The Use of High-Pressure Nuclear Magnetic Resonance to Study Protein Folding

  • Michael W. Lassalle
  • Kazuyuki Akasaka
Part of the Methods in Molecular Biology™ book series (MIMB, volume 350)

Abstract

Recent development of high-pressure cells for a variety of spectroscopic methods has enabled the use of pressure as one of the commonly used perturbations along with temperature and chemical perturbations to study folding/unfolding reactions of proteins. Although various high-pressure spectroscopy techniques have their own significance, high-pressure nuclear magnetic resonance (NMR) is unique in that it allows one to gain residue-specific and atom-detailed information from proteins under pressure. Furthermore, because of a peculiar volume property of a protein, high-pressure NMR allows one to obtain structural information of a protein in a wide conformational space from the bottom to the upper region of the folding funnel, giving structural reality for the “open” state of a protein proposed from hydrogen exchange. The method allows a link between equilibrium folding intermediates and the kinetic intermediates, and manifests a new view of proteins as dynamic entities amply fluctuating among the folded, intermediate, and unfolded sub ensembles. This chapter briefly summarizes the technique, the principle, and the ways to use high-pressure NMR for studying protein folding.

Key Words

Pressure protein folding thermodynamic stability volume change structures of folding intermediates high-pressure NMR pressure-jump 

References

  1. 1.
    Fujisawa, T., Kato, M., and Inoko, Y. (1999) Structural characterization of lactate dehydrogenase dissociation under high pressure studied by synchrotron high pressure small-angle x-ray scattering. Biochemistry 38, 6411–6418.CrossRefPubMedGoogle Scholar
  2. 2.
    Winter, R. (2002) Synchrotron X-ray and neutron small-angle scattering of lyotropic lipid mesophases, model biomembranes and proteins in solution at high pressure. Biochim. Biophys. Acta 1595, 160–184.CrossRefPubMedGoogle Scholar
  3. 3.
    Ruan, K. and Balny, C. (2002) High pressure static fluorescence to study macromolecular structure-function. Biochim. Biophys. Acta 1595, 94–102.CrossRefPubMedGoogle Scholar
  4. 4.
    Ikeuchi, Y., Suzuki, A., Oota, T., et al. (2002) Fluorescence study of the high pressure-induced denaturation of skeletal muscle actin. Eur. J. Biochem. 269, 364–371.CrossRefPubMedGoogle Scholar
  5. 5.
    Di Venere, A., Salucci, M. L., van Zadelhoff, G., et al. (2003) Structure-to-function relationship of mini-lipoxygenase, a 60-kda fragment of soybean lipoxygenase-1 with lower stability but higher enzymatic activity. J. Biol. Chem. 278, 18,281–18,288.CrossRefPubMedGoogle Scholar
  6. 6.
    Herberhold, H., Marchal, S., Lange, R., Scheying, C., Vogel, R. F., and Winter, R. (2003) Characterization of the pressure-induced intermediated and unfolded state of red-shifted green fluorescent protein-a static and kinetic FTIR, UV-VIS and fluorescence spectroscopy study. J. Mol. Biol. 330, 1153–1164.CrossRefPubMedGoogle Scholar
  7. 7.
    Dzwolak, W., Kato, M., and Taniguchi, Y. (2002) Fourier-transform infrared spectroscopy in high pressure studies on proteins. Biochim. Biophys. Acta 1595, 131–144.CrossRefPubMedGoogle Scholar
  8. 8.
    Smeller, L., Meersmann, F., Fidy, J., and Heremans, K. (2003) High pressure FTIR study of the stability of horseradish peroxidase. Effect of heme substitution, ligand binding, Ca++ removal, and reduction of the disulfide bonds. Biochemistry 42, 553–561.CrossRefPubMedGoogle Scholar
  9. 9.
    Meersman, F., Smeller, L., and Heremans, K. (2002) Comparative fourier transform infrared spectroscopy study of cold-, pressure-, and heat-induced unfolding and aggregation of myoglobin. Biophys. J. 82, 2635–2644.CrossRefPubMedGoogle Scholar
  10. 10.
    Jung, C., Kozin, S. A., Canny, B., Chervin, J. C., and Hoa, G. H. (2003) Compressibility and uncoupling of cytochrome P450cam: high pressure FTIR and activity studies. Biochem. Biophys. Res. Commun. 312, 197–203.CrossRefPubMedGoogle Scholar
  11. 11.
    Lange, R. and Balny, C. (2002) UV-visible derivative spectroscopy under high pressure. Biochim. Biophys. Acta 1595, 80–93.CrossRefPubMedGoogle Scholar
  12. 12.
    Pappenberger, G., Saudan, C., Becker, M., Merbach, A. E., and Kiefhaber, T. (2000) Denaturant-induced movement of the transition state of protein folding revealed by high-pressure stopped-flow measurements. Proc. Natl. Acad. Sci. USA 97, 17–22.CrossRefPubMedGoogle Scholar
  13. 13.
    Jung, C., Bec, N., and Lange, R. (2002) Substrates modulate the rate-determining step for CO binding in cytochrome P450cam (CYP101). Eur. J. Biochem. 269, 2989–2996.CrossRefPubMedGoogle Scholar
  14. 14.
    Kitahara, R., Royer, C., Yamada, H., et al. (2002) Equilibrium and pressure-jump relaxation studies of the conformational transitions of P13MTCP1. J. Mol. Biol. 320, 609–628.CrossRefPubMedGoogle Scholar
  15. 15.
    Desai, G., Panick, G., Zein, M., Winter, R., and Royer, C. A. (1999) Pressure-jump studies of the folding/unfolding of trp repressor. J. Mol. Biol. 288, 461–475.CrossRefPubMedGoogle Scholar
  16. 16.
    Woenckhaus, J., Koehling, R., Thiyagarajan, P., et al. (2001) Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding. Biophys. J. 80, 1518–1523.CrossRefPubMedGoogle Scholar
  17. 17.
    Kitamura, Y. and Itoh, T. (1987) Reaction volume of protonic ionization for buffering agents. Prediction of pressure dependence of pH and pOH. J. Solution Chemistry 16, 715–725.CrossRefGoogle Scholar
  18. 18.
    Jonas, J. (2002) High-resolution nuclear magnetic resonance studies of proteins. Biochim. Biophys. Acta 1595, 145–159.CrossRefPubMedGoogle Scholar
  19. 19.
    Akasaka, K. and Yamada, H. (2001) On-line cell high-pressure nuclear magnetic resonance technique: application to protein studies. Methods Enzymol. 338, 134–158.PubMedGoogle Scholar
  20. 20.
    Arnold, M. R., Kalbitzer, H. R., and Kremer, W. (2003) High-sensitivity sapphire cells for high pressure NMR spectroscopy on proteins. J. Magnetic Resonance 161, 127–131.CrossRefGoogle Scholar
  21. 21.
    Urbauer, J. L., Ehrhardt, M. R., Bieber, R. J., Flynn, P. F., and Wand, J. A. (1996) High-resolution triple-resonance NMR spectroscopy of a novel calmodulin peptide complex at kilobar pressures. J. Am. Chem. Soc. 118, 11,329–11,330.CrossRefGoogle Scholar
  22. 22.
    Royer, C. A., Hinck, A. P., Loh, S. N., et al. (1993) Effects of amino acid substitutions on the pressure denaturation of staphylococcal nuclease as monitored by fluorescence and nuclear magnetic resonance spectroscopy. Biochemistry 32, 5222–5232.CrossRefPubMedGoogle Scholar
  23. 23.
    Yamada, H., Nishikawa, M., Honda, M., Shimura, T., Akasaka, K., and Tabayashi, K. (2001) Pressure-resisting cell for high-pressure, high-resolution nuclear magnetic resonance measurements at very high magnetic fields. Rev. Sci. Instrum. 72, 1463–1471.CrossRefGoogle Scholar
  24. 24.
    Kamatari, Y. O., Kitahara, R., Yamada, H., Yokoyama, S., and Akasaka, K. (2004) High-pressure NMR spectroscopy for characterizing folding intermediates and denatured states of proteins. Methods 34, 133–143.CrossRefPubMedGoogle Scholar
  25. 25.
    Kuwata, K., Kamatari, Y. O., Akasaka, K., and James, T. L. (2004) Slow conformational dynamics in the hamster prion protein. Biochemistry 43, 4439–4446.CrossRefPubMedGoogle Scholar
  26. 26.
    Kuwata, K., Li, H., Yamada, H., and Legname, G. (2002) Locally disordered conformer of the hamster prion protein: a crucial intermediate to PrPSc? Biochemistry 41, 12,277–12,283.CrossRefPubMedGoogle Scholar
  27. 27.
    Kitahara, R. and Akasaka, K. (2003) Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding. Proc. Natl. Acad. Sci. USA 100, 3167–3172.CrossRefPubMedGoogle Scholar
  28. 28.
    Lassalle, M. W., Yamada, H., Morii, H., Ogata, K., Sarai, A., and Akasaka, K. (2001) Filling a cavity dramatically increases pressure stability of the c-myb R2 subdomain. Proteins 45, 96–101.CrossRefPubMedGoogle Scholar
  29. 29.
    Lassalle, M. W., Yamada, H., and Akasaka, K. (2000) The pressure-temperature free energy-landscape of staphylococcal nuclease monitored by 1H NMR. J. Mol. Biol. 298, 293–302.CrossRefPubMedGoogle Scholar
  30. 30.
    Niraula, T. N., Konno, T., Li, H., Yamada, H., Akasaka, K., and Tachibana, H. (2004) Pressure-dissociable reversible assembly of intrinsically denatured lysozyme is a precursor for amyloid fibrils. Proc. Natl. Acad. Sci. USA 101, 4089–4093.CrossRefPubMedGoogle Scholar
  31. 31.
    Akasaka, K. (2003) Highly fluctuating protein structure revealed by variable-pressure nuclear magnetic resonance. Biochemistry 42, 10,875–10,885.CrossRefPubMedGoogle Scholar
  32. 32.
    Chan, H. S. and Dill, K. A. (1998) Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30, 2–33.CrossRefPubMedGoogle Scholar
  33. 33.
    Smeller, L. and Heremans, K. (1997) Some thermodynamic and kinetic consequences of the phase diagram of protein denaturation. In: High-Pressure Research in the Biosciences and Biotechnology (Heremans, K., ed.), Leuven University Press, Leuven, Belgium, pp. 55–58.Google Scholar
  34. 34.
    Panick, G., Vidugiris, G. J. A., Malessa, R., Rapp, G., Winter, R., and Royer, C. A. (1999) Exploring the temperature-pressure phase diagram of staphylococcal nuclease. Biochemistry 38, 4157–4164.CrossRefPubMedGoogle Scholar
  35. 35.
    Panick, G., Malessa, R., Winter, R., Rapp, G., Frye, K. J., and Royer, C. A. (1998) Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle x-ray scattering and fourier-transform infrared spectroscopy. J. Mol. Biol. 275, 389–402.CrossRefPubMedGoogle Scholar
  36. 36.
    Akasaka, K. (2003) Exploring the entire conformational space of proteins by high-pressure NMR. Pure. Appl. Chem. 75, 927–936.CrossRefGoogle Scholar
  37. 37.
    Chalikian, T. V. (2003) Volumetric properties of proteins. Annu. Rev. Biophys. Biomol. Struct. 32, 207–235.CrossRefPubMedGoogle Scholar
  38. 38.
    Frye, K. and Royer, C. A. (1998) Probing the contribution of internal cavities to the volume change of protein unfolding under pressure. Protein Sci. 7, 2217–2222.CrossRefPubMedGoogle Scholar
  39. 39.
    Imai, T., Harano, Y., Kovalenko, A., and Hirata, F. (2001) Theoretical study for volume changes associated with the helix-coil transition of peptides. Biopolymers 59, 512–519.CrossRefPubMedGoogle Scholar
  40. 40.
    Royer, C. (2002) Revisiting volume changes in pressure induced proteins unfolding. Biochim. Biophys. Acta 1595, 201–209.CrossRefPubMedGoogle Scholar
  41. 41.
    Ogata, K., Kanei-Ishii, C., Sasaki, M., et al. (1996) The cavity in the hydrophobic core of Myb-DNA-binding domain is reserved for DNA recognition and transactivation. Nat. Struct. Biol. 3, 178–187.CrossRefPubMedGoogle Scholar
  42. 42.
    Kuwata, K., Li, H., Yamada, H., Batt, C.A., Goto, Y., and Akasaka, K. (2001) High pressure NMR reveals a variety of fluctuating conformers in β-lactoglobulin. J. Mol. Biol. 305, 1073–1083.CrossRefPubMedGoogle Scholar
  43. 43.
    Forge, V., Hoshino, M., Kuwata, K., et al. (2000) Is folding of β-lactoglobulin non-hierarchic? Intermediate with native-like β-sheet and non-native α-helix. J. Mol. Biol. 296, 1039–1051.CrossRefPubMedGoogle Scholar
  44. 44.
    Briggs, M. S. and Roder, H. (1992) Early hydrogen-bonding events in the folding reaction of ubiquitin. Proc. Natl. Acad. Sci. USA 89, 2017–2021.CrossRefPubMedGoogle Scholar
  45. 45.
    Kamatari, Y. O., Yokoyama, S., Tachibana, H., and Akasaka, K. (2005) Pressure-jump NMR study of dissociation and association of amyloid protofibrils, J. Mol. Biol. 349, 916–921.CrossRefPubMedGoogle Scholar
  46. 46.
    Kitahara, R., Yokoyama, S., and Akasaka, K. (2005) NMR snapshots of a fluctuating protein structure: Ubiquitin at 30 bar–3kbar. J. Mol. Biol. 347, 277–285.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Michael W. Lassalle
    • 1
  • Kazuyuki Akasaka
    • 2
  1. 1.Exploratory Research for Advanced Technology “Actin Filament Dynamics” ProjectJapan Science and Technology CorporationHyogoJapan
  2. 2.Department of Biotechnological Science, School of Biology-Oriented Science and TechnologyKinki UniversityKinokawa City, Wakayama PrefectureJapan

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