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© Research
Publication : Proceedings of the National Academy of Sciences of the United States of America

Experimental snapshots of a protein-DNA binding landscape

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Proceedings of the National Academy of Sciences of the United States of America - 27 Apr 2010

Sánchez IE, Ferreiro DU, Dellarole M, de Prat-Gay G

Link to Pubmed [PMID] – 20375284

Proc. Natl. Acad. Sci. U.S.A. 2010 Apr;107(17):7751-6

Protein recognition of DNA sites is a primary event for gene function. Its ultimate mechanistic understanding requires an integrated structural, dynamic, kinetic, and thermodynamic dissection that is currently limited considering the hundreds of structures of protein-DNA complexes available. We describe a protein-DNA-binding pathway in which an initial, diffuse, transition state ensemble with some nonnative contacts is followed by formation of extensive nonnative interactions that drive the system into a kinetic trap. Finally, nonnative contacts are slowly rearranged into native-like interactions with the DNA backbone. Dissimilar protein-DNA interfaces that populate along the DNA-binding route are explained by a temporary degeneracy of protein-DNA interactions, centered on “dual-role” residues. The nonnative species slow down the reaction allowing for extended functionality.

http://www.ncbi.nlm.nih.gov/pubmed/20375284