Skip to main content
NCBI home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1999 Oct;8(10):1946–1953. doi: 10.1110/ps.8.10.1946

Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

K Akasaka 1, H Li 1, H Yamada 1, R Li 1, T Thoresen 1, C K Woodward 1
PMCID: PMC2144150  PMID: 10548039

Abstract

The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place.

Full Text

The Full Text of this article is available as a PDF (1.3 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akasaka K., Tezuka T., Yamada H. Pressure-induced changes in the folded structure of lysozyme. J Mol Biol. 1997 Sep 5;271(5):671–678. doi: 10.1006/jmbi.1997.1208. [DOI] [PubMed] [Google Scholar]
  2. Berndt K. D., Güntert P., Orbons L. P., Wüthrich K. Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures. J Mol Biol. 1992 Oct 5;227(3):757–775. doi: 10.1016/0022-2836(92)90222-6. [DOI] [PubMed] [Google Scholar]
  3. Brunne R. M., van Gunsteren W. F. Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm. FEBS Lett. 1993 Jun 1;323(3):215–217. doi: 10.1016/0014-5793(93)81342-w. [DOI] [PubMed] [Google Scholar]
  4. Cioni P., Strambini G. B. Pressure effects on the structure of oligomeric proteins prior to subunit dissociation. J Mol Biol. 1996 Nov 15;263(5):789–799. doi: 10.1006/jmbi.1996.0616. [DOI] [PubMed] [Google Scholar]
  5. Cooper A. Thermodynamic fluctuations in protein molecules. Proc Natl Acad Sci U S A. 1976 Aug;73(8):2740–2741. doi: 10.1073/pnas.73.8.2740. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fuentes E. J., Wand A. J. Local stability and dynamics of apocytochrome b562 examined by the dependence of hydrogen exchange on hydrostatic pressure. Biochemistry. 1998 Jul 14;37(28):9877–9883. doi: 10.1021/bi980894o. [DOI] [PubMed] [Google Scholar]
  7. Gekko K., Hasegawa Y. Compressibility-structure relationship of globular proteins. Biochemistry. 1986 Oct 21;25(21):6563–6571. doi: 10.1021/bi00369a034. [DOI] [PubMed] [Google Scholar]
  8. Gross M., Jaenicke R. Proteins under pressure. The influence of high hydrostatic pressure on structure, function and assembly of proteins and protein complexes. Eur J Biochem. 1994 Apr 15;221(2):617–630. doi: 10.1111/j.1432-1033.1994.tb18774.x. [DOI] [PubMed] [Google Scholar]
  9. Hawley S. A. Reversible pressure--temperature denaturation of chymotrypsinogen. Biochemistry. 1971 Jun 22;10(13):2436–2442. doi: 10.1021/bi00789a002. [DOI] [PubMed] [Google Scholar]
  10. Heremans K., Smeller L. Protein structure and dynamics at high pressure. Biochim Biophys Acta. 1998 Aug 18;1386(2):353–370. doi: 10.1016/s0167-4838(98)00102-2. [DOI] [PubMed] [Google Scholar]
  11. Hitchens T. K., Bryant R. G. Pressure dependence of amide hydrogen-deuterium exchange rates for individual sites in T4 lysozyme. Biochemistry. 1998 Apr 28;37(17):5878–5887. doi: 10.1021/bi972950b. [DOI] [PubMed] [Google Scholar]
  12. Huang J., Ridsdale A., Wang J., Friedman J. M. Kinetic hole burning, hole filling, and conformational relaxation in heme proteins: direct evidence for the functional significance of a hierarchy of dynamical processes. Biochemistry. 1997 Nov 25;36(47):14353–14365. doi: 10.1021/bi9700274. [DOI] [PubMed] [Google Scholar]
  13. Inoue K., Yamada H., Imoto T., Akasaka K. High pressure NMR study of a small protein, gurmarin. J Biomol NMR. 1998 Nov;12(4):535–541. doi: 10.1023/a:1008374109437. [DOI] [PubMed] [Google Scholar]
  14. Iwanaga S., Morita T., Kato H., Harada T., Adachi N., Sugo T., Maruyama I., Takada K., Kimura T., Sakakibara S. Fluorogenic peptide substrates for proteases in blood coagulation, kallikrein-kinin and fibrinolysis systems. Adv Exp Med Biol. 1979;120A:147–163. doi: 10.1007/978-1-4757-0926-1_15. [DOI] [PubMed] [Google Scholar]
  15. Jonas J., Jonas A. High-pressure NMR spectroscopy of proteins and membranes. Annu Rev Biophys Biomol Struct. 1994;23:287–318. doi: 10.1146/annurev.bb.23.060194.001443. [DOI] [PubMed] [Google Scholar]
  16. Kharakoz D. P. Partial volumes and compressibilities of extended polypeptide chains in aqueous solution: additivity scheme and implication of protein unfolding at normal and high pressure. Biochemistry. 1997 Aug 19;36(33):10276–10285. doi: 10.1021/bi961781c. [DOI] [PubMed] [Google Scholar]
  17. Kharakoz D. P., Sarvazyan A. P. Hydrational and intrinsic compressibilities of globular proteins. Biopolymers. 1993 Jan;33(1):11–26. doi: 10.1002/bip.360330103. [DOI] [PubMed] [Google Scholar]
  18. Kim K. S., Fuchs J. A., Woodward C. K. Hydrogen exchange identifies native-state motional domains important in protein folding. Biochemistry. 1993 Sep 21;32(37):9600–9608. doi: 10.1021/bi00088a012. [DOI] [PubMed] [Google Scholar]
  19. Kitchen D. B., Reed L. H., Levy R. M. Molecular dynamics simulation of solvated protein at high pressure. Biochemistry. 1992 Oct 20;31(41):10083–10093. doi: 10.1021/bi00156a031. [DOI] [PubMed] [Google Scholar]
  20. Kobayashi N., Yamato T., Go N. Mechanical property of a TIM-barrel protein. Proteins. 1997 May;28(1):109–116. doi: 10.1002/(sici)1097-0134(199705)28:1<109::aid-prot11>3.0.co;2-n. [DOI] [PubMed] [Google Scholar]
  21. Kowalski J. M., Parekh R. N., Wittrup K. D. Secretion efficiency in Saccharomyces cerevisiae of bovine pancreatic trypsin inhibitor mutants lacking disulfide bonds is correlated with thermodynamic stability. Biochemistry. 1998 Feb 3;37(5):1264–1273. doi: 10.1021/bi9722397. [DOI] [PubMed] [Google Scholar]
  22. Kundrot C. E., Richards F. M. Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres. J Mol Biol. 1987 Jan 5;193(1):157–170. doi: 10.1016/0022-2836(87)90634-6. [DOI] [PubMed] [Google Scholar]
  23. Le H., Oldfield E. Correlation between 15N NMR chemical shifts in proteins and secondary structure. J Biomol NMR. 1994 May;4(3):341–348. doi: 10.1007/BF00179345. [DOI] [PubMed] [Google Scholar]
  24. Li H., Yamada H., Akasaka K. Effect of pressure on individual hydrogen bonds in proteins. Basic pancreatic trypsin inhibitor. Biochemistry. 1998 Feb 3;37(5):1167–1173. doi: 10.1021/bi972288j. [DOI] [PubMed] [Google Scholar]
  25. Llinás M., Horsley W. J., Klein M. P. Nitrogen-15 nuclear magnetic resonance spectrum of alumichrome. Detection by a double resonance Fourier transform technique. J Am Chem Soc. 1976 Nov 24;98(24):7554–7558. doi: 10.1021/ja00440a018. [DOI] [PubMed] [Google Scholar]
  26. Makhatadze G. I., Kim K. S., Woodward C., Privalov P. L. Thermodynamics of BPTI folding. Protein Sci. 1993 Dec;2(12):2028–2036. doi: 10.1002/pro.5560021204. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Mozhaev V. V., Heremans K., Frank J., Masson P., Balny C. High pressure effects on protein structure and function. Proteins. 1996 Jan;24(1):81–91. doi: 10.1002/(SICI)1097-0134(199601)24:1<81::AID-PROT6>3.0.CO;2-R. [DOI] [PubMed] [Google Scholar]
  28. Paladini A. A., Jr, Weber G. Pressure-induced reversible dissociation of enolase. Biochemistry. 1981 Apr 28;20(9):2587–2593. doi: 10.1021/bi00512a034. [DOI] [PubMed] [Google Scholar]
  29. Panick G., Malessa R., Winter R., Rapp G., Frye K. J., Royer C. A. 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. 1998 Jan 16;275(2):389–402. doi: 10.1006/jmbi.1997.1454. [DOI] [PubMed] [Google Scholar]
  30. Parekh R. N., Shaw M. R., Wittrup K. D. An integrating vector for tunable, high copy, stable integration into the dispersed Ty delta sites of Saccharomyces cerevisiae. Biotechnol Prog. 1996 Jan-Feb;12(1):16–21. doi: 10.1021/bp9500627. [DOI] [PubMed] [Google Scholar]
  31. Prehoda K. E., Mooberry E. S., Markley J. L. Pressure denaturation of proteins: evaluation of compressibility effects. Biochemistry. 1998 Apr 28;37(17):5785–5790. doi: 10.1021/bi980384u. [DOI] [PubMed] [Google Scholar]
  32. Royer C. A., Hinck A. P., Loh S. N., Prehoda K. E., Peng X., Jonas J., Markley J. L. Effects of amino acid substitutions on the pressure denaturation of staphylococcal nuclease as monitored by fluorescence and nuclear magnetic resonance spectroscopy. Biochemistry. 1993 May 18;32(19):5222–5232. doi: 10.1021/bi00070a034. [DOI] [PubMed] [Google Scholar]
  33. Smith P. E., van Schaik R. C., Szyperski T., Wüthrich K., van Gunsteren W. F. Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. J Mol Biol. 1995 Feb 17;246(2):356–365. doi: 10.1006/jmbi.1994.0090. [DOI] [PubMed] [Google Scholar]
  34. Takeda N., Kato M., Taniguchi Y. Pressure- and thermally-induced reversible changes in the secondary structure of ribonuclease A studied by FT-IR spectroscopy. Biochemistry. 1995 May 2;34(17):5980–5987. doi: 10.1021/bi00017a027. [DOI] [PubMed] [Google Scholar]
  35. Tüchsen E., Woodward C. Assignment of asparagine-44 side-chain primary amide 1H NMR resonances and the peptide amide N1H resonance of glycine-37 in basic pancreatic trypsin inhibitor. Biochemistry. 1987 Apr 7;26(7):1918–1925. doi: 10.1021/bi00381a020. [DOI] [PubMed] [Google Scholar]
  36. 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. 1980 Apr 7;112(2):280–284. doi: 10.1016/0014-5793(80)80198-0. [DOI] [PubMed] [Google Scholar]
  37. Wagner G., Braun W., Havel T. F., Schaumann T., Go N., Wüthrich K. Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J Mol Biol. 1987 Aug 5;196(3):611–639. doi: 10.1016/0022-2836(87)90037-4. [DOI] [PubMed] [Google Scholar]
  38. Wishart D. S., Bigam C. G., Holm A., Hodges R. S., Sykes B. D. 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J Biomol NMR. 1995 Jan;5(1):67–81. doi: 10.1007/BF00227471. [DOI] [PubMed] [Google Scholar]
  39. Wishart D. S., Bigam C. G., Yao J., Abildgaard F., Dyson H. J., Oldfield E., Markley J. L., Sykes B. D. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR. 1995 Sep;6(2):135–140. doi: 10.1007/BF00211777. [DOI] [PubMed] [Google Scholar]
  40. Wlodawer A., Deisenhofer J., Huber R. Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. J Mol Biol. 1987 Jan 5;193(1):145–156. doi: 10.1016/0022-2836(87)90633-4. [DOI] [PubMed] [Google Scholar]
  41. Wlodawer A., Nachman J., Gilliland G. L., Gallagher W., Woodward C. Structure of form III crystals of bovine pancreatic trypsin inhibitor. J Mol Biol. 1987 Dec 5;198(3):469–480. doi: 10.1016/0022-2836(87)90294-4. [DOI] [PubMed] [Google Scholar]
  42. Wroblowski B., Díaz J. F., Heremans K., Engelborghs Y. Molecular mechanisms of pressure induced conformational changes in BPTI. Proteins. 1996 Aug;25(4):446–455. doi: 10.1002/prot.5. [DOI] [PubMed] [Google Scholar]
  43. Yamaguchi T., Yamada H., Akasaka K. Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR. J Mol Biol. 1995 Jul 28;250(5):689–694. doi: 10.1006/jmbi.1995.0408. [DOI] [PubMed] [Google Scholar]
  44. Zhang J., Peng X., Jonas A., Jonas J. NMR study of the cold, heat, and pressure unfolding of ribonuclease A. Biochemistry. 1995 Jul 11;34(27):8631–8641. doi: 10.1021/bi00027a012. [DOI] [PubMed] [Google Scholar]
  45. Zipp A., Kauzmann W. Pressure denaturation of metmyoglobin. Biochemistry. 1973 Oct 9;12(21):4217–4228. doi: 10.1021/bi00745a028. [DOI] [PubMed] [Google Scholar]
  46. Zollfrank J., Friedrich J., Vanderkooi J. M., Fidy J. Conformational relaxation of a low-temperature protein as probed by photochemical hole burning. Horseradish peroxidase. Biophys J. 1991 Feb;59(2):305–312. doi: 10.1016/S0006-3495(91)82224-X. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES