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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1983 Jul;80(14):4315–4319. doi: 10.1073/pnas.80.14.4315

Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data.

W F van Gunsteren, H J Berendsen, J Hermans, W G Hol, J P Postma
PMCID: PMC384028  PMID: 6576339

Abstract

The structure and dynamics of the full unit cell of a protein (bovine pancreatic trypsin inhibitor) containing 4 protein molecules and 560 water molecules have been simulated by using the molecular dynamics method. The obtained structure, atom positional fluctuations, and structure factors are compared with x-ray values. A way of calculating the motional contributions to structure factors is proposed.

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Selected References

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  1. Anderson C. M., Zucker F. H., Steitz T. A. Space-filling models of kinase clefts and conformation changes. Science. 1979 Apr 27;204(4391):375–380. doi: 10.1126/science.220706. [DOI] [PubMed] [Google Scholar]
  2. Artymiuk P. J., Blake C. C., Grace D. E., Oatley S. J., Phillips D. C., Sternberg M. J. Crystallographic studies of the dynamic properties of lysozyme. Nature. 1979 Aug 16;280(5723):563–568. doi: 10.1038/280563a0. [DOI] [PubMed] [Google Scholar]
  3. Fehlhammer H., Bode W., Huber R. Crystal structure of bovine trypsinogen at 1-8 A resolution. II. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin. J Mol Biol. 1977 Apr 25;111(4):415–438. doi: 10.1016/s0022-2836(77)80062-4. [DOI] [PubMed] [Google Scholar]
  4. Frauenfelder H., Petsko G. A., Tsernoglou D. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature. 1979 Aug 16;280(5723):558–563. doi: 10.1038/280558a0. [DOI] [PubMed] [Google Scholar]
  5. Gurd F. R., Rothgeb T. M. Motions in proteins. Adv Protein Chem. 1979;33:73–165. doi: 10.1016/s0065-3233(08)60459-3. [DOI] [PubMed] [Google Scholar]
  6. Hagler A. T., Moult J. Computer simulation of the solvent structure around biological macromolecules. Nature. 1978 Mar 16;272(5650):222–226. doi: 10.1038/272222a0. [DOI] [PubMed] [Google Scholar]
  7. Karplus M., McCammon J. A. Protein structural fluctuations during a period of 100 ps. Nature. 1979 Feb 15;277(5697):578–578. doi: 10.1038/277578a0. [DOI] [PubMed] [Google Scholar]
  8. Karplus M., McCammon J. A. The internal dynamics of globular proteins. CRC Crit Rev Biochem. 1981;9(4):293–349. doi: 10.3109/10409238109105437. [DOI] [PubMed] [Google Scholar]
  9. Levitt M. Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein. Nature. 1981 Nov 26;294(5839):379–380. doi: 10.1038/294379a0. [DOI] [PubMed] [Google Scholar]
  10. Matthews D. A., Alden R. A., Bolin J. T., Filman D. J., Freer S. T., Hamlin R., Hol W. G., Kisliuk R. L., Pastore E. J., Plante L. T. Dihydrofolate reductase from Lactobacillus casei. X-ray structure of the enzyme methotrexate.NADPH complex. J Biol Chem. 1978 Oct 10;253(19):6946–6954. [PubMed] [Google Scholar]
  11. McCammon J. A., Gelin B. R., Karplus M. Dynamics of folded proteins. Nature. 1977 Jun 16;267(5612):585–590. doi: 10.1038/267585a0. [DOI] [PubMed] [Google Scholar]
  12. McCammon J. A., Wolynes P. G., Karplus M. Picosecond dynamics of tyrosine side chains in proteins. Biochemistry. 1979 Mar 20;18(6):927–942. doi: 10.1021/bi00573a001. [DOI] [PubMed] [Google Scholar]
  13. Northrup S. H., Pear M. R., McCammon J. A., Karplus M. Molecular dynamics of ferrocytochrome c. Nature. 1980 Jul 17;286(5770):304–305. doi: 10.1038/286304a0. [DOI] [PubMed] [Google Scholar]
  14. Northrup S. H., Pear M. R., McCammon J. A., Karplus M., Takano T. Internal mobility of ferrocytochrome c. Nature. 1980 Oct 16;287(5783):659–660. doi: 10.1038/287659a0. [DOI] [PubMed] [Google Scholar]
  15. Northrup S. H., Pear M. R., Morgan J. D., McCammon J. A., Karplus M. Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J Mol Biol. 1981 Dec 25;153(4):1087–1109. doi: 10.1016/0022-2836(81)90469-1. [DOI] [PubMed] [Google Scholar]
  16. Phillips S. E. Structure and refinement of oxymyoglobin at 1.6 A resolution. J Mol Biol. 1980 Oct 5;142(4):531–554. doi: 10.1016/0022-2836(80)90262-4. [DOI] [PubMed] [Google Scholar]
  17. Watenpaugh K. D., Sieker L. C., Jensen L. H. Crystallographic refinement of rubredoxin at 1 x 2 A degrees resolution. J Mol Biol. 1980 Apr 15;138(3):615–633. doi: 10.1016/s0022-2836(80)80020-9. [DOI] [PubMed] [Google Scholar]
  18. van Gunsteren W. F., Karplus M. Effect of constraints, solvent and crystal environment on protein dynamics. Nature. 1981 Oct 22;293(5834):677–678. doi: 10.1038/293677a0. [DOI] [PubMed] [Google Scholar]
  19. van Gunsteren W. F., Karplus M. Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. Biochemistry. 1982 May 11;21(10):2259–2274. doi: 10.1021/bi00539a001. [DOI] [PubMed] [Google Scholar]

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