European Biophysics Journal

, Volume 15, Issue 4, pp 237–249 | Cite as

Low temperature X-ray investigation of structural distributions in myoglobin

  • F. Parak
  • H. Hartmann
  • K. D. Aumann
  • H. Reuscher
  • G. Rennekamp
  • H. Bartunik
  • W. Steigemann
Article

Abstract

The results of X-ray structure analysis of metmyoglobin at 300 K, 185 K, 165 K, 115 K and 80 K are reported. The lattice vectorsa andb decrease linearly with temperature whilec shows non-linearity above 180 K, indicating some type of phase transition. Cooling does change the myoglobin structure but only within the structural distribution as determined by individual 〈x2〉 at room temperature. Two residues showed significant alternative positions for sidechains at higher temperatures while only one position is occupied at low temperatures. In the case of LEU 61 a jump between different positions of the side-chain reduces the potential barrier for the entrance of the O2 molecule to the heme pocket.

The mean square displacements, 〈x2〉, of the individual residues decrease linearly with temperature in most cases, indicating a parabolic envelope for the potential responsible for motions. A separation of rotational and translational disorder of the entire molecule is discussed. Comparison with Mössbauer spectroscopy indicates that protein dynamics on a time scale faster than 10-7 s is not simply a harmonic process. Extrapolation of the structural distributions toT=0 K shows that a large zero point distribution of the myoglobin structure exists, thus proving that there is no absolute energy minimum for one well defined conformation.

Key words

Protein crystallography Debye-Waller factor intramolecular motion oxygen path 

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References

  1. Ansari A, Berendzen J, Bowne SF, Frauenfelder H, Iben IET, Sauke TB, Shyamsunder E, Young RD (1985) Protein states and protein quakes. Proc Natl Acad Sci USA 82:5000–5004Google Scholar
  2. Artymiuk PJ, Blake CCF, Grace DEP, Oatley SJ, Phillips DC, Sternberg MJE (1979) Crystallographic studies of dynamic properties of lysozyme. Nature (London) 280:563–568Google Scholar
  3. Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, Gunsalus IC (1975) Dynamics of ligand binding to myoglobin. Biochemistry 14:5355–5373Google Scholar
  4. Bartunik HD, Schubert P (1982) Crystal cooling for protein crystallography with synchrotron radiation. J Appl Cryst 15:227–231Google Scholar
  5. Case DA, Karplus M (1979) Dynamics of ligand binding to heme proteins. J Mol Biol 132:343–368Google Scholar
  6. Figgis BN, Reynolds PA, Lehner N (1983) cis-bis(bipyridy)dichloroiron (III) tetrachloroferrate (III), [Fe(bpy)2 Cl2][FeCl4]; structure at 4.2 and at 115 K by neutron diffraction. Acta Cryst B 39:711–717Google Scholar
  7. Frauenfelder H (1985) Ligand binding and protein dynamics. In: Clementi E, Corongiu G, Sarma MH, Sarma RH (eds), Structure and motions: membranes, nucleic acids and proteins. Adenine Press, pp 205–217Google Scholar
  8. Frauenfelder H, Petsko GA, Tsernoglou D (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280:558–563Google Scholar
  9. Frauenfelder H, Hartmann H, Karplus M, Kuntz ID, Kuriyan J, Parak F, Petsko GA, Ringe D, Tilton RF, Connolly MI, Max N (1987) The thermal expansion of a protein. Biochemistry 26:254–261Google Scholar
  10. Hartmann H, Parak F, Steigemann W, Petsko GA, Ringe Ponzi D, Frauenfelder H (1982) Conformational substates in a protein; structure and dynamics of metmyoglobin at 80 K. Proc Natl Acad Sci USA 79:4967–4971Google Scholar
  11. Hartmann H, Steigemann W, Reuscher H, Parak F (1986) Structural disorder in proteins: a comparison of myoglobin and erythrocruorin. Eur Biophys J 14:337–348Google Scholar
  12. Jones TA, Liljas L (1984) Crystallographic refinement of macromolecules having noncrystallographic symmetry. Acta Cryst A 40:50–57Google Scholar
  13. Kendrew JC, Parrish RG (1956) The crystal structure of myoglobin III. Sperm-whale myoglobin. Proc Roy Soc 238A: 305–324Google Scholar
  14. Konnert JH (1976) A restrained parameter structure factor least-squares refinement procedure for large asymmetric units. Acta Crystallogr A 32:614–617Google Scholar
  15. Konnert JH, Hendrickson WA (1980) A restrained thermal factor refinement procedure. Acta Crystallogr A 36:344–349Google Scholar
  16. Krupyanskii Yu F, Parak F, Goldanskii VI, Mössbauer RL, Gaubmann F, Engelmann H, Suzdalev IP (1982) Investigation of large intramolecular movements within metmyoglobin by Rayleigh scattering of Mössbauer radiation (RSMR). Z. Naturforsch 37c:57–62Google Scholar
  17. Levy RM, Sheridan RP, Keepers JW, Dubey GS, Swaminathan S, Karplus M (1985) Molecular dynamics of myoglobin at 298 K. Biophys J 48:509–518Google Scholar
  18. Nienhaus GU, Parak F (1986) Rayleigh scattering of Mössbauer radiation on metmyoglobin. Hyperfine Interactions 29:1451–1454Google Scholar
  19. Nienhaus GU, Drepper F, Parak F, Mössbauer RL, Bade D, Hoppe W (1987) A multiwire proportional counter with spherical drift chamber for protein crystallography with X-rays and gamma-rays. Nucl Instrum Methods A256:581–586Google Scholar
  20. Nyborg J, Wonacott AJ (1977) In: Arnd UW, Wonacott AJ (eds) The rotation method in crystallography. North-Holland, Amsterdam, pp 139–145Google Scholar
  21. Parak F, Knapp EW (1984) A consistent picture of protein dynamics. Proc Natl Acad Sci USA 81:7088–7092Google Scholar
  22. Parak F, Thomanek UF, Bade D, Wintergerst B (1977) The orientation of the electric field gradient tensor in CO-liganded myoglobin. Z Naturforsch 32c:507–512Google Scholar
  23. Parak F, Knapp EW, Kucheida D (1982) Protein dynamics. Mössbauer spectroscopy on deoxymyoglobin crystals. J Mol Biol 161:177–194Google Scholar
  24. Parak F, Fischer M, Graffweg E, Formanek H (1987a) Distributions and fluctuations of protein structures investigated by X-ray analysis and Mössbauer spectroscopy. In: Clementi E, Chin S (eds) Structure and dynamics of nucleic acids, proteins and membranes. Plenum, New York, pp 139–148Google Scholar
  25. Parak F, Hartmann H, Nienhaus GU, Heidemeier J (1987b) Structural fluctuations in myoglobin. In: Ehrenberg A, Rigler R, Gräslund A, Nilsson L (eds) Structure, dynamics and function of biomolecules. Springer, Berlin Heidelberg New York Tokyo, pp 30–33Google Scholar
  26. Phillips SEV (1980) Structure and refinement of oxymyoglobin at 1.6 A resolution. J Mol Biol 142:531–554 Coordinates taken from the Protein Data BankGoogle Scholar
  27. Reinisch L, Heidemeier J, Parak F (1985) Determination of the second order Doppler shift of iron in myoglobin by Mössbauer spectroscopy. Eur Biophys J 12:167–172Google Scholar
  28. Ringe D, Petsko GA, Kerr DE, de Montellano PRO (1984) Reaction of myoglobin with phenylhydrazine: a molecular doorstop. Biochemistry 23:2–4Google Scholar
  29. Schwager P, Bartels K (1975) Refinement of setting angles in screenless film methods. J Appl Crystallogr 8:275–280Google Scholar
  30. Schwager P, Bartels K (1977) In: Arnd UW, Wonacott AJ (eds) The rotation method in crystallography. North-Holland, Amsterdam, pp 105–117, 139–151Google Scholar
  31. Steigemann W (1974) Dissertation TU München. Die Entwicklung und Anwendung von Rechenverfahren und Rechenprogrammen zur Strukturanalyse von Proteinen am Beispiel des Trypsin-Trypsininhibitor-Komplexes, des freien Inhibitors und derl-AsparaginaseGoogle Scholar
  32. Swaminathan S, Craven BM, McMullan RK (1984) The crystal structure and molecular thermal motion of urea at 12, 60 and 123 K from neutron diffraction. Acta Crystallor B 40:300–306Google Scholar
  33. Takano R (1977a) Structure of myoglobin refined at 2.0 A resolution. Crystallographic refinement of metmyoglobin from sperm whale. J Mol Biol 110:537–568 Coordinates taken from the Protein Data BankGoogle Scholar
  34. Takano R (1977b) Structure of myoglobin refined at 2.0 A resolution. Structure of deoxymyoglobin from sperm whale. J Mol Biol 110:569–584 Coordinates taken from the Protein Data BankGoogle Scholar

Copyright information

© Springer-Verlag 1987

Authors and Affiliations

  • F. Parak
    • 1
  • H. Hartmann
    • 1
  • K. D. Aumann
    • 1
  • H. Reuscher
    • 1
  • G. Rennekamp
    • 1
  • H. Bartunik
    • 2
  • W. Steigemann
    • 3
  1. 1.Institut für Physikalische Chemie der Universität MünsterMünsterFederal Republic of Germany
  2. 2.Max-Planck-InstitutHamburgFederal Republic of Germany
  3. 3.Max-Planck-Institut für BiochemieMartinsriedFederal Republic of Germany

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