Advertisement

Internal Dynamics of Proteins and DNA: Analogy to Glass-Forming Systems

  • A. P. Sokolov
  • R. B. Gregory
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)

Keywords

Mode Coupling Theory Dynamic Structure Factor Boson Peak Neutron Spectroscopy Quasielastic Scattering 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    J. Perez, J.M. Zanotti, D. Durand, Biophys. J. 77 (1999), 454CrossRefGoogle Scholar
  2. 2.
    M. Tarek, D.A. Neumann, D.J. Tobias, Chem. Phys. 292 (2003), 435CrossRefGoogle Scholar
  3. 3.
    A.P. Sokolov, H. Grimm, A. Kisliuk, A.J. Dianoux, J. Biol. Phys. 27 (2001), 313CrossRefGoogle Scholar
  4. 4.
    J.H. Roh, G. Caliskan, A.P. Sokolov, R. Gregory, et al. (unpublished)Google Scholar
  5. 5.
    C.L. Brooks III, M. Karplus, B.M. Pettitt, in Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (Wiley Interscience, 1988) p. 19Google Scholar
  6. 6.
    S. Longeville, W. Doster, G. Kali, Chem. Phys. 292 (2003), 413CrossRefGoogle Scholar
  7. 7.
    W. Doster, S. Cusack, W. Petry, Phys. Rev. Lett. 65 (1990), 1080CrossRefADSGoogle Scholar
  8. 8.
    J. Fitter, R.E. Lechner, N.A. Dencher, Biophys. J. 73 (1997), 2126CrossRefGoogle Scholar
  9. 9.
    A.P. Sokolov, H. Grimm, R. Kahn, J. Chem. Phys. 110 (1999), 7053CrossRefADSGoogle Scholar
  10. 10.
    M. Tarek, D.J. Tobias, J. Chem. Phys. 115 (2001), 1607CrossRefADSGoogle Scholar
  11. 11.
    F.G. Parak, Rep. Prog. Phys. 66 (2003), 103CrossRefADSGoogle Scholar
  12. 12.
    G. Caliskan, A. Kisliuk, A. Sokolov, J. Non-Crystallogr. Sol. 307–310 (2002), 868CrossRefGoogle Scholar
  13. 13.
    C.P. Lindsey, G.D. Patterson, J. Chem. Phys. 73 (1980), 3348CrossRefADSGoogle Scholar
  14. 14.
    J.L. Green, J. Fan, C.A. Angell, J. Am. Chem. Soc. 98 (1994), 13780Google Scholar
  15. 15.
    C.A. Angell, Science 267 (1995), 1924ADSCrossRefGoogle Scholar
  16. 16.
    W. Doster, M. Settles, in Workshop on Hydration Processes in Biology: Theoretical and Experimental Approaches, M.C. Bellissent-Funel (Ed.) (Les Houches, IOS Press, 1999) p. 177Google Scholar
  17. 17.
    D. Richter, et al., J. Phys. Condens. Matter 11 (1999), A297CrossRefADSGoogle Scholar
  18. 18.
    J. Colmenero, et al., J. Phys. Condens. Matter 11 (1999), A363CrossRefADSGoogle Scholar
  19. 19.
    F. Volino, A.J. Dianoux, Mol. Phys. 41 (1980), 271ADSCrossRefGoogle Scholar
  20. 20.
    A.L. Tournier, J.C. Smith, Phys. Rev. Lett. 91 (2003), 208106CrossRefADSGoogle Scholar
  21. 21.
    J.A. Rupley, P. Yang, G. Tollin, in Water in Polymers, S.P. Rowland (Ed.) (Am. Chem. Soc., Washington, DC, 1980) pp. 111–132CrossRefGoogle Scholar
  22. 22.
    O.V. Belonogova, E.N. Frolov, S.A. Krasnopol’skaya, B.P. Atanasov, V.K. Gins, E.N. Mukhin, A.A. Levina, A.P. Andreeva, G.I. Likhtenshtein, V.I. Goldanskii, Dokl. Akad. Nauk USSR 241 (1978), 219Google Scholar
  23. 23.
    G.I. Likhtenshtein, V.R. Bogatyrenko, A.V. Kulikov, Appl. Magn. Reson. 4 (1993), 513CrossRefGoogle Scholar
  24. 24.
    F. Parak, Methods Enzymol. 127 (1986), 196CrossRefGoogle Scholar
  25. 25.
    G.B. Strambini, E. Gabellieri, Photochem. Photobiol. 39 (1984), 725Google Scholar
  26. 26.
    N.K. Shah, R.D. Ludescher, Photochem. Photobiol. 58 (1993), 169CrossRefGoogle Scholar
  27. 27.
    R.B. Gregory, M. Gangoda, R.K. Gilpin, W. Su, Biopolymers 33 (1993), 513CrossRefGoogle Scholar
  28. 28.
    P.L. Poole, J.L. Finney, Int. J. Biol. Macromol. 5 (1983), 308CrossRefGoogle Scholar
  29. 29.
    J.E. Schinkel, N.W. Downer, J.A. Rupley, Biochemistry 24 (1985), 352CrossRefGoogle Scholar
  30. 30.
    S. Bone, R.J. Pethig, Mol. Biol. 181 (1985), 323CrossRefGoogle Scholar
  31. 31.
    R. Pethig, in Protein-Solvent Interactions, R.B. Gregory (Ed.) (Marcel Dekker, New York, 1995) pp. 265–288Google Scholar
  32. 32.
    V.I. Goldanskii, Y.F. Krupyanskii: Rev. Biophys. 22 (1989), 39; V.I. Goldanskii, Y.F. Krupyanskii, in Protein-Solvent Interactions, R.B. Gregory (Ed.) (Marcel Dekker, New York, 1995) pp. 289–326CrossRefGoogle Scholar
  33. 33.
    M. Diehl, W. Doster, W. Petry, A. Schulte, Biophys. J. 73 (1997), 2726CrossRefGoogle Scholar
  34. 34.
    R.B. Gregory, in Protein-Solvent Interactions, R.B. Gregory (Ed.) (Marcel Dekker, New York, 1995) pp. 191–264Google Scholar
  35. 35.
    R.W. Lumry, A. Rosenberg, Colloques. Int. CNRS 246 (1975), 53Google Scholar
  36. 36.
    M. Tarek, D.J. Tobias, Phys. Rev. Lett. 88 (2002), 138101CrossRefADSGoogle Scholar
  37. 37.
    A.L. Tournier, J. Xu, J.C. Smith, Biophys. J. 85 (2003), 1871CrossRefGoogle Scholar
  38. 38.
    D. Vitkup, D. Ringe, G.A. Petsko, M. Karplus, Nat. Struct. Biol. 7 (2000), 34–38CrossRefGoogle Scholar
  39. 39.
    A. Ansari, C.M. Jones, E.R. Henry, J. Hofrichter, W.A. Eaton, Science 256 (1992), 1796ADSCrossRefGoogle Scholar
  40. 40.
    T. Kleinert, et al., Biochemistry 37 (1998), 717CrossRefGoogle Scholar
  41. 41.
    H. Lichtenegger, et al., Biophys. J. 76 (1999), 414ADSCrossRefGoogle Scholar
  42. 42.
    B. Gavish, M.M. Werber, Biochem. 18 (1979), 1269CrossRefGoogle Scholar
  43. 43.
    D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M.C. Marden, L. Reinish, A.H. Reynolds, L.B. Sorensen, K.T. Yue, Biochem. 19 (1980), 5147CrossRefGoogle Scholar
  44. 44.
    M. Settles, W. Doster, F. Kremer, F. Post, W. Schirmacher, Philos. Mag. 65 (1992), 861CrossRefGoogle Scholar
  45. 45.
    R.H. Austin, K.W. Beeson, L. Eisenstein, H. Frauenfelder, I.C. Gunsalus, Biochem. 14 (1975), 5355CrossRefGoogle Scholar
  46. 46.
    B. Gavish, S. Yedgar, in Protein-Solvent Interactions, R.B. Gregory (Ed.) (Marcel Dekker, New York, 1995) pp. 343–373Google Scholar
  47. 47.
    S.N. Timasheff, in Protein-Solvent Interactions, R.B. Gregory (Ed.) (Marcel Dekker, New York, 1995) pp. 445–482Google Scholar
  48. 48.
    R. Gregory, Biopolymers 27 (1988), 1699CrossRefGoogle Scholar
  49. 49.
    W. Doster, S. Cusak, W. Petry, Nature 337 (1989), 754CrossRefADSGoogle Scholar
  50. 50.
    B.F. Rasmussen, et al., Nature 357 (1992), 423CrossRefADSGoogle Scholar
  51. 51.
    A.M. Tsai, D.A. Neumann, L.N. Bell, Biophys. J. 79 (2000), 2728CrossRefGoogle Scholar
  52. 52.
    M. Ferrand, A.J. Dianoux, W. Petry, G. Zaccai, Proc. Natl Acad. Sci. USA 90 (1993), 9668ADSCrossRefGoogle Scholar
  53. 53.
    R.M. Daniel, J.C. Smith, M. Ferrand, S. Hery, R. Dunn, J. Finney, Biophys. J. 75 (1998), 2504CrossRefGoogle Scholar
  54. 54.
    L. Cordone, M. Ferrand, E. Vitrano, G. Zaccai, Biophys. J. 76 (1999), 1043CrossRefGoogle Scholar
  55. 55.
    W. Gotze, L. Sjogren, Rep. Prog. Phys. 55 (1992), 241CrossRefADSGoogle Scholar
  56. 56.
    see, for example, Transp. Theory Stat. Phys. 24 (1995), Special issue devoted to Relaxation Kinetics in Supercooled Liquids — Mode Coupling Theory and Its Experimental TestsGoogle Scholar
  57. 57.
    W. Stefen, A. Patkowski, H. Glaser, G. Meier, E.W. Fischer, Phys. Rev. E 49 (1994), 2992CrossRefADSGoogle Scholar
  58. 58.
    A.P. Sokolov, W. Steffen, E. Rössler, Phys. Rev. E 52 (1995), 5105CrossRefADSGoogle Scholar
  59. 59.
    A.P. Sokolov, Science 273 (1996), 1675; Endeavour 21 (1997), 109ADSCrossRefGoogle Scholar
  60. 60.
    A.P. Sokolov, J. Hurst, D. Quitmann, Phys. Rev. B 51 (1995), 12865CrossRefADSGoogle Scholar
  61. 61.
    E. Rössler, A.P. Sokolov, A. Kisliuk, D. Quitmann, Phys. Rev. B 49 (1994), 14967CrossRefADSGoogle Scholar
  62. 62.
    A.P. Sokolov, J. Non-Crystallogr. Solids 235–237 (1998), 190Google Scholar
  63. 63.
    N.V. Surovtsev, J. Wiedersich, V.N. Novikov, E. Rössler, A.P. Sokolov, Phys. Rev. B 58 (1998), 14888CrossRefADSGoogle Scholar
  64. 64.
    J. Fitter, Biophys. J. 76 (1999), 1034ADSCrossRefGoogle Scholar
  65. 65.
    P.G. Debenedetti, F.H. Stillinger, Nature 410 (2001), 259CrossRefADSGoogle Scholar
  66. 66.
    J.W. Mack, M.G. Usha, J. Long, R.G. Griffin, R.J. Wittebort, Biopolymers 53 (2000), 9CrossRefGoogle Scholar
  67. 67.
    G. Caliskan, A. Kisliuk, V.N. Novikov, A.P. Sokolov, J. Chem. Phys. 114 (2001), 10189CrossRefADSGoogle Scholar
  68. 68.
    G. Caliskan, A. Kisliuk, A. Tsai, C. Soles, A.P. Sokolov, J. Chem. Phys. 118 (2003), 4230CrossRefADSGoogle Scholar
  69. 69.
    M.T. Cicerone, A. Tellington, L. Trost, A. Sokolov, Bioprocess Int. 1 (2003), 2Google Scholar
  70. 70.
    V. Reat, H. Patzelt, C. Pfister, M. Ferrand, D. Oesterhelt, G. Zaccai, PNAS USA 95 (1998), 4970CrossRefADSGoogle Scholar
  71. 71.
    A. Orecchini, A. Paciaroni, A.R. Bizzarri, S. Canistraro, J. Phys. Chem. B 106 (2002), 7348CrossRefGoogle Scholar
  72. 72.
    Information about the ILL-EMBL Deuteration Laboratory can be found on the web: www.ill.fr/deuterationGoogle Scholar
  73. 73.
    Y. Zhou, D. Vitkup, M. Karplus, J. Mol. Biol. 285 (1999), 1371CrossRefGoogle Scholar
  74. 74.
    S. Dellerue, A.J. Petrescu, J.C. Smith, M.C. Bellissent-Funel, Biophys. J. 81 (2001), 1666CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • A. P. Sokolov
    • 1
  • R. B. Gregory
    • 2
  1. 1.Department of Polymer ScienceThe University of AkronAkronUSA
  2. 2.Department of ChemistryKent State UniversityKentUSA

Personalised recommendations