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. 1999 Oct;8(10):2033–2040. doi: 10.1110/ps.8.10.2033

X-ray crystal structures of a severely desiccated protein.

J A Bell 1
PMCID: PMC2144124  PMID: 10548049

Abstract

Unlike most protein crystals, form IX of bovine pancreatic ribonuclease A diffracts well when severely dehydrated. Crystal structures have been solved after 2.5 and 4 days of desiccation with CaSO4, at 1.9 and 2.0 A resolution, respectively. The two desiccated structures are very similar. An RMS displacement of 1.6 A is observed for main-chain atoms in each structure when compared to the hydrated crystal structure with some large rearrangements observed in loop regions. The structural changes are the result of intermolecular contacts formed by strong electrostatic interactions in the absence of a high dielectric medium. The electron density is very diffuse for some surface loops, consistent with a very disordered structure. This disorder is related to the conformational changes. These results help explain conformational changes during the lyophilization of protein and the associated phenomena of denaturation and molecular memory.

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Selected References

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  1. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  2. Carpenter J. F., Pikal M. J., Chang B. S., Randolph T. W. Rational design of stable lyophilized protein formulations: some practical advice. Pharm Res. 1997 Aug;14(8):969–975. doi: 10.1023/a:1012180707283. [DOI] [PubMed] [Google Scholar]
  3. Costantino H. R., Griebenow K., Mishra P., Langer R., Klibanov A. M. Fourier-transform infrared spectroscopic investigation of protein stability in the lyophilized form. Biochim Biophys Acta. 1995 Nov 15;1253(1):69–74. doi: 10.1016/0167-4838(95)00156-o. [DOI] [PubMed] [Google Scholar]
  4. Costantino H. R., Schwendeman S. P., Langer R., Klibanov A. M. Deterioration of lyophilized pharmaceutical proteins. Biochemistry (Mosc) 1998 Mar;63(3):357–363. [PubMed] [Google Scholar]
  5. Dong A., Meyer J. D., Kendrick B. S., Manning M. C., Carpenter J. F. Effect of secondary structure on the activity of enzymes suspended in organic solvents. Arch Biochem Biophys. 1996 Oct 15;334(2):406–414. doi: 10.1006/abbi.1996.0472. [DOI] [PubMed] [Google Scholar]
  6. Dung M. H., Bell J. A. Structure of crystal form IX of bovine pancreatic ribonuclease A. Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):419–425. doi: 10.1107/S0907444997000929. [DOI] [PubMed] [Google Scholar]
  7. Evans S. V. SETOR: hardware-lighted three-dimensional solid model representations of macromolecules. J Mol Graph. 1993 Jun;11(2):134-8, 127-8. doi: 10.1016/0263-7855(93)87009-t. [DOI] [PubMed] [Google Scholar]
  8. Gregory R. B., Gangoda M., Gilpin R. K., Su W. The influence of hydration on the conformation of bovine serum albumin studied by solid-state 13C-NMR spectroscopy. Biopolymers. 1993 Dec;33(12):1871–1876. doi: 10.1002/bip.360331212. [DOI] [PubMed] [Google Scholar]
  9. Griebenow K., Klibanov A. M. Lyophilization-induced reversible changes in the secondary structure of proteins. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10969–10976. doi: 10.1073/pnas.92.24.10969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hooft R. W., Vriend G., Sander C., Abola E. E. Errors in protein structures. Nature. 1996 May 23;381(6580):272–272. doi: 10.1038/381272a0. [DOI] [PubMed] [Google Scholar]
  11. Hsu C. C., Ward C. A., Pearlman R., Nguyen H. M., Yeung D. A., Curley J. G. Determining the optimum residual moisture in lyophilized protein pharmaceuticals. Dev Biol Stand. 1992;74:255–271. [PubMed] [Google Scholar]
  12. Jones T. A. Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. Methods Enzymol. 1985;115:157–171. doi: 10.1016/0076-6879(85)15014-7. [DOI] [PubMed] [Google Scholar]
  13. Kachalova G. S., Morozov V. N., Morozova TYa, Myachin E. T., Vagin A. A., Strokopytov B. V., Nekrasov YuV Comparison of structures of dry and wet hen egg-white lysozyme molecule at 1.8 A resolution. FEBS Lett. 1991 Jun 17;284(1):91–94. doi: 10.1016/0014-5793(91)80769-y. [DOI] [PubMed] [Google Scholar]
  14. Kishan R. V., Chandra N. R., Sudarsanakumar C., Suguna K., Vijayan M. Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme. Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):703–710. doi: 10.1107/S0907444994014794. [DOI] [PubMed] [Google Scholar]
  15. Matthews B. W. Solvent content of protein crystals. J Mol Biol. 1968 Apr 28;33(2):491–497. doi: 10.1016/0022-2836(68)90205-2. [DOI] [PubMed] [Google Scholar]
  16. Morris A. L., MacArthur M. W., Hutchinson E. G., Thornton J. M. Stereochemical quality of protein structure coordinates. Proteins. 1992 Apr;12(4):345–364. doi: 10.1002/prot.340120407. [DOI] [PubMed] [Google Scholar]
  17. Nagendra H. G., Sukumar N., Vijayan M. Role of water in plasticity, stability, and action of proteins: the crystal structures of lysozyme at very low levels of hydration. Proteins. 1998 Aug 1;32(2):229–240. doi: 10.1002/(sici)1097-0134(19980801)32:2<229::aid-prot9>3.0.co;2-f. [DOI] [PubMed] [Google Scholar]
  18. Prestrelski S. J., Pikal K. A., Arakawa T. Optimization of lyophilization conditions for recombinant human interleukin-2 by dried-state conformational analysis using Fourier-transform infrared spectroscopy. Pharm Res. 1995 Sep;12(9):1250–1259. doi: 10.1023/a:1016296801447. [DOI] [PubMed] [Google Scholar]
  19. Rupley J. A., Careri G. Protein hydration and function. Adv Protein Chem. 1991;41:37–172. doi: 10.1016/s0065-3233(08)60197-7. [DOI] [PubMed] [Google Scholar]
  20. Shah N. K., Ludescher R. D. Influence of hydration on the internal dynamics of hen egg white lysozyme in the dry state. Photochem Photobiol. 1993 Aug;58(2):169–174. doi: 10.1111/j.1751-1097.1993.tb09544.x. [DOI] [PubMed] [Google Scholar]
  21. Steinbach P. J., Brooks B. R. Protein hydration elucidated by molecular dynamics simulation. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):9135–9139. doi: 10.1073/pnas.90.19.9135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Walter R. L., Thiel D. J., Barna S. L., Tate M. W., Wall M. E., Eikenberry E. F., Gruner S. M., Ealick S. E. High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation. Structure. 1995 Aug 15;3(8):835–844. doi: 10.1016/s0969-2126(01)00218-0. [DOI] [PubMed] [Google Scholar]

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