JCP Nameplate
  • Volume/Page
  • Keyword
  • DOI
  • Citation
  • Advanced
   
 
 
 

You Tube Flickr Twitter UniPHY Group iResearch App Facebook

Journal of Chemical Physics / Volume 133 / Issue 8 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 133, 085101 (2010); http://dx.doi.org/10.1063/1.3481089 (8 pages)

Depth dependent dynamics in the hydration shell of a protein

J. Servantie, C. Atilgan, and A. R. Atilgan

Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli 34956 Tuzla, Istanbul 34956, Turkey

View MapView Map

(Received 2 April 2010; accepted 28 July 2010; published online 26 August 2010)

We study the dynamics of hydration water/protein association in folded proteins using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition that corresponds to the onset of amplified atomic fluctuations in proteins. The results indicate that the number of water molecules within a cutoff distance of each residue scales linearly with protein depth index and is not affected by the local dynamics of the backbone. Keeping track of the water molecules within the cutoff sphere, we observe an effective residence time, scaling inversely with depth index at physiological temperatures while the diffusive escape is highly reduced below the transition. A depth independent orientational memory loss is obtained for the average dipole vector of the water molecules within the sphere when the protein is functional. While below the transition temperature, the solvent is in a glassy state, acting as a solid crust around the protein, inhibiting any large scale conformational fluctuations. At the transition, most of the hydration shell unfreezes and water molecules collectively make the protein more flexible.

© 2010 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. NUMERICAL METHODS
  3. RESULTS AND DISCUSSION
    1. Hyration levels and water residence times
    2. Depth dependent relaxation times in the hydration layer
    3. Gradual unfreezing of the hydration layer
  4. CONCLUSION

RELATED DATABASES

To view database links for this article, you need to log in.

KEYWORDS and PACS

Keywords

biochemistry, molecular biophysics, molecular configurations, molecular dynamics method, proteins, solvation, water

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3481089

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    W. Doster, S. Busch, A. M. Gaspar, M. -S. Appavou, J. Wuttke, and H. Scheer, Phys. Rev. Lett. 104, 098101 (2010).

    M. Tarek and D. J. Tobias, Phys. Rev. Lett. 88, 138101 (2002).

    P. Kumar, Z. Yan, L. Xu, M. G. Mazza, S. V. Buldyrev, S. -H. Chen, S. Sastry, and H. E. Stanley, Phys. Rev. Lett. 97, 177802 (2006).

    D. van der Spoel, P. J. van Maaren, and H. J. C. Berendsen, J. Chem. Phys. 108, 10220 (1998)JCPSA6000108000024010220000001.

    P. Höchtl, S. Boresch, W. Bitomsky, and O. Steinhauser, J. Chem. Phys. 109, 4927 (1998)JCPSA6000109000012004927000001.

    D. N. LeBard and D. V. Matyushov, Phys. Rev. E 78, 061901 (2008).

    I. Brovchenko, A. Geiger, and A. Oleinikova, J. Chem. Phys. 123, 044515 (2005)JCPSA6000123000004044515000001.

    S. Viscardy, J. Servantie, and P. Gaspard, J. Chem. Phys. 126, 184512 (2007)JCPSA6000126000018184512000001.


For access to citing articles, you need to log in.


Figures (11)

Access to article objects (figures, tables, multimedia) requires a subscription; log in to view available files.
(Access to supplementary files, where available, is free for this journal.)


Close

Google Calendar

ADVERTISEMENT

Your Recent History Recent History Help

Recently Viewed

  1. Depth dependent dynamics in the hydration shell of a protein
  2. Time- and frequency-resolved photoionization of the C 2A2 state of the benzyl radical, C7H7
  3. Monte Carlo simulation of a single ring among linear chains: Structural and dynamic heterogeneity
  4. Concerted electron and proton transfer in ionic crystals mapped by femtosecond x-ray powder diffraction
  5. On the paradoxical relation between the melting temperature and forbidden energy gap of nanoparticles
Go to AIP Home
Copyright © American Institute of Physics
close