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Protein Studies by High-Pressure NMR

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Experimental Approaches of NMR Spectroscopy

Abstract

High-pressure NMR spectroscopy is a method that allows NMR measurements of any target samples under variable pressure. When applied to proteins, the method extends the conformational space that NMR spectroscopy can handle, from the space limited to the basic folded paradigm into the extensive conformational space that spans the entire high-energy paradigm of protein structure from the folded to the unfolded. The success of the experiment is ensured by the strong coupling between the volume and the conformation of a protein such that the partial molar volume of a protein decreases in parallel with the loss of its conformational order (the “volume theorem of protein”) as advocated by Akasaka. The validity of this principle arises from the fact that a globular protein generally has a significant vacant space (sometimes called “void” or “cavities”) inside its folded architecture into which water molecules may penetrate to reduce its partial molar volume and its conformational order simultaneously. Thanks to this principle, pressure provides a simple, clean, systematic and often efficient means of investigating the high-energy conformers of a protein, which is essential for understanding its folding, function, interaction, fibrillation, adaptation and evolution.

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References

  1. Bloch, F.: Nuclear induction. Phys. Rev. 70(7–8), 460–474 (1946)

    Article  CAS  Google Scholar 

  2. Purcell, E.M., Torrey, H.C., Pound, R.V.: Resonance absorption by nuclear magnetic moments in a solid. Phys. Rev. 69(1–2), 37–38 (1946)

    Article  CAS  Google Scholar 

  3. Hahn, E.L.: Spin echoes. Phys. Rev. 80(4), 580–594 (1950)

    Article  Google Scholar 

  4. Ernst, R.R., Bodenhausen, G., Wokaun, A.: Principles of Nuclear Magnetic Resonance in One and Two Dimensions (International Series of Monographs on Chemistry),  Oxford Univ. Press, London/New York (1991)

    Google Scholar 

  5. Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181(4096), 223–230 (1973)

    Article  CAS  Google Scholar 

  6. Wüthrich, K.: NMR of Proteins and Nucleic Acids. Wiley, Hoboken (1986)

    Google Scholar 

  7. Cooper, A.: Thermodynamic fluctuations in protein molecules. Biochemistry 73(8), 2740–2741 (1976)

    CAS  Google Scholar 

  8. Hirata, F., Akasaka, K.: Structural fluctuation of proteins induced by thermodynamic perturbation. J. Chem. Phys. 142(4), 44110 (2015)

    Article  Google Scholar 

  9. Gekko, K., Hasegawa, Y.: Compressibility–structure relationship of globular proteins. Biochemistry 25(21), 6563–6571 (1986)

    Article  CAS  Google Scholar 

  10. Frauenfelder, H., et al.: Proteins and pressure. J. Phys. Chem. 94, 1024–1037 (1990)

    Google Scholar 

  11. Yamada, H.: High resolution NMR measurement under high pressure and pressure dependence of the proton chemical shifts. Chem. Lett. 1(9), 747–750 (1972)

    Article  Google Scholar 

  12. Yamada, H.: Pressure-resisting glass cell for high pressure, high resolution NMR measurement. Rev. Sci. Instrum. 45(5), 640–642 (1974)

    Article  CAS  Google Scholar 

  13. Morishima, I., Hara, M.: High-pressure NMR studies of hemoproteins. Pressure-induced structural changes in the heme environments of cyanometmyoglobin. J. Am. Chem. Soc. 104(24), 6833–6834 (1982)

    Article  CAS  Google Scholar 

  14. Wagner, G.: Activation volumes for the rotational motion of interior aromatic rings in globular proteins determined by high resolution 1H NMR at variable pressure. FEBS Lett. 112(2), 280–284 (1980)

    Article  CAS  Google Scholar 

  15. Jonas, J., Jonas, A.: High-pressure NMR spectroscopy of proteins and membranes. Annu. Rev. Biophys. Biomol. Struct. 23(1), 287–318 (1994)

    Article  CAS  Google Scholar 

  16. Jonas, J., Ballard, L., Nash, D.: High-resolution, high-Pressure NMR studies of proteins. Biophys. J. 75(1), 445–452 (1998)

    Article  CAS  Google Scholar 

  17. Yamada, H., Nishikawa, K., Honda, M., Shimura, T., Akasaka, K., Tabayashi, K.: Pressure-resisting cell for high-pressure, high-resolution nuclear magnetic resonance measurements at very high magnetic fields. Rev. Sci. Instrum. 72(2), 1463 (2001)

    Article  CAS  Google Scholar 

  18. Akasaka, K., Yamada, H.: On-line cell high-pressure nuclear magnetic resonance technique: application to protein studies. Methods Enzymol. 338, 134–158 (2001)

    Google Scholar 

  19. Akasaka, K., Li, H.: Low-lying excited states of proteins revealed from nonlinear pressure shifts in 1H and 15N NMR. Biochemistry 40(30) 8665–8671 (2001)

    Google Scholar 

  20. Akasaka, K.: Exploring the entire conformational space of proteins by high-pressure NMR. Pure Appl. Chem. 75(7), 927–936 (2003)

    Article  CAS  Google Scholar 

  21. Akasaka, K.: Highly fluctuating protein structures revealed by variable-pressure nuclear magnetic resonance. Biochemistry 42(37), 10875–10885 (2003)

    Article  CAS  Google Scholar 

  22. Kamatari, Y., Kitahara, R., Yamada, H., Yokoyama, S., Akasaka, K.: High-pressure NMR spectroscopy for characterizing folding intermediates and denatured states of proteins. Methods 34(1), 133–143 (2004)

    Article  CAS  Google Scholar 

  23. Li, H., Akasaka, K.: Conformational fluctuations of proteins revealed by variable pressure NMR. Biochim. Biophys. Acta Proteins Proteom. 1764(3), 331–345 (2006)

    Article  CAS  Google Scholar 

  24. Akasaka, K.: Probing conformational fluctuation of proteins by pressure perturbation. Chem. Rev. 106(5), 1814–1835 (2006)

    Article  CAS  Google Scholar 

  25. Lassalle, M.W., Akasaka, K.: The use of high-pressure nuclear magnetic resonance to study protein folding. Methods Mol. Biol. 350, 21–38 (2007)

    CAS  Google Scholar 

  26. Akasaka, K.: High pressure NMR study of proteins-seeking roots for function, evolution, disease and food applications. High Press. Res. 30(4), 453–457 (2010)

    Google Scholar 

  27. Akasaka, K., Kitahara, R., Kamatari, Y.O.: Exploring the folding energy landscape with pressure. Arch. Biochem. Biophys. 531(1–2), 110–115 (2013)

    Article  CAS  Google Scholar 

  28. Kitahara, R., Hata, K., Li, H., Williamson, M.P., Akasaka, K.: Pressure-induced chemical shifts as probes for conformational fluctuations in proteins. Prog. Nucl. Magn. Reson. Spectrosc. 71, 35–58 (2013)

    Article  CAS  Google Scholar 

  29. Akasaka, K.: Pressure and protein dynamism. High Press. Res. 34(2), 222–235 (2014)

    Article  CAS  Google Scholar 

  30. Akasaka, K.: High pressure NMR spectroscopy. In: Akasaka, K., Matsuki, H. (eds.) High Pressure Bioscience-Basic Concepts, Applications and Frontiers, pp. 707–721. Springer, Amsterdam (2015)

    Chapter  Google Scholar 

  31. Kalbitzer, H.R.: High pressure NMR methods for characterizing functional substates in proteins. In: Akasaka, K., Matsuki, H. (eds.) High Pressure Bioscience-Basic Concepts, Applications and Frontiers, pp. 179–197. Springer, Amsterdam (2015)

    Chapter  Google Scholar 

  32. Kremer, W.: High pressure NMR studies in proteins. In: Annual Reports on NMR Spectroscopy, 57,177–203. Elsevier, Amsterdam (2006)

    Google Scholar 

  33. Fourme, R., Girard, E., Akasaka, K.: High-pressure macromolecular crystallography and NMR: status, achievements and prospects. Curr. Opin. Struct. Biol. 22(5), 636–642 (2012)

    Article  CAS  Google Scholar 

  34. Nguyen, L.M., Roche, J.: High-pressure NMR techniques for the study of protein dynamics, folding and aggregation. J. Magn. Reson. 277(April), 179–185 (2017)

    Article  CAS  Google Scholar 

  35. Maeno, A., Matsuo, H., Akasaka, K.: The pressure–temperature phase diagram of hen lysozyme at low pH. BIOPHYSICS (J. Biophys. Soc. Japan) 5, 1–9 (2009)

    Google Scholar 

  36. Kitahara, R., Yamada, H., Akasaka, K., Wright, P.E.: High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded. J. Mol. Biol. 320(2), 311–319 (2002)

    Article  CAS  Google Scholar 

  37. Hawley, S.A.: Reversible pressure–temperature denaturation of chymotrypsinogen. Biochemistry 10(13), 2436–2442 (1971)

    Article  CAS  Google Scholar 

  38. Smeller, L.: Protein denaturation on p-T axes-thermodynamics and analysis. In: Akasaka, K., Matsuki, H. (eds.) High Pressure Bioscience-Basic Concepts, Applications and Frontiers, pp. 19–39. Springer, Amsterdam (2015)

    Chapter  Google Scholar 

  39. Gekko, K.: Volume and compressibility of proteins. In: Akasaka, K., Matsuki, H. (eds.) High Pressure Bioscience-Basic Concepts, Applications and Frontiers, pp. 75–108. Springer, Amsterdam (2015)

    Chapter  Google Scholar 

  40. Soda, K., Shimbo, Y., Seki, Y., Taiji, M.: Structural characteristics of hydration sites in lysozyme. Biophys. Chem. 156(1), 31–42 (2011)

    Article  CAS  Google Scholar 

  41. Kamatari, Y.O., Smith, L.J., Dobson, C.M., Akasaka, K.: Cavity hydration as a gateway to unfolding: An NMR study of hen lysozyme at high pressure and low temperature. Biophys. Chem. 156(1), 24–30 (2011)

    Article  CAS  Google Scholar 

  42. Kitahara, R., Okuno, A., Kato, M., Taniguchi, Y., Yokoyama, S., Akasaka, K.: Cold denaturation of ubiquitin at high pressure. Magn. Reson. Chem. 44(S1), S108–S113 (2006)

    Article  CAS  Google Scholar 

  43. Royer, C.A.: Revisiting volume changes in pressure-induced protein unfolding. Biochim. Biophys. Acta 1595(1–2), 201–209 (2002)

    Article  CAS  Google Scholar 

  44. Kalbitzer, H.R., Görler, A., Li, H., Dubovskii,, P.V., Hengstenberg, W., Kowolik, C., Yamada, H., Akasaka, K.: 15N and 1H NMR study of histidine containing protein (HPr) from Staphylococcus carnosus at high pressure. Protein Sci. 9:693–703 (2000)

    Google Scholar 

  45. Benedek, G.B., Purcell, E.M.: Nuclear magnetic resonance in liquids under high pressure. J. Chem. Phys. 22(12), 2003–2012 (1954)

    Article  CAS  Google Scholar 

  46. Royer, C.A., et al.: Effects of amino acid substitutions on the pressure denaturation of staphylococcal nuclease as monitored by fluorescence and nuclear magnetic resonance spectroscopy. Biochemistry 32(19), 5222–5232 (1993)

    Article  CAS  Google Scholar 

  47. Akasaka, K., Tezuka, T., Yamada, H.: Pressure-induced changes in the folded structure of lysozyme. J. Mol. Biol. 271, 671–678 (1997)

    Google Scholar 

  48. Refaee, M., Tezuka, T., Akasaka, K., Williamson, M.P.: Pressure-dependent changes in the solution structure of hen egg-white lysozyme. J. Mol. Biol. 327(4), 857–865 (2003)

    Google Scholar 

  49. Urbauer, J.L., Ehrhardt, M.R., Bieber, R.J., Flynn, P.F., Wand, A.J.: High-resolution triple-resonance NMR spectroscopy of a novel calmodulin‚ peptide complex at kilobar pressures. J. Amer. Chem. Soc. 118, 11329–11330 (1996)

    Google Scholar 

  50. Akasaka, K., Yamada, H.: On-line cell high-pressure nuclear magnetic resonance technique: application to protein studies. Methods Enzymol. 338, 134–158 (2001)

    Article  CAS  Google Scholar 

  51. Erlach, M.B., et al.: Ceramic cells for high pressure NMR spectroscopy of proteins. J. Magn. Reson. 204(2), 196–199 (2010)

    Article  CAS  Google Scholar 

  52. Yamada, H.: Pressure-resisting glass cell for high pressure, high resolution NMR measurement. 45, 640–642 (1974)

    Google Scholar 

  53. Akasaka, K.: High pressure NMR spectroscopy. In: Akasaka, K., Matsuki, H. (eds.) High Pressure Bioscience-Basic Concepts, Applications and Frontiers, pp. 707–721. Springer, Amsterdam (2015)

    Google Scholar 

  54. Arnold, M.R., Kalbitzer, H.R., Kremer, W.: High-sensitivity sapphire cells for high pressure NMR spectroscopy on proteins. J. Magn. Reson. 161(2), 127–131 (2003)

    Article  Google Scholar 

  55. Akasaka, K., Maeno, A., Yamazaki, A.: Direct high-pressure NMR observation of dipicolinic acid leaking from bacterial spore: a crucial step for thermal inactivation. Biophys. Chem. (2017) Apr 19.  doi: 10.1016/j.bpc.2017.04.008

  56. Li, H., Yamada, H., Akasaka, K.: Effect of pressure on the tertiary structure and dynamics of folded basic pancreatic trypsin inhibitor. Biophys. J. 77, 2801–2812 (1999)

    Article  CAS  Google Scholar 

  57. Li, H., Yamada, H., Akasaka, K.: Effect of pressure on individual hydrogen bonds in proteins. Basic pancreatic trypsin inhibitor. Biochemistry 37(5), 1167–1173 (1998)

    Article  CAS  Google Scholar 

  58. Akasaka, K., Naito, A., Imanari, M.: Novel method for NMR spectral correlation between the native and the denatured states of a protein. Application to ribonuclease A. J. Am. Chem. Soc. 113(12), 4688–4689 (1991)

    Article  CAS  Google Scholar 

  59. Kamatari, Y.O., Yamada, H., Akasaka, K., Jones, J.A., Dobson, C.M., Smith, L.J.: Response of native and denatured hen lysozyme to high pressure studied by (15)N/(1)H NMR spectroscopy. Eur. J. Biochem. 268(6), 1782–1793 (2001)

    Article  CAS  Google Scholar 

  60. Hattori, M., et al.: Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips. Protein Sci. 13(12), 3104–3114 (2004)

    Article  CAS  Google Scholar 

  61. Kitahara, R., Yokoyama, S., Akasaka, K.: NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar–3 kbar. J. Mol. Biol. 347(2), 277–285 (2005)

    Google Scholar 

  62. Imai, T., Sugita, Y: Dynamic correlation between pressure-induced protein structural transition and water penetration. J. Phys. Chem. B 114(6), 2281–2286 (2010)

    Google Scholar 

  63. ​Niraula, T.N., Haraoka, K., Ando, Y., Li, H., Yamada, H., Akasaka, K.: Decreased thermodynamic stability as a crucial factor for familial amyloidotic polyneuropathy. J. Mol. Biol. 320(2), 333–342 (2002)

    Google Scholar 

  64. Kuwata, K., Li, H., Yamada, H., Legname, G., Prusiner, S.B., Akasaka, K., James, T.L.: Locally Disordered Conformer of the Hamster Prion Protein: A Crucial Intermediate to PrPSc?. Biochemistry 41(41), 12277–12283 (2002)

    Google Scholar 

  65. Kuwata, K. et al.: Hot spots in prion protein for pathogenic conversion. Proc. Natl. Acad. Sci. (USA) 104(29), 11921–11926 (2007)

    Google Scholar 

  66. Akasaka, K., Latif, A.R.A., Nakamura, A., Matsuo, K., Tachibana, H., Gekko, K.: Amyloid protofibril is highly voluminous and compressible. Biochemistry 46(37), 10444–10450 (2007)

    Google Scholar 

  67. Akasaka, K., et al.: Pressure-assisted dissociation and degradation of proteinase K-resistant fibrils prepared by seeding with scrapieinfecte hamster prion protein. Prion 8(4), 314–318 (2014)

    Google Scholar 

  68. Kitahara, R., Akasaka, K.: Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding. Proc. Natl. Acad. Sci. USA 100 (6), 3167–3172 (2003)

    Google Scholar 

  69. Roche, J., Dellarole, M., Royer, C. A., Roumestand, C.: Exploring the protein foding pathway with high-pressure NMR: Steady-state an kinetics studies. In: Akasaka, K., Matsuki, H. (eds.) High Pressure Bioscience-Basic Concepts, Applications and Frontiers, pp. 261–278 Springer, Amsterdam (2015)

    Google Scholar 

  70. Vallurupalli, P., Hansen, D.F., Kay, L.E.: Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci USA. 19;105(33):11766−11771 (2008)

    Google Scholar 

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  1. Kyoto Prefectural University of Medicine, Kyoto, Japan

    Kazuyuki Akasaka

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  1. Kazuyuki Akasaka
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Correspondence to Kazuyuki Akasaka .

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    The Nuclear Magnetic Resonance Society of Japan

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Akasaka, K. (2018). Protein Studies by High-Pressure NMR. In: The Nuclear Magnetic Resonance Society of Japan (eds) Experimental Approaches of NMR Spectroscopy. Springer, Singapore. https://doi.org/10.1007/978-981-10-5966-7_1

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