help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Biophys. J. BioFAST: First Published March 24, 2006. doi:10.1529/biophysj.105.080226
© 2006 by the Biophysical Society.

A more recent version of this article appeared on June 15, 2006.
This Article
Right arrow Full Text (Rapid PDF)
Right arrow All Versions of this Article:
biophysj.105.080226v1
90/12/4305    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow Author home page(s):
Lars Nordenskiöld
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Korolev, N.
Right arrow Articles by Nordenskiöld, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Korolev, N.
Right arrow Articles by Nordenskiöld, L.

BIOPHYSICAL THEORY AND MODELING

Computer Modeling Demonstrates that Electrostatic Attraction of Nucleosomal DNA is Mediated by Histone Tails

Nikolay Korolev 1, Alexander P. Lyubartsev 2 and Lars Nordenskiöld 1*

1 Nanyang Technological University
2 Stockholm University

* To whom correspondence should be addressed. E-mail: larsnor{at}ntu.edu.sg.

Submitted on December 21, 2005
Revised on January 23, 2006
Accepted on 1 March 2006


  Abstract
Molecular dynamics (MD) computer simulations of charged histone tail-DNA interactions in systems mimicking nucleosome core particles (NCP) have been conducted. In a coarse-grained model, the NCP is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. The size, charge and distribution of the tails relative to the core were built mimicking real NCP. In this way, we incorporate attractive ion-ion correlation effects due to fluctuations in the ion cloud and the attractive entropic and energetic tail bridging effects. In agreement with experimental data, increase of monovalent salt content from salt-free to physiological concentration leads to formation of NCP aggregates; and likewise in the presence of MgCl2 the NCPs form condensed systems via histone tail bridging and accumulation of counterions. More detailed mechanisms of the histone tail - DNA interactions and dynamics have been obtained from all-atom MD simulations (including water) comprising three DNA 22-mers and 14 short fragments of the H4 histone tail (amino acids from 5 to 12) carrying three positive charges on lysine+ interacting with DNA. We found correlation of the DNA-DNA distance with the presence and association of the histone tail between the DNA molecules.

Key Words: DNA compaction, chromatin folding, coarse-grained modeling, molecular dynamics, polyelectrolytes




This article has been cited by other articles:


Home page
 Biophys. JHome page
A. Bertin, S. Mangenot, M. Renouard, D. Durand, and F. Livolant
Structure and Phase Diagram of Nucleosome Core Particles Aggregated by Multivalent Cations
Biophys. J., November 15, 2007; 93(10): 3652 - 3663.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Bertin, M. Renouard, J. S. Pedersen, F. Livolant, and D. Durand
H3 and H4 Histone Tails Play a Central Role in the Interactions of Recombinant NCPs
Biophys. J., April 1, 2007; 92(7): 2633 - 2645.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Copyright © 2006 by the Biophysical Society.