Skip to main content
SpringerLink
Log in

Computational Studies of Protein Dynamics

  • Chapter
Water and Biomolecules

Part of the book series: Biological and Medical Physics, Biomedical ((BIOMEDICAL))

  • 825 Accesses

Abstract

Theoretical and computational studies of protein function have reached the point at which they are making important contributions to drug discovery and other practical applications. At the same time, they are deepening our understanding of the principles of protein activity, including the dynamical features that give rise to NMR and other experimental measurements, and the time-dependent aspects of biological function.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. S.A. Adcock, J.A. McCammon, Chem. Revs. 106, 1589 (2006)

    Article  CAS  Google Scholar 

  2. R.E. Amaro, R. Baron, J.A. McCammon, J. Comput. Aid. Mol. Des. 22, 693 (2008)

    Article  CAS  Google Scholar 

  3. Y. Bourne, P. Taylor, P. Marchot, Cell 83, 502 (1995)

    Article  Google Scholar 

  4. P.A. Carr, H.P. Erickson, A.G. Palmer, Structure 5, 949 (1997)

    Article  PubMed  CAS  Google Scholar 

  5. C.E. Chang, T. Shen, J. Trylska, V. Tozzini, J.A. McCammon, Biophys. J. 90, 3880 (2006)

    Article  PubMed  CAS  Google Scholar 

  6. V.P. Denisov, J. Peters, H.D. Horlein, B. Halle, Nat. Struct. Biol. 3, 505 (1996)

    Article  PubMed  CAS  Google Scholar 

  7. R.M. Dickson, A.B. Cubitt, R.Y. Tsien, W.E. Moerner, Nature 388, 355 (1997)

    Article  PubMed  CAS  Google Scholar 

  8. H. Frauenfelder, S.G. Sligar, P.G. Wolynes, Science 254, 1598 (1991)

    Article  PubMed  CAS  Google Scholar 

  9. A.A. Gorfe, C.E. Chang, I. Ivanov, J.A. McCammon, Biophys. J. 94, 1144 (2008)

    Article  PubMed  CAS  Google Scholar 

  10. A.A. Gorfe, B.J. Grant, J.A. McCammon, Structure 16, 885 (2008)

    Article  PubMed  CAS  Google Scholar 

  11. D. Hamelberg, J. Mongan, J.A. McCammon, J. Chem. Phys. 120, 11919 (2004)

    Article  PubMed  CAS  Google Scholar 

  12. D. Hamelberg, T. Shen, J.A. McCammon, J. Chem. Phys. 122, 241103 (2005)

    Article  PubMed  Google Scholar 

  13. D. Hamelberg, T. Shen, J.A. McCammon, J. Chem. Phys. 125, 094905 (2006)

    Article  PubMed  Google Scholar 

  14. Y.W. Jia, A. Sytnik, L.Q. Li, S. Vladimirov, B.S. Cooperman, R.M. Hochstrasser, Proc. Natl. Acad. Sci. USA 94, 7932 (1997)

    Article  PubMed  CAS  Google Scholar 

  15. H. Kojima, E. Muto, H. Higuchi, T. Yanagida, Biophys. J. 73, 2012 (1997)

    Article  PubMed  CAS  Google Scholar 

  16. S.J. Landry, N.K. Steede, K. Maskos, Biochemistry 36, 10975 (1997)

    Article  PubMed  CAS  Google Scholar 

  17. P.R.L. Markwick, G. Bouvignies, M. Blackledge, J. Am. Chem. Soc. 129, 4724 (2007)

    Article  PubMed  CAS  Google Scholar 

  18. J.A. McCammon, S.H. Northrup, Nature 293, 316 (1981)

    Article  PubMed  CAS  Google Scholar 

  19. W. Min, B.P. English, G. Luo, B.J. Cherayil, S.C. Kou, X.S. Xie, Acc. Chem. Res. 38, 923 (2005)

    Article  PubMed  CAS  Google Scholar 

  20. D.D.L. Minh, C.E. Chang, J. Trylska, V. Tozzini, J.A. McCammon, J. Am. Chem. Soc. 128, 6006 (2006)

    Article  PubMed  CAS  Google Scholar 

  21. W.W. Parson, Z.T. Chu, A. Warshel, Biophys. J. 74, 182 (1998)

    Article  PubMed  CAS  Google Scholar 

  22. T.D. Pollard, I. Goldberg, W.H. Schwarz, J. Biol. Chem. 267, 20339 (1992)

    PubMed  CAS  Google Scholar 

  23. M.R. Sawaya, J. Kraut, Biochemistry 36, 586 (1997)

    Article  PubMed  CAS  Google Scholar 

  24. J. Schames, R.H. Henchman, J.S. Siegel, C.A. Sotriffer, H. Ni, J.A. McCammon, J. Med. Chem. 47, 1879 (2004)

    Article  PubMed  CAS  Google Scholar 

  25. T. Shen, K. Tai, R.H. Henchman, J.A. McCammon, Acc. Chem. Res. 35, 332 (2002)

    Article  PubMed  CAS  Google Scholar 

  26. L.R. Solomon, P.A. Rubenstein, J. Biol. Chem. 262, 11382 (1987)

    PubMed  CAS  Google Scholar 

  27. D.A. Steinhauer, J. Martin, Y.P. Lin, S.A. Wharton, M.B.A. Oldstone, J.J. Skehel, D.C. Wiley, Proc. Natl. Acad. Sci. USA 93, 12873 (1996)

    Article  PubMed  CAS  Google Scholar 

  28. J.L. Sussman, M. Harel, F. Frolow, C. Oefner, A. Goldman, L. Toker, I. Silman, Science 253, 872 (1991)

    Article  PubMed  CAS  Google Scholar 

  29. D. Thorn Leeson, D.A. Wiersma, K. Fritsch, J. Friedrich, J. Phys. Chem. B 101, 6331 (1997)

    Article  Google Scholar 

  30. H. Ueno, T. Suzuki, K. Kinosita Jr., M. Yoshida, Proc. Natl. Acad. Sci. USA 102, 1333 (2005)

    Article  PubMed  CAS  Google Scholar 

  31. J. van Beek, R. Callender, M.R. Gunner, Biophys. J. 72, 619 (1997)

    Article  PubMed  Google Scholar 

  32. R.C. Wade, B.A. Luty, E. Demchuk, J.D. Madura, M.E. Davis, J.M. Briggs, J.A. McCammon, Nat. Struct. Biol. 1, 65 (1994)

    Article  PubMed  CAS  Google Scholar 

  33. S. Wennmalm, L. Edman, R. Rigler, Proc. Natl. Acad. Sci. USA 94, 10641 (1997)

    Article  PubMed  CAS  Google Scholar 

  34. S.T. Wlodek, T.W. Clark, L.R. Scott, J.A. McCammon, J. Am. Chem. Soc.119, 9513 (1997)

    Article  CAS  Google Scholar 

  35. P.G. Wolynes, Q. Rev. Biophys. 38, 405 (2005)

    Article  PubMed  CAS  Google Scholar 

  36. W. Wriggers, K. Schulten, Proteins 35, 262 (1999)

    Article  PubMed  CAS  Google Scholar 

  37. H.X. Zhou, J. Chem. Phys. 108, 8146 (1998)

    Article  CAS  Google Scholar 

  38. H.X. Zhou, Phys. Biol. 2, R1 (2005)

    Article  PubMed  CAS  Google Scholar 

  39. H.X. Zhou, S.T. Wlodek, J.A. McCammon, Proc. Natl. Acad. Sci. USA 95, 9280 (1998)

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Department of Pharmacology, Center for Theoretical Biological Physics, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093-0365, USA

    J. A. McCammon

Authors
  1. J. A. McCammon
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan

    Kunihiro Kuwajima

  2. Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Yuji Goto

  3. Institute for Molecular Science Department for Theoretical and Computational Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan

    Fumio Hirata

  4. Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-6 Takayama, Ikoma, Nara, 630-0192, Japan

    Mikio Kataoka

  5. Graduate School of Science, Department of Chemistry, Kyoto University, Oiwakecho, Kitashirakawa, Kyoto, 606-8502, Japan

    Masahide Terazima

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

McCammon, J.A. (2009). Computational Studies of Protein Dynamics. In: Kuwajima, K., Goto, Y., Hirata, F., Kataoka, M., Terazima, M. (eds) Water and Biomolecules. Biological and Medical Physics, Biomedical . Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88787-4_11

Download citation

Publish with us

Policies and ethics

Search

Navigation