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Molecular Simulations of Protein Structure, Dynamics and Thermodynamics

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Computer Modelling of Fluids Polymers and Solids

Part of the book series: NATO ASI Series ((ASIC,volume 293))

Abstract

Proteins display a rich variety of structural, dynamic and chemically functional character. It is the wide range of chemical functionality provided by the twenty amino acids composing proteins which is responsible for the importance of these macromolecules in biology. The chemical nature of protein function is controlled by the structural arrangement and motions of chemically labile groups. Thus, the detailed investigation of the motions and structure of a single protein molecule is of importance in understanding the reactive nature of protein chemistry.

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References

  1. J. A. McCammon, B. R. Gelin and M. Karplus, Nature 267, 585 (1977).

    Article  ADS  Google Scholar 

  2. B. J. Alder and T. E. Wainright, J. Chem. Phys. 31, 459 (1959).

    Article  MathSciNet  ADS  Google Scholar 

  3. A. Rahman, Phys. Rev. A136, 405 (1964).

    Article  ADS  Google Scholar 

  4. J. A. McCammon and M. Karplus, Proc. Natl. Acad. Sci. USA 76, 3585 (1979).

    Article  ADS  Google Scholar 

  5. J. A. McCammon and M. Karplus, Biopolymers 19, 1375 (1980).

    Article  Google Scholar 

  6. S. H. Northrup, M. R. Pear, C. Y. Lee, J. A. McCammon and M. Karplus, Proc. Natl. Acad. Sci. USA 79, 4035 (1982).

    Article  ADS  Google Scholar 

  7. C. L. Brooks III, M. Karplus and B. M. Pettitt, Proteins: A Theoretical Perspective on Structure Dynamics and Thermodynamics, complete volume in Adv. Chem. Phys., 71 (1988).

    Google Scholar 

  8. J. A. McCammon and S. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press (1987).

    Google Scholar 

  9. C. L. Brooks III and M. Karplus, Methods in Enzymology 127, 369 (1986).

    Article  Google Scholar 

  10. G. Careri, P. Fasella and E. Gratton, Ann. Rev. Biophys. Bioeng. 8, 69 (1979).

    Article  Google Scholar 

  11. J. A. McCammon and M. Karplus, Ann. Rev. Phys. Chem. 31, 29 (1980).

    Article  ADS  Google Scholar 

  12. M. Karplus and J. A. McCammon, Ann. Rev. Biochem. 53, 263 (1983).

    Article  Google Scholar 

  13. M. Levitt, Ann. Rev. Biophys. Bioeng. 11, 251 (1982).

    Article  Google Scholar 

  14. W. van Gunsteren and H. J. C. Berendsen, Biochem. Soc. Trans. 10, 301 (1982).

    Google Scholar 

  15. O. Edholm, L. Nilsson, O. Bery, M. Elnenberg, F. Closens, A. Gräslund, B. Jönsson and O. Teleman, Reviews of Biophysics, 17, 125 (1984).

    Article  Google Scholar 

  16. R. M. Levy, R. P. Sheridan, J. W. Keepers, G. S. Dubey, S. Swaminathan and M. Karplus, Biophys. J. 48, 509 (1985).

    Article  Google Scholar 

  17. R. M. Levy, M. Karplus and J. A. McCammon, J. Am. Chem. Soc. 103, 994 (1981).

    Article  Google Scholar 

  18. T. Ichiye and M. Karplus, Biochemistry 2, 2884 (1982).

    Google Scholar 

  19. J. Kuriyan, G. Petsko, R. M. Levy and M. Karplus, J. Mol. Biol. 190, 227 (1986).

    Article  Google Scholar 

  20. A. T. Brünger, J. Kuriyan and M. Karplus, Science, 235, 459 (1987).

    ADS  Google Scholar 

  21. J. A. Pople, B. T. Luke, M. J. Frisch and J. S. Binkley, J. Phys. Chem. 89, 2198 (1985).

    Article  Google Scholar 

  22. See, for example, J-K. Hwang, E. King, S. Creighton and A. Wonshal, J. Am. Chem. Soc, 110, 5297 (1988).

    Article  Google Scholar 

  23. U. Burkhart and N. L. Allinger, Molecular Mechanics (Am. Chem. Soc, Washington, D.C., 1982).

    Google Scholar 

  24. B. R. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan and M. Karplus, J. Comp. Chem. 4, 187 (1983).

    Article  Google Scholar 

  25. S. J. Weiner, P. Kollman, D. T. Nuguyen and D. Case, J. Comp. Chem. 7, 230 (1986).

    Article  Google Scholar 

  26. A. Dwivedi and S. Krimm, Biopolymers, 23, 923 (1984).

    Article  Google Scholar 

  27. A. T. Hagler, D. J. Osguthorpe, P. Dauber-Osguthorpe and J. C. Hempel, Science 227, 1309 (1985).

    Article  ADS  Google Scholar 

  28. K. D. Gibson, H. A. Scheraga, Proc. Nat. Acad. Sci, USA 58, 420 (1967);

    Article  ADS  Google Scholar 

  29. L. Dunfield, A. Burgess and H. Scheraga, J. Phys. Chem. 82, 2609 (1978).

    Article  Google Scholar 

  30. A. J. Stone and S. L. Price, J. Phys. Chem., 92, 3325 (1988).

    Article  Google Scholar 

  31. W. Jorgensen, J. Am. Chem. Soc. 103, 335 (1981)

    Article  Google Scholar 

  32. W. Jorgensen, J. Am. Chem. Soc. 103, 341 (1981).

    Article  Google Scholar 

  33. C. Singh and P. A. Kollman, J. Comp. Chem., 5, 129 (1984).

    Article  Google Scholar 

  34. L. Chirlian and M. Frank, J. Comp. Chem., 8, 894 (1987).

    Article  Google Scholar 

  35. B.R. Brooks. Supercomputer Research in Chemistry and Chemical Engineering, editors, Kutensen and B. Truhlar, Chap. 8 (1987).

    Google Scholar 

  36. C.L. Brooks, B.M. Pettitt and M. Karplus, J. Chem. Phys., 83, 5897 (1985)

    Article  ADS  Google Scholar 

  37. A. Brünger, C. L. Brooks III and M. Karplus, Chem. Phys. Lett. 105, 495 (1984).

    Article  ADS  Google Scholar 

  38. C. L. Brooks III, A. Brünger and M. Karplus, Biopolymers 24, 434 (1985).

    Article  Google Scholar 

  39. L. Verlet, Phys. Rev. 159, 98 (1967).

    Article  ADS  Google Scholar 

  40. R. W. Hockney and J. W. Easfwasel, Computer Simulations Using Particles (McGraw Hill, New York, 1981).

    Google Scholar 

  41. D. Beeman, J. Comp. Phys. 20, 130 (1976).

    Article  ADS  Google Scholar 

  42. H. C. Andersen, J. Chem. Phys. 72, 2384 (1980).

    Article  ADS  Google Scholar 

  43. S. Nose, J. Chem. Phys., 81, 511 (1984);

    Article  ADS  Google Scholar 

  44. W. G. Hoover, Phys. Rev. A, 31, 1695 (1985);

    Article  ADS  Google Scholar 

  45. D. J. Evans and B.L. Hollan, J. Chem. Phys., 83, 4069 (1985).

    Article  ADS  Google Scholar 

  46. D.J. Evans and G.P. Morris, Chem. Phys., 77, 63 (1983).

    Article  ADS  Google Scholar 

  47. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).

    Article  ADS  Google Scholar 

  48. M. Ferrano and J. P. Rychaert, Mol. Phys., 54, 587 (1985).

    Article  ADS  Google Scholar 

  49. B. M. Pettitt and M. Karplus, Chem. Phys. Lett. 121, 194 (1985).

    Article  ADS  Google Scholar 

  50. S. A. Adelman, Adv. Chem. Phys. 53, 62 (1984).

    Google Scholar 

  51. R. Pastor, B. R. Brooks and A. Szabo, Mol. Phys., to be published.

    Google Scholar 

  52. C. L. Brooks III and M. Karplus, J. Mol. Biol., 208, 159 (1989).

    Article  Google Scholar 

  53. C. L. Brooks III and M. Karplus, J. Chem. Phys. 79, 6312 (1983).

    Article  ADS  Google Scholar 

  54. W. van Gunsteren and M. Karplus, Biochemistry 21, 2259 (1982).

    Article  Google Scholar 

  55. H. Yu and M. Karplus, unpublished results.

    Google Scholar 

  56. H. J. C. Berendesen, W. F. van Gunsteren, H. R. S. Zwindermann and R. G. Geurten, Ann. NY Acad. Sci., 482, 269 (1986).

    Article  ADS  Google Scholar 

  57. W. F. van Gunsteren and H. J. C. Berendsen, J. Mol. Biol. 176, 559 (1984).

    Article  Google Scholar 

  58. T. Head-Gordon and C. L. Brooks III, unpublished results.

    Google Scholar 

  59. T. Ichiye and M. Karplus, Proteins, 2, 236 (1987).

    Article  Google Scholar 

  60. A. Brünger, C.L. Brooks III and M. Karplus, Proc. Natl. Acad. Sci., 82, 8456 (1985).

    Article  ADS  Google Scholar 

  61. C. L. Brooks III, A. T. Brünger, M. France, K. Haydock, L. C. Allen and M. Karplus, International Symposium on Bioorganic Chemistry editor R. Breslow (The New York Academy of Sciences, 1986) p. 295.

    Google Scholar 

  62. G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4546 (1982).

    Article  Google Scholar 

  63. L. X. Q. Chen, R. A. Eugh, A. T. Brunger, D. T. Nguyen, M. Karplus and G. R. Fleming, Biochemistry, 27, 6908 (1988).

    Article  Google Scholar 

  64. M. Mezei and D. L. Beveridge, Annals NY Acad. Sci., 483, 1(1986).

    Article  ADS  Google Scholar 

  65. S. H. Fleischman and C. L. Brooks III, J. Chem. Phys., 87, 3029(1987).

    Article  ADS  Google Scholar 

  66. W. L. Jorgensen and C. Ravimohan, J. Chem. Phys., 83, 3050 (1985).

    Article  ADS  Google Scholar 

  67. P. A. Bash, U. C. Singh, F. K. Brown, R. Language and P. A. Kollman, Science, 235, 574 (1987);

    Article  ADS  Google Scholar 

  68. b) U. C. Singh, F. K. Brown, P. A. Bash and P. A. Kollman, J. Am. Chem. Soc, 109, 1607 (1987).

    Article  Google Scholar 

  69. C. F. Wong and J. A. McCammon, J. Am. Chem. Soc., 108, 3830 (1986);

    Article  Google Scholar 

  70. b) T. P. Lybrand, J. A. McCammon and G. Wipff, Proc. Natl. Acad.Sci. USA, 83, 833 (1986).

    Article  ADS  Google Scholar 

  71. S. H. Fleischman and C. L. Brooks III, Proteins, to be published.

    Google Scholar 

  72. R. W. Zwanzig, J. Chem. Phys., 22, 1420 (1954).

    Article  ADS  Google Scholar 

  73. B. L. Tembe and J. A. McCammon, Comput. Chem., 8, 281 (1984).

    Article  Google Scholar 

  74. S. H. Fleischman, B. Tidor, C. L. Brooks III and M. Karplus, J. Comp.Chem., manuscript in preparation.

    Google Scholar 

  75. C. L. Brooks III, J. Phys. Chem., 90, 6680 (1986); b) There were typographical errors in equations 8 and 9 of the above reference, the corrected relationships are given in equations 25 and 26 of the present paper.

    Article  Google Scholar 

  76. C. Singh, Proc Natl. Acad. Sci., 85, 4280 (1988).

    Article  ADS  Google Scholar 

  77. D. J. Tobias and C. L. Brooks III, Chem. Phys. Lett., 142, 472(1987);

    Article  ADS  Google Scholar 

  78. D. J. Tobias and C. L. Brooks III, J. Chem. Phys., 89, 5115 (1988);

    Article  ADS  Google Scholar 

  79. D. J. Tobias, C. L. Brooks III and S. H. Fleischman, Chem. Phys. Lett. 156, 256 (1989)

    Article  ADS  Google Scholar 

  80. C.L. Brooks III, Intl. J. Quant. Chem., proceedings from the Sanibel Symposium, 15, 221 (1988).

    Article  MathSciNet  Google Scholar 

  81. A. Ben-Naim and Y. Marcus, J. Chem. Phys., 81, 2016 (1984);

    Article  ADS  Google Scholar 

  82. S. F. Dec and S. J. Gill, J. Solution Chem., 13, 27 (1984).

    Article  Google Scholar 

  83. J. Smith and M. Karplus, J. Comp. Chem., to be submitted.

    Google Scholar 

  84. W. L. Jorgensen, J. D. Madura and C. J. Swenson, J. Am. Chem. Soc., 106, 6638 (1984).

    Article  Google Scholar 

  85. W. Mendenhall, Introduction to Probability and Statistics, Duxbury Press, North Scituate, Massachusetts, 1975.

    Google Scholar 

  86. C.F. Wong and J.A. McCammon, Isr. J. Chem., 27, 211 (1986).

    Google Scholar 

  87. D. A. Matthews, J. T. Bolin, J. M. Burridge, D. J. Filman, K. W. Volz, B. T. Kaufman, C. R. Beddell, J. M. Champness, D. K. Stammers and J. Kraut, J. Biol. Chem., 280, 381 (1985);

    Google Scholar 

  88. D. A. Matthews, J. T. Bolin, J. M. Burridge, D. J. Filman, K. W. Volz and J. Kraut, J. Biol. Chem., 280, 392 (1985).

    Google Scholar 

  89. D. J. Tobias and C. L. Brooks III, work in progress.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA

    Charles L. Brooks III

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  1. Charles L. Brooks III
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Editor information

Editors and Affiliations

  1. Davy Faraday Research Laboratory, The Royal Institution, London, UK

    C. R. A. Catlow

  2. Department of Chemistry, University of Bath, Bath, UK

    S. C. Parker

  3. H.H. Wills Physics Laboratory, University of Bristol, Bristol, UK

    M. P. Allen

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© 1990 Kluwer Academic Publishers

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Brooks, C.L. (1990). Molecular Simulations of Protein Structure, Dynamics and Thermodynamics. In: Catlow, C.R.A., Parker, S.C., Allen, M.P. (eds) Computer Modelling of Fluids Polymers and Solids. NATO ASI Series, vol 293. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-2484-0_12

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  • DOI: https://doi.org/10.1007/978-94-009-2484-0_12

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-7621-0

  • Online ISBN: 978-94-009-2484-0

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