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Wiley, Journal of Computational Chemistry, 15(29), p. 2582-2592, 2008

DOI: 10.1002/jcc.21014

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Insights on protein-DNA recognition by coarse grain modelling

Journal article published in 2008 by Pierre Poulain ORCID, Brigitte Hartmann, Adrien Saladin, Chantal Prevost
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This paper is available in a repository.

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Abstract

Coarse grain modelling of macromolecules is a new approach potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein–DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein–DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acids side chains strengthen the binding. Overall, this work demonstrates that coarse grain modelling can reveal itself a precious auxiliary for a general and complete description and understanding of protein–DNA association mechanisms.