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Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

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Abstract

A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Moreover, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.

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References

  1. J. Randall, H.D. Middendorf, H.L. Crespi, A.D. Taylor, Nature 276, 636 (1978).

    Article  ADS  Google Scholar 

  2. B. Jacrot, S. Cusack, A.J. Dianoux, D.M. Engelman, Nature 300, 84 (1982).

    Article  ADS  Google Scholar 

  3. A.J.D.D.M. Engelman, S. Cusack, B. Jacrot, Basic Life Sci. 27, 365 (1984).

    Google Scholar 

  4. J.C. Smith, S. Cusack, P. Poole, J. Finney, J. Biomol. Struct. Dyn. 4, 583 (1987).

    Article  Google Scholar 

  5. J.C. Smith, S. Cusack, U. Pezzeca, B. Brooks, M. Karplus, J. Chem. Phys. 85, 3636 (1986).

    Article  ADS  Google Scholar 

  6. J.C. Smith, S. Cusack, B. Tidor, M. Karplus, J. Chem. Phys. 93, 2974 (1990).

    Article  ADS  Google Scholar 

  7. S. Cusack, J.C. Smith, J. Finney, B. Tidor, M. Karplus, J. Mol. Biol. 202, 903 (1988).

    Article  Google Scholar 

  8. W. Doster, S. Cusack, W. Petry, Nature 337, 754 (1989).

    Article  ADS  Google Scholar 

  9. F. Parak, E.N. Frolov, R.L. Mossbauer, V.I. Goldanskii, J. Mol. Biol. 145, 825 (1981).

    Article  Google Scholar 

  10. J.C. Smith, K. Kuczera, M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 87, 1601 (1990).

    Article  ADS  Google Scholar 

  11. M. Ferrand, A.J. Dianoux, W. Petry, G. Zaccai, Proc. Natl. Acad. Sci. U.S.A. 90, 9668 (1993).

    Article  ADS  Google Scholar 

  12. V. Reat, H. Patzelt, M. Ferrand, C. Pfister, D. Oesterhelt, G. Zaccai, Proc. Natl. Acad. Sci. U.S.A. 95, 4970 (1998).

    Article  ADS  Google Scholar 

  13. K. Wood, U. Lehnert, B. Kessler, G. Zaccai, D. Oesterhelt, Biophys. J. 95, 194 (2008).

    Article  Google Scholar 

  14. L. Cordone, M. Ferrand, E. Vitrano, G. Zaccai, Biophys. J. 76, 1043 (1999).

    Article  Google Scholar 

  15. G. Zaccai, Science 288, 1604 (2000).

    Article  ADS  Google Scholar 

  16. Y.T. Lee, R.F. Wilson, I. Rupniewski, D.B. Goodin, Biochemistry-Us 49, 3412 (2010).

    Article  Google Scholar 

  17. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 26, 1781 (2005).

    Article  Google Scholar 

  18. Y. Miao, J. Baudry, Biophys. J. 101, 1493 (2011).

    Article  ADS  Google Scholar 

  19. Z. Yi, Y.L. Miao, J. Baudry, N. Jain, J.C. Smith, J. Phys. Chem. B 116, 5028 (2012).

    Article  Google Scholar 

  20. Y. Miao, Z. Yi, C. Cantrell, D. Glass, J. Baudry, N. Jain, J.C. Smith, Biophys. J. 103, 2167 (2012).

    Article  ADS  Google Scholar 

  21. Y. Miao, Z. Yi, D.C. Glass, L. Hong, M. Tyagi, J. Baudry, N. Jain, J.C. Smith, J. Am. Chem. Soc. 134, 19576 (2012).

    Article  Google Scholar 

  22. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys. 103, 8577 (1995).

    Article  ADS  Google Scholar 

  23. J.-P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, J. Comput. Phys. 23, 327 (1977).

    Article  ADS  Google Scholar 

  24. E. Lindahl, B. Hess, D. van der Spoel, J. Mol. Model 7, 306 (2001).

    Google Scholar 

  25. T. Becker, J.C. Smith, Phys. Rev. E 67, 021904 (2003).

    Article  ADS  Google Scholar 

  26. L. Hong, X. Cheng, D.C. Glass, J.C. Smith, Phys. Rev. Lett. 108, 238102 (2012).

    Article  ADS  Google Scholar 

  27. K. Wood, F.-X. Gallat, R. Otten, A.J. van Heel, M. Lethier, L. van Eijck, M. Moulin, M. Haertlein, M. Weik, F.A.A. Mulder, Angew. Chem. Int. Ed. 52, 665 (2013).

    Article  Google Scholar 

  28. A.L. Tournier, J.C. Smith, Phys. Rev. Lett. 91, 20 (2003).

    Article  Google Scholar 

  29. D.J. Bicout, G. Zaccai, Biophys. J. 80, 1115 (2001).

    Article  ADS  Google Scholar 

  30. L. Hong, D.C. Glass, J.D. Nickels, S. Perticaroli, Z. Yi, M. Tyagi, H. O’Neill, Z. Qiu, A.P. Sokolov, J.C. Smith, Phys. Rev. Lett. 110, 028104 (2013).

    Article  ADS  Google Scholar 

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Correspondence to Jeremy C. Smith.

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Contribution to the Topical Issue “Neutron Biological Physics”, edited by Giovanna Fragneto and Frank Gabel.

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Miao, Y., Hong, L., Yi, Z. et al. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein. Eur. Phys. J. E 36, 72 (2013). https://doi.org/10.1140/epje/i2013-13072-5

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  • DOI: https://doi.org/10.1140/epje/i2013-13072-5

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