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 alpha, most often involved in alphagamma transitions, makes the most significant energetic contribution. This type of transition is twice as costly as those involving beta, or coupled epsilonzeta changes. Sugar amplitude changes are also energetically significant, in contrast to changes in phase angles.
Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, 75005 Paris, France.
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Zakrzewska
D018360:Crystallography, X-Ray / Q000706:statistics & numerical data; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D016208:Databases, Factual; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D013816:Thermodynamics
D004268:DNA-Binding Proteins; D004247:DNA