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Nonsequence‐specific arginine interactions in the nucleosome core particle

Nonsequence‐specific arginine interactions in the nucleosome core particle We have analyzed the relative orientation of basic amino acid side chains towards DNA in the nucleosome core particle. The electric field created by DNA phosphates has no apparent preferential orientation: no favored orientation of the arginine guanidinium group is found. Arginine may be either directly hydrogen bonded to a phosphate oxygen or stabilized in the minor groove by van der Waals contacts and the local negative electric field. On the other hand, the phosphate oxygen atoms hydrogen bonded to arginines are always found close to the plane defined by the guanidinium group. Thus it can be concluded that the interactions of arginine are strongly directional, those of phosphate are not. We also find that a highly charged fragment of histone H2B, which is placed between two DNA turns, has a very variable conformation. An increase in protein positive charge density apparently allows multiple nonspecific protein conformations when interacting with DNA. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 432–439, 2003 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Biopolymers Wiley

Nonsequence‐specific arginine interactions in the nucleosome core particle

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References (16)

Publisher
Wiley
Copyright
Copyright © 2003 Wiley Periodicals, Inc., A Wiley Company
ISSN
0006-3525
eISSN
1097-0282
DOI
10.1002/bip.10389
pmid
12879489
Publisher site
See Article on Publisher Site

Abstract

We have analyzed the relative orientation of basic amino acid side chains towards DNA in the nucleosome core particle. The electric field created by DNA phosphates has no apparent preferential orientation: no favored orientation of the arginine guanidinium group is found. Arginine may be either directly hydrogen bonded to a phosphate oxygen or stabilized in the minor groove by van der Waals contacts and the local negative electric field. On the other hand, the phosphate oxygen atoms hydrogen bonded to arginines are always found close to the plane defined by the guanidinium group. Thus it can be concluded that the interactions of arginine are strongly directional, those of phosphate are not. We also find that a highly charged fragment of histone H2B, which is placed between two DNA turns, has a very variable conformation. An increase in protein positive charge density apparently allows multiple nonspecific protein conformations when interacting with DNA. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 432–439, 2003

Journal

BiopolymersWiley

Published: Aug 1, 2003

Keywords: lysine; arginine; protamines; nucleosome core particle; histones; x‐ray crystallography; protein–DNA interactions

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