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© Research
Publication : The Journal of biological chemistry

Free energy contributions to direct readout of a DNA sequence

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in The Journal of biological chemistry - 16 Sep 2005

Ferreiro DU, Dellarole M, Nadra AD, de Prat-Gay G

Link to Pubmed [PMID] – 16000299

J. Biol. Chem. 2005 Sep;280(37):32480-4

The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol(-1)), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol(-1) from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as “indirect readout.” Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of “hot spots,” such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and “wet” protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken.

http://www.ncbi.nlm.nih.gov/pubmed/16000299