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DNA deformation energetics and protein binding
Author(s) -
Zakrzewska K.
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10476
Subject(s) - chemistry , deformation (meteorology) , energetics , stacking , crystallography , distortion (music) , chemical physics , dna , base pair , helix (gastropod) , molecular physics , thermodynamics , physics , amplifier , ecology , biochemistry , optoelectronics , organic chemistry , cmos , biology , meteorology , snail
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