (2003)

    ADS  Article  Google Scholar 

  5. Mukamel, S. Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. Annu. Rev. Phys. Chem. 51, 691–729 (2000)

    ADS  CAS  Article  Google Scholar 

  6. Mukherjee, P., Kass, I., Arkin, I. & Zanni, M. T. Picosecond dynamics of a membrane protein revealed by 2D IR. Proc. Natl Acad. Sci. USA 103, 3528–3533 (2006)

    ADS  CAS  Article  Google Scholar 

  7. Golonzka, O., Khalil, M., Demirdoven, N. & Tokmakoff, A. Vibrational anharmonicities revealed by coherent two-dimensional infrared spectroscopy. Phys. Rev. Lett. 86, 2154–2157 (2001)

    ADS  CAS  Article  Google Scholar 

  8. Cowan, M. L. et al. Ultrafast memory loss and energy redistribution in the hydrogen bond network of liquid H2O. Nature 434, 199–202 (2005)

    ADS  CAS  Article  Google Scholar 

  9. Hamm, P., Lim, M. & Hochstrasser, R. M. Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J. Phys. Chem. B 102, 6123–6138 (1998)

    CAS  Article  Google Scholar 

  10. Woutersen, S. & Hamm, P. Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy. J. Phys. Chem. B 104, 11316–11320 (2000)

    CAS  Article  Google Scholar 

  11. Woutersen, S. & Hamm, P. Nonlinear two-dimensional vibrational spectroscopy of peptides. J. Phys. Condens. Matter 14, R1035–R1062 (2002)

    ADS  CAS  Article  Google Scholar 

  12. Bredenbeck, J. et al. Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide. J. Phys. Chem. B 107, 8654–8660 (2003)

    CAS  Article  Google Scholar 

  13. Bredenbeck, J., Helbing, J. & Hamm, P. Transient two-dimensional infrared spectroscopy: exploring the polarization dependence. J. Chem. Phys. 121, 5943–5957 (2004)

    ADS  CAS  Article  Google Scholar 

  14. Bieri, O. et al. The speed limit for protein folding measured by triplet-triplet energy transfer. Proc. Natl Acad. Sci. USA 96, 9597–9601 (1999)

    ADS  CAS  Article  Google Scholar 

  15. Kolano, C., Gomann, K. & Sander, W. Small cyclic disulfide peptides: Synthesis in preparative amounts and characterization by means of NMR and FT-IR spectroscopy. Eur. J. Org. Chem. 20, 4167–4176 (2004)

    Article  Google Scholar 

  16. Volk, M. et al. Peptide conformational dynamics and vibrational stark effects following photoinitiated disulfide cleavage. J. Phys. Chem. B 101, 8607–8616 (1997)

    CAS  Article  Google Scholar 

  17. Lu, H. S. M. et al. Aminothiotyrosine disulfide, an optical trigger for initiation of protein folding. J. Am. Chem. Soc. 119, 7173–7180 (1997)

    CAS  Article  Google Scholar 

  18. Bredenbeck, J. et al. Picosecond conformational transition and equilibration of a cyclic peptide. Proc. Natl Acad. Sci. USA 100, 6452–6457 (2003)

    ADS  CAS  Article  Google Scholar 

  19. Bredenbeck, J., Helbing, J., Kumita, J. R., Woolley, G. A. & Hamm, P. α-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy. Proc. Natl Acad. Sci. USA 102, 2379–2384 (2005)

    ADS  CAS  Article  Google Scholar 

  20. Hamm, P., Ohline, S. M. & Zinth, W. Vibrational cooling after ultrafast photoisomerization of azobenzene measured by femtosecond infrared spectroscopy. J. Chem. Phys. 106, 519–529 (1997)

    ADS  CAS  Article  Google Scholar 

  21. Pimentel, G. C. & McClellan, A. L. The Hydrogen Bond 67–141 (W. H. Freeman, San Francisco, 1960)

    Google Scholar 

  22. Nguyen, P. H., Gorbunov, R. D. & Stock, G. Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study. Biophys. J. 91, 1224–1234 (2006)

    ADS  CAS  Article  Google Scholar 

  23. Mohanty, D., Elber, R., Thirumalai, D., Beglov, D. & Roux, B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272, 423–442 (1997)

    CAS  Article  Google Scholar 

  24. Mohanty, D., Elber, R. & Thirumalai, D. Probing the role of local propensity in peptide turn formation. Int. J. Quantum Chem. 80, 1125–1128 (2000)

    CAS  Article  Google Scholar 

  25. Kubelka, J., Hofrichter, J. & Eaton, W. A. The protein folding 'speed limit'. Curr. Opin. Struct. Biol. 14, 76–88 (2004)

    CAS  Article  Google Scholar 

  26. Sadqi, M., Fushman, D. & Munoz, V. Atom-by-atom analysis of global downhill protein folding. Nature 442, 317–321 (2006)

    ADS  CAS  Article  Google Scholar 

  27. Yang, W. Y. & Gruebele, M. Folding at the speed limit. Nature 423, 193–197 (2003)

    ADS  CAS  Article  Google Scholar 

  28. Satzger, H. et al. Picosecond dynamics in water-soluble azobenzene-peptides. Chem. Phys. Lett. 396, 191–197 (2004)

    ADS  CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was financially supported by a Postdoctoral Research Fellowship from the Deutsche Forschungsgemeinschaft to C.K.; by grants from the SNF to P.H.; and grants from the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie to W.S. Author Contributions C.K. designed the molecule together with W.S., C.K. synthesized it and ran the experiment together with J.H. C.K., J.H. and P.H. wrote the manuscript. M.K. and P.H. were responsible for the molecular dynamics simulations. 2D-IR and transient 2D-IR spectroscopy is a major theme of the group of P.H.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Christoph Kolano or Peter Hamm.

Ethics declarations

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains Supplementary Figures 1–3, Supplementary Movie Legend, Experimental Methods, Computational Methods. (PDF 648 kb)

Supplementary Movie 1

MD simulation of the cyclic disulfide–bridged peptide cyclo(Boc–Cys–Pro–Aib–Cys–OMe). (MPG 5943 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kolano, C., Helbing, J., Kozinski, M. et al. Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy. Nature 444, 469–472 (2006). https://doi.org/10.1038/nature05352

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature05352

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing