@article {2015|1766, title = {Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key}, journal = {Structure}, volume = {23}, number = {8}, year = {2015}, month = {aug}, pages = {1373{\textendash}1374}, doi = {10.1016/j.str.2015.07.004}, author = {S Sacquin-Mora and Chantal Pr{\'e}vost} } @article {2009|1636, title = {Deforming DNA: from physics to biology}, journal = {Chemphyschem}, volume = {10}, year = {2009}, month = {jul}, pages = {1399{\textendash}404}, abstract = {

The DNA double helix has become a modern icon which symbolizes our understanding of the molecular basis of life. It is less widely recognized that the double helix proposed by Watson and Crick more than half a century ago is a remarkably adaptable molecule that can undergo major conformational rearrangements without being irreversibly damaged. Indeed, DNA deformation is an intrinsic feature of many of the biological processes in which it is involved. Over the last two decades, single-molecule experiments coupled with molecular modeling have transformed our understanding of DNA flexibility, while the accumulation of high-resolution structures of DNA-protein complexes have demonstrated how organisms can exploit this property as a useful feature for preserving, reading, replicating, and packaging the genetic message. In this Minireview we summarize the information now available on the extreme\–and the less extreme\–deformations of the double helix.

}, doi = {10.1002/cphc.200900253}, author = {Chantal Pr{\'e}vost and M. Takahashi and Richard Lavery} } @article {2003|1663, title = {Docking macromolecules with flexible segments}, journal = {J. Comput. Chem.}, volume = {24}, year = {2003}, month = {nov}, pages = {1910{\textendash}20}, abstract = {

We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide Wenqing, X. et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA.

}, doi = {10.1002/jcc.10329}, author = {Bastard, Karine and Thureau, Aur{\'e}lien and Richard Lavery and Chantal Pr{\'e}vost} } @article {1997|1819, title = {Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: An internal coordinate molecular modeling study}, journal = {J. Biomol. Struct. Dyn.}, volume = {14}, number = {6}, year = {1997}, month = {jun}, pages = {703{\textendash}714}, abstract = {

A trans-diamminedichloroplatinum(II) (trans-DDP) intrastrand adduct within the sequence d(TCTG*TG*TC).d(GACACAGA) (where G* represents a platinated guanine) is modeled on the basis of qualitative experimental data concerning global unwinding and curvature as well as information on base pairing. Modeling is performed using the internal coordinate JUMNA program, specific to nucleic acids, and modified to include the possibility of covalently bound ligands. Calibration of the energy functions representing the Pt-N7 bond with guanine is described. The platinum atom and the platinum-nitrogen bonds are parameterized for use in the H{\"u}ckel Del Re method to calculate monopoles at each atom. These monopoles are consistent with the Flex force field included in Jumna. By developing an appropriate minimization protocol we are able to generate stable, distorted three-dimensional structures compatible with the experimental data and including an unusually high global unwinding. No a priori geometric assumptions are made in generating these structures.

}, doi = {10.1080/07391102.1997.10508173}, author = {Chantal Pr{\'e}vost and Boudvillain, M and Beudaert, P and Leng, M and Lavery, R and Vovelle, F} }