Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

DNA deformation energetics and protein binding

DNA deformation energetics and protein binding The formation of protein‐DNA complexes often involves deformation of the DNA double helix. We have calculated the energy necessary to produce this deformation in 71 crystallographically determined complexes, using internal coordinate energy optimization with the JUMNA program and a generalized Born continuum solvent treatment. An analysis of the data allows deformation energy to be interpreted in terms of both local and global structural changes. We find that, in the majority of complexes, roughly 60% of the deformation energy corresponds to backbone distortion. It is also found that large changes in stacking and pairing energies are often compensated for by other, longer range, stabilizing factors. Some deformations, such as base opening, can be large, but only‐produce local energetic effects. In terms of backbone distortions, the angle α, most often involved in αγ transitions, makes the most significant energetic contribution. This type of transition is twice as costly as those involving β, or coupled εζ changes. Sugar amplitude changes are also energetically significant, in contrast to changes in phase angles. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 414–423, 2003 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Biopolymers Wiley

DNA deformation energetics and protein binding

Biopolymers , Volume 70 (3) – Nov 1, 2003

Loading next page...
 
/lp/wiley/dna-deformation-energetics-and-protein-binding-XrFOKw9DOj

References (15)

Publisher
Wiley
Copyright
Copyright © 2003 Wiley Periodicals, Inc., A Wiley Company
ISSN
0006-3525
eISSN
1097-0282
DOI
10.1002/bip.10476
pmid
14579313
Publisher site
See Article on Publisher Site

Abstract

The formation of protein‐DNA complexes often involves deformation of the DNA double helix. We have calculated the energy necessary to produce this deformation in 71 crystallographically determined complexes, using internal coordinate energy optimization with the JUMNA program and a generalized Born continuum solvent treatment. An analysis of the data allows deformation energy to be interpreted in terms of both local and global structural changes. We find that, in the majority of complexes, roughly 60% of the deformation energy corresponds to backbone distortion. It is also found that large changes in stacking and pairing energies are often compensated for by other, longer range, stabilizing factors. Some deformations, such as base opening, can be large, but only‐produce local energetic effects. In terms of backbone distortions, the angle α, most often involved in αγ transitions, makes the most significant energetic contribution. This type of transition is twice as costly as those involving β, or coupled εζ changes. Sugar amplitude changes are also energetically significant, in contrast to changes in phase angles. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 414–423, 2003

Journal

BiopolymersWiley

Published: Nov 1, 2003

Keywords: protein‐DNA complexes; DNA distortion; binding energy; molecular modeling

There are no references for this article.