Advertisement

Proteins Studied by Computer Simulations

  • Ulrich H. E. Hansmann
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7125)

Abstract

Computer simulations can complement experiments in molecular biology; and are sometimes the only instrument to probe fundamental processes in the cell. However, their use is hampered by poor convergence. I summarize a number of now widely utilized algorithms that help to alleviate these sampling difficulties, and review recent results that demonstrate the power of these techniques in protein simulations.

Keywords

Root Mean Square Deviation Exchange Move Menkes Disease Parallel Tempering Replica Exchange 
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.
    Banci, L., Bertini, I., Cantini, F., Migliardi, M., Rosato, A., Wang, S.: J. Mol. Biol. 352, 409–417 (2005)CrossRefGoogle Scholar
  2. 2.
    Berg, B.A., Neuhaus, T.: Phys. Lett. B267, 249–253 (1991)CrossRefGoogle Scholar
  3. 3.
    Buchete, N.V., Hummer, G.: Biophysical Journal 92, 3032–3039 (2007)CrossRefGoogle Scholar
  4. 4.
    Cannon, M.J., Williams, A.D., Wetzel, R., Myszka, D.J.: Anal. Biochem.  328, 67–75 (2004)Google Scholar
  5. 5.
    Chikenji, G., Fujitsukab, Y., Takada, S.: Chem. Phys.  307, 157–162 (2004)Google Scholar
  6. 6.
    Chikenji, G., Kikuchi, M.: Proc. Natl. Acad. Sci. USA 97, 14273–14277 (2000)CrossRefGoogle Scholar
  7. 7.
    Esler, W.P., Stimson, E.R., Jennings, J.M., Vinters, H.V., Ghilardi, J.R., Lee, J.P., Manthy, P.W., Maggio, J.E.: Biochemistry 39, 6288–6295 (2000)CrossRefGoogle Scholar
  8. 8.
    Ferrenberg, A.M., Swendsen, R.H.: Phys. Rev. Lett. 61, 2635–2638 (1988); Phys. Rev. Lett. 63, 1195–1198 (1989)CrossRefGoogle Scholar
  9. 9.
    Hamada, D., Segawa, S., Goto, Y.: Nat. Struc. Biol. 3, 868–873 (1996)CrossRefGoogle Scholar
  10. 10.
    Han, M., Hansmann, U.H.E.: J. Chem. Phys. 135, 065101 (2011)CrossRefGoogle Scholar
  11. 11.
    Hansmann, U.H.E.: Computers in Science and Engineering 5, 64–69 (2003)Google Scholar
  12. 12.
    Hansmann, U.H.E.: Chem. Phys. Lett.  281, 140–150 (1997)Google Scholar
  13. 13.
    Hansmann, U.H.E., Okamoto, Y.: The Generalized-Ensemble Approach for Protein Folding Simulations. In: Stauffer, D. (ed.) Annual Reviews of Computational Physics, vol. VI, pp. 129–157. World Scientific, Singapore (1999)Google Scholar
  14. 14.
    Hansmann, U.H.E., Okamoto, Y.: Physica A  212, 415–437 (1994)Google Scholar
  15. 15.
    Hansmann, U.H.E., Wille, L.T.: Phys. Rev. Lett. 88, 68105 (2002)CrossRefGoogle Scholar
  16. 16.
    Hukushima, K., Nemoto, K.: J. Phys. Soc. (Japan) 65, 1604–1608 (1996); Geyer, G.J., Thompson, E.A.: J. Am. Stat. Assn 90 (431), 909–920 (1995)Google Scholar
  17. 17.
    Kar, P., Nadler, W., Hansmann, U.H.E.: Phys. Rev. E 80, 056703 (2009)CrossRefGoogle Scholar
  18. 18.
    Kouza, M., Gowtham, S., Seel, M., Hansmann, U.H.E.: Physical Chemistry – Chemical Physics 12, 11390 (2010)CrossRefGoogle Scholar
  19. 19.
    Kouza, M., Hansmann, U.H.E.: J. Chem. Phys 134, 044124 (2011)CrossRefGoogle Scholar
  20. 20.
    Kuwata, K., Hoshino, M., Era, S., Batt, C.A., Goto, Y.: J. Mol. Biol. 283, 731–739 (1998)CrossRefGoogle Scholar
  21. 21.
    Kuwata, K., Shastry, R., Cheng, H., Hoshino, M., Batt, C.A., Goto, Y., Roder, H.: Nat. Struc. Biol. 8, 151–155 (2001)CrossRefGoogle Scholar
  22. 22.
    Kwak, W., Hansmann, U.H.E.: Phys. Rev. Lett. 95, 138102 (2005)CrossRefGoogle Scholar
  23. 23.
    Laio, A., Parrinello, M.: Proc. Natl. Acad. Sci. USA 99, 12562–12566 (2002)CrossRefGoogle Scholar
  24. 24.
    Lutsenko, S., Petrukhin, K., Cooper, M.J., Gilliam, C.T., Kaplan, J.H.: J. Biol. Chem. 272, 18939–18944 (1997)CrossRefGoogle Scholar
  25. 25.
    Lührs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Döbeli, H., Schubert, D., Riek, R.: Proc. Natl. Acad. Sci. USA 102, 17342–17347 (2005)CrossRefGoogle Scholar
  26. 26.
    Menkes, J.H., Alter, M., Steigleder, G.K., Weakley, D.R., Sung, J.H.: Pediatrics 29, 764–779 (1962)Google Scholar
  27. 27.
    Mohanty, S., Meinke, J.H., Zimmermann, O., Hansmann, U.H.E.: Proc. Nat. Acad. Sci. USA 105, 8004–8008 (2008)CrossRefGoogle Scholar
  28. 28.
    Nadler, W., Hansmann, U.H.E.: Phys. Rev. E 75, 026109 (2007)CrossRefGoogle Scholar
  29. 29.
    Nadler, W., Hansmann, U.H.E.: Phys. Rev. E. 76, 057102 (2007)CrossRefGoogle Scholar
  30. 30.
    Okur, A., Wickstrom, L., Layten, M., Geney, R., Song, K., Hornak, V., Simmerling, C.: J. Chem. Theory Comput. 2, 420–424 (2006)CrossRefGoogle Scholar
  31. 31.
    Peng, Y., Hansmann, U.H.E.: Helix versus sheet formation in a small peptide. Phys. Rev. E 68, 041911 (2000)CrossRefGoogle Scholar
  32. 32.
    Petkova, A.T., Buntkowsky, G., Dyda, F., Leapman, R.D., Yau, W.M., Tycko, R.: J. Mol. Biol. 335, 247–260 (2004)Google Scholar
  33. 33.
    Plotkin, S.S.: Protein Struct. Func. Genet. 45, 337–345 (2001)CrossRefGoogle Scholar
  34. 34.
    Puig, S., Thiele, D.J.: Curr. Opin. Chem. Biol. 6, 171–180 (2002)CrossRefGoogle Scholar
  35. 35.
    Scheraga, H.A., Khalili, M., Liwo, A.: Annual Review of Physical Chemistry 58, 57–83 (2007)CrossRefGoogle Scholar
  36. 36.
    Trebst, S., Troyer, M., Hansmann, U.H.E.: J. Chem. Phys. 124, 174903 (2006)CrossRefGoogle Scholar
  37. 37.
    Tumer, Z., Lund, C., Tolshave, J., Vural, B., Tonnesen, T., Horn, N.: Am. J. Hum. Genet. 60, 63–71 (1997)Google Scholar
  38. 38.
    Vulpe, C.D., Levinson, B., Whitney, S., Packman, S., Gitschier, J.: Nature Genet. 3, 7–13 (1993)CrossRefGoogle Scholar
  39. 39.
    Wang, J., Zhu, W., Li, G., Hansmann, U.H.E.: J. Chem. Phys. 135, 084115 (2011)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Ulrich H. E. Hansmann
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of OklahomaNormanUSA

Personalised recommendations