Advertisement

The European Physical Journal D

, Volume 51, Issue 1, pp 33–40 | Cite as

Computer simulation of proteins: thermodynamics and structure prediction

  • J. H. Meinke
  • S. Mohanty
  • W. Nadler
  • O. Zimmermann
  • U. H.E. HansmannEmail author
Dynamics of Bio Macromolecules

Abstract

Over the last decade, computer simulations have become an increasingly important tool to study proteins. They now regularly complement experimental investigations and often are the only instrument to probe processes in the cell. Here, we summarize some of the algorithmic advances and review recent results that exemplify the progress over the last years. Our focus is on the thermodynamics and structure prediction of proteins, with information on the kinetics and dynamics inferred only indirectly.

PACS

87.15.Cc Folding and sequence analysis 87.15.Ak Monte Carlo simulations 87.15.-v Biomolecules: structure and physical properties 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. B.A. Berg, T. Neuhaus, Phys. Lett. B 267, 249 (1991)Google Scholar
  2. Z.W. Salsburg, J.D. Jacobson, W. Fickett, W.W. Wood, J. Chem. Phys. 30, 65 (1959)Google Scholar
  3. G.M. Torrie, J.P. Valleau, Chem. Phys. Lett. 28, 578 (1974)Google Scholar
  4. A.M. Ferrenberg, R.H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988); A.M. Ferrenberg, R.H. Swendsen, Phys. Rev. Lett. 63, 1603(E) (1089), and references given in that erratumGoogle Scholar
  5. U.H.E. Hansmann, Y. Okamoto, Physica A 212, 415 (1994)Google Scholar
  6. B.A. Berg, Comput. Phys. Commun. 153, 397 (2003)Google Scholar
  7. U.H.E. Hansmann, L.T. Wille, Phys. Rev. Lett. 88, 068105 (2002)Google Scholar
  8. C.J. Geyer, A. Thompson, J. Am. Stat. Assoc. 90, 909 (1995)Google Scholar
  9. K. Hukushima, K. Nemoto, J. Phys. Soc. (Jpn) 65, 1604 (1996)Google Scholar
  10. U.H.E. Hansmann, Chem. Phys. Lett. 281, 140 (1997)Google Scholar
  11. S. Trebst, D.A. Huse, M. Troyer, Phys. Rev. E 70, 046701 (2004)Google Scholar
  12. H.G. Katzgraber, S. Trebst, D.A. Huse, M. Troyer, J. Stat. Mech. Theor. Exp. P03018 (2006)Google Scholar
  13. S. Trebst, M. Troyer, U.H.E. Hansmann, J. Chem. Phys. 124, 174903 (2006)Google Scholar
  14. W. Nadler, U.H.E. Hansmann, Phys. Rev. E 75, 026109 (2007)Google Scholar
  15. D.A. Kofke, J. Chem. Phys. 117, 6911 (2002); Erratum: J. Chem. Phys. 120, 10852 (2004)Google Scholar
  16. C. Predescu, M. Predescu, C. Ciabanu, J. Chem. Phys. 120, 4119 (2004)Google Scholar
  17. D.A. Kofke, J. Chem. Phys. 121, 1167 (2004)Google Scholar
  18. A. Kone, D.A. Kofke, J. Chem. Phys. 122, 206101 (2005)Google Scholar
  19. W. Nadler, U.H.E. Hansmann, Phys. Rev. E 76, 065701R (2007)Google Scholar
  20. W. Nadler, U.H.E. Hansmann, Phys. Rev. E 76, 057102 (2007)Google Scholar
  21. Y. Sugita, Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999)Google Scholar
  22. W. Kwak, U.H.E. Hansmann, Phys. Rev. Lett. 95, 138102 (2005)Google Scholar
  23. J. Chen, W. Im, C.L. Brooks III, J. Comp. Chem. 26, 1565 (2005)Google Scholar
  24. J.M. Carr, D.J. Wales, J. Chem. Phys. 123, 234901 (2005)Google Scholar
  25. M. Nanias, M. Chinchio, J. Pillardy, D.R. Ripoll, H.A. Scheraga, Proc. Natl. Acad. Sci. USA 100, 1706 (2003)Google Scholar
  26. J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll, P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga, J. Phys. Chem. B 105, 7299 (2001)Google Scholar
  27. A. Verma, A. Schug, K.H. Lee, W. Wenzel, J. Chem. Phys. 124, 044515 (2006)Google Scholar
  28. A. Verma, W. Wenzel, J. Phys. Cond. Mat. 19, 285213 (2007)Google Scholar
  29. D. Gront, A. Kolinski, U.H.E. Hansmann, Int. J. Quant. Chem. 105, 826 (2005)Google Scholar
  30. U.H.E. Hansmann, Y. Okamoto, J. Chem. Phys. 110, 1267 (1999)Google Scholar
  31. F. Eisenmenger, U.H.E. Hansmann, S. Hayryan, C.-K. Hu, Comput. Phys. Commun. 138, 192 (2001)Google Scholar
  32. F. Eisenmenger, U.H.E. Hansmann, S. Hayryan, C.-K. Hu, Comput. Phys. Commun. 174, 422 (2006)Google Scholar
  33. J.H. Meinke, S. Mohanty, F. Eisenmenger, U.H.E. Hansmann, Comput. Phys. Commun. DOI:10.1016/j.cpc.2007.11.004. Google Scholar
  34. G. Nemethy, K.D. Gibson, K.A. Palmer, C.N. Yoon, G. Paterlini, A. Zagari, S. Rumsey, H.A. Scheraga, J. Phys. Chem. 96, 6472 (1992)Google Scholar
  35. T. Ooi, M. Oobatake, G. Nemethy, H.A. Scheraga, Proc. Natl. Acad. Sci. USA 84 3086 (1987)Google Scholar
  36. B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, D. Baker, Science 302, 1364 (2003)Google Scholar
  37. J.D. Bryngelson, P.G. Wolynes, Proc. Natl Acad. Sci. USA 84, 7524 (1987)Google Scholar
  38. J.N. Onuchic, Z. Luhey-Schulten, P.G. Wolynes, Ann. Rev. Phys. Chem. 48, 545 (1997)Google Scholar
  39. K.A. Dill, H.S. Chan, Nat. Struct. Biol. 4, 10 (1997)Google Scholar
  40. E.I. Shakhnovitch, Curr. Opin. Struc. Biol. 7, 29 (1997)Google Scholar
  41. T. Veitshans, D. Klimov, D. Thirumalai, Fold. Des. 2, 1 (1997)Google Scholar
  42. T. Herges, W. Wenzel, Structure 13, 661 (2005)Google Scholar
  43. P. Pokarowski, A. Kolinski, J. Skolnick, Biophys. J. 84, 1518 (2003)Google Scholar
  44. A. Liwo, P. Arukowicz, C. Czaplewski, S. Oldziej, J. Pillardi, H.A. Scheraga, Proc. Natl. Acad. Sci. USA 99, 1937 (2002)Google Scholar
  45. D.A. Evans, D.J. Wales, J. Chem. Phys. 121, 1080 (2004)Google Scholar
  46. K.W. Plaxco, K.T. Simons, D. Baker, J. Mol. Biol. 277, 985 (1998)Google Scholar
  47. D.E. Kim, H. Gu, D. Baker, Proc. Natl. Acad. Sci. USA 95, 4982 (1998)Google Scholar
  48. A. Matouschek, J. Kellis Jr, L. Serrano, A.R. Fersht, Nature 340, 122 (1989)Google Scholar
  49. D. Baker, Nature 405, 39 (2000)Google Scholar
  50. A. Zarrine-Afsar, S.M. Larson, A.R. Davidson, Curr. Opin. Struct. Biol. 15, 42 (2005)Google Scholar
  51. C. Simmerling, B. Strockbine, A.E. Roitberg, J. Am. Chem. Soc. 124, 11258 (2002)Google Scholar
  52. S. Mohanty, U.H.E. Hansmann, Biophys. J. 92, 3573 (2006)Google Scholar
  53. R. Zhou, B.J. Berne, R. Germain, Proc. Natl. Acad. Sci. USA 98, 14931 (2001)Google Scholar
  54. W.Y. Yang, J.W. Pitera, W.C. Swope, M. Gruebele, J. Mol. Biol. 336, 241 (2004)Google Scholar
  55. W. Wenzel, Europhys. Lett. 76, 156 (2006)Google Scholar
  56. X. Wu, B.R. Brooks, Biophys. J. 86, 1946 (2004)Google Scholar
  57. S. Mohanty, U.H.E. Hansmann, Phys. Rev. E 76, 1539 (2007)Google Scholar
  58. S. Mohanty, J. Meinke, O. Zimmermann, U.H.E. Hansmann, Proc. Natl. Acad. Sci. USA, DOI: 10.1073/pnas.0708411105 Google Scholar
  59. D. Hamada, S. Segawa, Y. Goto, Nat. Struct. Biol. 3, 868 (1996)Google Scholar
  60. K. Kuwata, M. Hoshino, S. Era, C.A. Batt, Y. Goto, J. Mol. Biol. 283, 731 (1998)Google Scholar
  61. K. Kuwata, R. Shastry, H. Cheng, M. Hoshino, C.A. Batt, Y. Goto, H. Roder, Nat. Struct. Biol. 8, 151 (2001)Google Scholar
  62. G. Chikenji, M. Kikuchi, Proc. Natl. Acad. Sci. USA 97, 14273 (2000)Google Scholar
  63. G. Chikenji, Y. Fujitsukab, S. Takada, Chem. Phys. 307, 157 (2004)Google Scholar
  64. S.S. Plotkin, Protein Struct. Func. Genet. 45, 337 (2001)Google Scholar
  65. J. Shimada, E. Kussell, E.I. Shakhnovich, J. Mol. Biol. 308, 79 (2001)Google Scholar
  66. E. Kussell, E.I. Shakhnovich, Phys. Rev. Lett. 89, 168101 (2002)Google Scholar
  67. Y. Wei, W. Nadler, U.H.E. Hansmann, J. Chem. Phys. 125, 164902 (2006)Google Scholar
  68. Y. Wei, W. Nadler, U.H.E. Hansmann, J. Phys. Chem. B 111, 4244 (2007)Google Scholar
  69. Y. Wei, W. Nadler, U.H.E. Hansmann, J. Chem. Phys. 126, 204307 (2007)Google Scholar
  70. P. Dugourd, R.R. Hudgins, D.E. Clemmer, M.F. Jarrold, Rev. Sci. Instrum. 68, 1122 (1997)Google Scholar
  71. R.R. Hudgins, J. Woenckhaus, M.F. Jarrold, Int. J. Mass. Spectrom. Ion. Proc. 165/166, 497 (1997)Google Scholar
  72. M. Kohtani, J.E. Schneider, T.C. Jones, M.F. Jarrold, J. Am. Chem. Soc. 126, 16981 (2004)Google Scholar
  73. M. Kohtani, M.F. Jarrold, J. Am. Chem. Soc. 126, 8454 (2004)Google Scholar
  74. B.S. Kinnear, D.T. Kaleta, M. Kohtani, R.R. Hudgins, M.F. Jarrold, J. Am. Chem. Soc. 122, 9243 (2000)Google Scholar
  75. C.J. McKnight, P.T. Matsudaira, P.S. Kim, Nat. Struct. Biol. 4, 180 (1997)Google Scholar
  76. Y. Wei, W. Nadler, U.H.E. Hansmann, J. Chem. Phys. 128, 025105 (2008)Google Scholar
  77. H. Lei, C. Wei, H. Liu, Y. Duan, Proc. Natl. Acad. Sci. USA 104, 4930 (2007)Google Scholar
  78. G.M.S. De Mori, G. Colombo, M. Micheletti, Proteins 58, 459 (2005)Google Scholar
  79. G. Jayachandran, V. Vishal, V.S. Pande, J. Chem. Phys. 124, 164902 (2006)Google Scholar
  80. J. Kubelka, W.A. Eaton, J. Hofrichter, J. Mol. Biol. 329, 625 (2003)Google Scholar
  81. A. Irbäck, S. Mohanty, J. Comput. Chem. 27, 1548 (2006)Google Scholar
  82. A. Irbäck, S. Mohanty, Biophys. J. 88, 1560 (2005)Google Scholar
  83. J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, T. Hubbard, A. Tramontano, Proteins 69, 3 (2007)Google Scholar
  84. K.T. Simons, C. Kooperberg, E. Huang, D. Baker, J. Mol. Biol. 268, 209225 (1997)Google Scholar
  85. Y. Zhang, Proteins S8, 108 (2007)Google Scholar
  86. A. Kolinski, Acta Biochim. Pol. 51, 349 (2004)Google Scholar
  87. Y. Zhang, A. Kolinski, J. Skolnick, Biophys. J. 85, 1145 (2003)Google Scholar
  88. Y. Zhang, D. Kihara, J. Skolnick, Proteins 48, 192 (2002)Google Scholar
  89. A. Verma, W. Wenzel, From Computational Biophysics to Systems Biology (CBSB07), edited by H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann, NIC Series, Vol. 36 (2007) pp. 283–286Google Scholar
  90. Y.I. Wolf, N.V. Grishin, E.V. Koonin, J. Mol. Biol. 299, 897 (2000)Google Scholar
  91. Y. Zhang, I.A. Hubner, A.K. Arakaki, E. Shakhnovich, J. Skolnick, Proc. Natl. Acad. Sci. USA 103, 2605 (2006)Google Scholar
  92. W.W. Chen, J.S. Yang, E.I. Shakhnovich, Proteins 66, 682 (2007)Google Scholar
  93. D.T. Jones, J. Mol. Biol. 292, 195 (1999)Google Scholar
  94. W. Kabsch, C. Sander, Biopolymers 22, 2577 (1983)Google Scholar
  95. M.J. Wood, J.D. Hirst, Proteins 59, 476 (2005)Google Scholar
  96. O. Dor, Y. Zhou, Proteins 68, 76 (2007)Google Scholar
  97. O. Zimmermann, U.H.E. Hansmann, Bioinformatics 22, 3009 (2006)Google Scholar
  98. B. Schökopf, A.J. Smola, Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond (MIT Press, Cambridge, MA, 2002)Google Scholar
  99. O. Zimmermann, L. Wang, U.H.E. Hansmann, In Silico Biol. 7, 0037 (2007)Google Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • J. H. Meinke
    • 1
  • S. Mohanty
    • 1
  • W. Nadler
    • 1
  • O. Zimmermann
    • 1
  • U. H.E. Hansmann
    • 2
    Email author
  1. 1.John-von-Neumann Institute for ComputingJülichGermany
  2. 2.Department of PhysicsMichigan Technological UniversityHoughtonU.S.A.

Personalised recommendations