- We use biophysical experimental techniques such as crystallography and cryo-EM to visualize at the atomic level the structure of molecules essential to life, such as DNA polymerases involved in DNA Repair and Cancer and ion channels involved in electric nerve signalling.
- We complement them with molecular and normal modes dynamics, so as to go beyond the essentially static pictures given by these methods.
- We also try to better understand the electrostatics of macromolecules and their interaction with the solvent, in order to be able to predict their binding properties.
- Our main goal is to design structure-inspired drugs (pharmacology) and re-design active site(s) to make them accept other substrates (synthetic biology).
Development of methods in computational structural biology
We are developing new computational methods to calculate the electrostatics of proteins, understand their dynamical properties and simulate transitions between two known conformations of the same macromolecule.
DNA Replication and Synthetic Biology
We work with archaeal DNA polymerases to make them accept xeno-nucleotides and synthesize variants of DNA and RNA in vivo.
DNA Repair and Cancer
We study the mechanism of DNA Repair of (DNA) Double Strand Breaks through the so-called Non-Homologous End Joining (NHEJ) process in mammals using x-ray crystallography and structural studies of pol mu and Tdt
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Inception Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues. Inception program uses Integrative Biology, Social Science […]
We have developed a new way to calculate electrostatics properties of biological macromolecules in a polarizable solvent: AquaSol. We can then compute the solvent density around proteins as well as their SAXS spectra: AquaSAXS.
2018Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands, in press.
2018Structural basis for a bimodal allosteric mechanism of general anesthetic modulation in pentameric ligand-gated ion channels, in press.
2018Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation, in press.
2017Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel., PLoS Biol. 2017 15(12):e2004470..
2017Ab initio sampling of transition paths by Conditioned Langevin Dynamics, J Chem Phys. 2017 Oct 21;147(15):152703..
2017The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems., J Chem Theory Comput. 2017 Mar 14;13(3):1424-1438..
2017Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State, J Biol Chem. 2017 Feb 3;292(5):1550-1558..
2016Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids, Front Mol Biosci 2016;3:85.
2016Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination., Structure. 2016 24(9):1452-63.
2016Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography., Nat Commun. 2016 Aug 22;7:12227.
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Marie de Tarragon
Phone: Ext. 86 96
Unite de Dynamique Structurales des Macromolecules Biologiques
25-28 Rue du Docteur Roux