@article {2015|1965,
	title = {An integrative approach to the study of filamentous oligomeric assemblies, with application to {R}ec{A}},
	journal = {Plos One},
	volume = {in press},
	year = {2015},
	pages = {e0116414},
	abstract = {<p>Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization. In our approach, local modes of association are sampled via docking or Monte Carlo simulations. This enables shedding new light on fiber morphologies that may be adopted by the RecA protein. Two distinct RecA helical morphologies, the so-called \&quot;extended\&quot; and \&quot;compressed\&quot; forms, are known to play a role in homologous recombination. We investigate the variability within each form in terms of helical parameters and steric accessibility. We also address possible helical discontinuities in RecA filaments due to multiple monomer-monomer association modes. By relating local interface organization to global filament morphology, the strategies developed here to study RecA self-assembly are particularly well suited to other DNA-binding proteins and to filamentous protein assemblies in general.</p>},
	doi = {10.1371/journal.pone.0116414},
	author = {Benjamin Boyer and Johann Ezelin and Pierre Poulain and A Saladin and Martin Zacharias and Charles H. Robert and Chantal Pr{\'e}vost}
}
@article {2008|1662,
	title = {Insights on protein-DNA recognition by coarse grain modelling},
	journal = {J. Comput. Chem.},
	volume = {29},
	year = {2008},
	month = {nov},
	pages = {2582{\textendash}92},
	abstract = {<p>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 acid side chains strengthen the binding. Overall, this work demonstrates that coarse grain modeling can reveal itself a precious auxiliary for a general and complete description and understanding of protein-DNA association mechanisms.</p>},
	doi = {10.1002/jcc.21014},
	author = {Poulain, P and A Saladin and Hartmann, B and Chantal Pr{\'e}vost}
}
