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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
. 1984 Nov;81(22):7088–7092. doi: 10.1073/pnas.81.22.7088

A consistent picture of protein dynamics.

F Parak, E W Knapp
PMCID: PMC392082  PMID: 6594683

Abstract

Information about the protein dynamics of myoglobin obtained by x-ray and Mössbauer investigations is analyzed and compared with computer simulations. Computer simulations give correct amplitudes of mean-square displacements but fail in the description of the time dependence of motions. Our model describes protein dynamics at physiological temperatures as an overdamped diffusion-like motion in a restricted space. The fluctuations occur around the average conformation determined by x-ray structure analysis. The gain in entropy drives the molecule into the transition state and, in this way, accounts for its flexibility.

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Selected References

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

  1. 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]
  2. Austin R. H., Beeson K. W., Eisenstein L., Frauenfelder H., Gunsalus I. C. Dynamics of ligand binding to myoglobin. Biochemistry. 1975 Dec 2;14(24):5355–5373. doi: 10.1021/bi00695a021. [DOI] [PubMed] [Google Scholar]
  3. Bauminger E. R., Cohen S. G., Nowik I., Ofer S., Yariv J. Dynamics of heme iron in crystals of metmyoglobin and deoxymyoglobin. Proc Natl Acad Sci U S A. 1983 Feb;80(3):736–740. doi: 10.1073/pnas.80.3.736. [DOI] [PMC free article] [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. Go N., Noguti T., Nishikawa T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci U S A. 1983 Jun;80(12):3696–3700. doi: 10.1073/pnas.80.12.3696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hartmann H., Parak F., Steigemann W., Petsko G. A., Ponzi D. R., Frauenfelder H. Conformational substates in a protein: structure and dynamics of metmyoglobin at 80 K. Proc Natl Acad Sci U S A. 1982 Aug;79(16):4967–4971. doi: 10.1073/pnas.79.16.4967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. Krupyanskii YuF, Parak F., Goldanskii V. I., Mössbauer R. L., Gaubman E. E., Engelmann H., Suzdalev I. P. Investigation of large intramolecular movement within metmyoglobin by Rayleigh scattering of Mössbauer radiation (RSMR). Z Naturforsch C. 1982 Jan-Feb;37(1-2):57–62. doi: 10.1515/znc-1982-1-211. [DOI] [PubMed] [Google Scholar]
  9. Levitt M. Protein conformation, dynamics, and folding by computer simulation. Annu Rev Biophys Bioeng. 1982;11:251–271. doi: 10.1146/annurev.bb.11.060182.001343. [DOI] [PubMed] [Google Scholar]
  10. Levy R. M., Perahia D., Karplus M. Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1346–1350. doi: 10.1073/pnas.79.4.1346. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Parak F., Frolov E. N., Mössbauer R. L., Goldanskii V. I. Dynamics of metmyoglobin crystals investigated by nuclear gamma resonance absorption. J Mol Biol. 1981 Feb 5;145(4):825–833. doi: 10.1016/0022-2836(81)90317-x. [DOI] [PubMed] [Google Scholar]
  12. Parak F., Knapp E. W., Kucheida D. Protein dynamics. Mössbauer spectroscopy on deoxymyoglobin crystals. J Mol Biol. 1982 Oct 15;161(1):177–194. doi: 10.1016/0022-2836(82)90285-6. [DOI] [PubMed] [Google Scholar]
  13. Peticolas W. L. Low frequency vibrations and the dynamics of proteins and polypeptides. Methods Enzymol. 1979;61:425–458. doi: 10.1016/0076-6879(79)61020-0. [DOI] [PubMed] [Google Scholar]
  14. Wagner G., DeMarco A., Wüthrich K. Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI). I. 1H NMR studies. Biophys Struct Mech. 1976 Aug 23;2(2):139–158. doi: 10.1007/BF00863706. [DOI] [PubMed] [Google Scholar]
  15. van Gunsteren W. F., Berendsen H. J., Hermans J., Hol W. G., Postma J. P. Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4315–4319. doi: 10.1073/pnas.80.14.4315. [DOI] [PMC free article] [PubMed] [Google Scholar]

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