Free energy contributions to direct readout of a DNA sequence.

FERREIRO, D.U., DELLAROLE, M., NADRA, A.D. AND PRAT GAY, G. DE

JOURNAL OF BIOLOGICAL CHEMISTRY

Año: 2005 vol. 280 p. 32480 - 32484

0021-9258

Free Energy Contributions to Direct Readout of a DNA Sequence* Received for publication, May 25, 2005, and in revised form, June 30, 2005 Published, JBC Papers in Press, July 5, 2005, DOI 10.1074/jbc.M505706200 Diego U. Ferreiro1,Mariano Dellarole, Alejandro D. Nadra2, and Gonzalo de Prat-Gay3 From the Instituto Leloir, Consejo Nacional de Investigaciones Científicas y Técnicas, and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Patricias Argentinas 435, 1405 Buenos Aires, Argentina The energetic contributions of individual DNA-contacting side chains to specificDNArecognition 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 toDNAbinding 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.