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High Pressure Macromolecular Crystallography

Part of the Subcellular Biochemistry book series (SCBI, volume 72)

Abstract

X-ray crystallography is a powerful tool for the high resolution structural study of biomacromolecules. One of the most important beneficial feature of the method is the possibility of the direct observation of hydration water structure. In recent years, significant development in high-pressure macromolecular crystallography (HPMX) using a diamond anvil cell (DAC) has been performed in combination with shorter wavelength X-ray of synchrotron radiation. The number of protein structures determined by HPMX at pressure ranging from several hundred MPa to 1 GPa is gradually growing. In this chapter, we describe DAC with its usage, and then an example of HPMX study on hydration structure of 3-isopropylmalate dehydrogenase (IPMDH).

Keywords

Diamond anvil cell DAC 3-Isopropylmalate dehydrogenase IPMDH 

Notes

Acknowledgements

This work was partially supported by a KAKENHI Grant-in-Aid for Challenging Exploratory Research (21657027), and has been performed with Dr. Takayuki Nagae, Nagoya University.

References

  1. Boehler R (2006) New diamond cell for single-crystal x-ray diffraction. Rev Sci Instrum 77:115103CrossRefGoogle Scholar
  2. Chavas LMG, Nagae T, Yamada H, Watanabe N, Yamada Y, Hiraki M, Matsugaki N (2013) New methodologies at PF AR-NW12A: implementation of high-pressure macromolecular crystallography. J Synchrotron Rad 20:838–842CrossRefGoogle Scholar
  3. Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM (2005) Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci USA 102:16668–16671PubMedCentralCrossRefPubMedGoogle Scholar
  4. Fourme R, Ascone I, Kahn R, Girard E, Hoerentrup C et al (2001) High pressure protein crystallography: instrumentation, methodology and results of data collection on lysozyme crystals. J Synchrotron Radiat 8:1149–1156Google Scholar
  5. Fourme R, Girard E, Dhaussy A-C, Medjoubi K, Prangé T, Ascone I, Mézouar M, Kahn R (2011) A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results. J Synchrotron Rad 18:31–36CrossRefGoogle Scholar
  6. Fourme R, Girard E, Kahn R, Dhaussy A-C, Ascone I (2009) Advances in high-pressure biophysics: status and prospects of macromolecular crystallography. Annu Rev Biophys 38:153–171CrossRefPubMedGoogle Scholar
  7. Girard E, Dhaussy A-C, Couzinet B, Chervin J-C, Mezouar M, Kahn R, Ascone I, Fourme R (2007a) Toward fully fledged high-pressure macromolecular crystallography. J Appl Crystallogr 40:912–918CrossRefGoogle Scholar
  8. Girard E, Kahn R, Mezouar M, Dhaussy A-C, Lin T, Johnson JE, Fourme R (2005) The first crystalstructure of a macromolecular assembly under 100 high pressure: CpMV at 330 MPa. Biophys J 88:3562–3571PubMedCentralCrossRefPubMedGoogle Scholar
  9. Girard E, Prange T, Dhaussy A-C, Migianu-Griffoni E, Lecouvey M, Chervin J-C, Mezouar M, Kahn R, Fourme R (2007b) Adaptation of the base-paired double-helix molecular architecture to extreme pressure. Nucleic Acids Res 35:4800–4808PubMedCentralCrossRefPubMedGoogle Scholar
  10. Kasahara R, Sato T, Tamegai H, Kato C (2009) Piezo-adapted 3-isopropylmalate dehydrogenase of the obligate piezophile Shewanella benthica DB21MT-2 isolated from the 11,000-m depth of the Mariana Trench. Biosci Biotech Biochem 3:2541–2543CrossRefGoogle Scholar
  11. Katrusiak A, Dauter Z (1996) Compressibility of lysozyme protein crystals by X-ray diffraction. Acta Crystallogr D52:607–608Google Scholar
  12. Kitamura Y, Itho T (1987) Reaction volume of protonic ionization for buffering agents. Prediction of pressure dependence of pH and pOH. J Solut Chem 16:715–725Google Scholar
  13. Kundrot CE, Richards FM (1987) Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres. J Mol Biol 193:157–170CrossRefPubMedGoogle Scholar
  14. Kurpiewska K, Lewinski K (2010) High pressure macromolecular crystallography for structural biology: a review. Cent Eur J Biol 5:531–542Google Scholar
  15. Merrill L, Bassett WA (1974) Miniature diamond anvil pressure cell for single crystal x-ray diffraction studies. Rev Sci Instrum 45:290–294CrossRefGoogle Scholar
  16. Mozhaev VV, Heremans K, Frank J, Masson P, Balny C (1996) High pressure effects on protein structure and function. Proteins Struct Funct Genet 24:81–91CrossRefPubMedGoogle Scholar
  17. Nagae T, Kawamura T, Chavas LMG, Niwa K, Hasegawa M, Kato C, Watanabe N (2012) High pressure induced water penetration into 3-isopropylmalate dehydrogenase. Acta Crystallogr D68:300–309Google Scholar
  18. Piermarini GJ, Block S, Barnett JD, Forman RA (1975) Calibration of the pressure dependence of the R1 Ruby fluorescence line to 195 kbar. J Appl Phys 46:2774–2780CrossRefGoogle Scholar
  19. Sazaki G, Nagatoshi Y, Suzuki Y, Durbin SD, Miyashita S, Nakada T et al (1999) Solubility of tetragonal and orthorhombic lysozyme crystals under high pressure. J Crystallogr Growth 196:204–209Google Scholar
  20. Suzuki Y, Tsukamoto M, Sakuraba H, Matsumoto M, Nagasawa M, Tamura K (2010) Design of a standalone-type beryllium vessel for high-pressure protein crystallography. Rev Sci Instrum 81:084302CrossRefPubMedGoogle Scholar
  21. Urayama P, Phillips GN, Gruner SM (2002) Probing substates in sperm whale myoglobin using high-pressure crystallography. Structure 10:51–60CrossRefPubMedGoogle Scholar
  22. Waghmare RY, Pan XJ, Glatz CE (2000) Pressure and concentration dependence of nucleation kinetics for crystallization of subtilisin. J Crystallogr Growth 210:746–757CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Synchrotron Radiation Research CenterNagoya UniversityNagoyaJapan

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