- 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 (cell-cell communications).
- 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 and ligands, 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).
- More details can be found at http://lorentz.dynstr.pasteur.fr or at http://www.dynstr.pasteur.fr
DNA Replisome in Archaea
We study the general architecture of the replisome in archaea, especially around the essential PolD, that we discovered to be unique among other DNA polymerases, as it has the fold of multi-subunit RNA polymerases, […]
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 Polymerases Engineering and Synthetic Biology
We work with archaeal DNA polymerases (PolB) that were evolved to accept xeno-nucleotides to understand the molecular basis of their changed specificity. We use this information to engineer new DNA polymerases to synthesize variants […]
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
Ligand-gated Ion channels
We study the structure and function of ligand-gated ion channels by X-ray crystallography to understand i) the gating mechanism (opening of the pore upon agonist binding) ii) the permeation mechanism (transport of ions through […]
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
IINCEPTION 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 (Official website here : https://www.inception-program.fr/en). Inception program […]
This software allows to calculate the most probable pathway between two conformational states of the same macromolecule, using the Elastic Network model for the Energy landscape of each of the two states. See http://lorentz.dynstr.pasteur.fr/joel/index.php
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.
2020Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution, Biomolecules . 2020 Dec 8;10(12):1647. doi: 10.3390/biom10121647..
2020Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel., Acta Crystallogr D Struct Biol 2020 Jul; 76(Pt 7): 668-675.
2020Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel., Proc. Natl. Acad. Sci. U.S.A. 2020 Jun; 117(24): 13437-13446.
2020Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA., Nat Commun 2020 03; 11(1): 1591.
2019Statistical Physics Approach to the Optimal Transport Problem., Phys. Rev. Lett. 2019 Jul; 123(4): 040603.
2019Structural evidence for an “in trans” base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction, J. Biol. Chem. 2019 Jul;294(27):10579-10595.
2019Rapid enzymatic synthesis of long RNA polymers: A simple protocol to generate RNA libraries with random sequences, Methods 2019 May;161:83-90.
2019Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases, PLoS Biol. 2019 Jan;17(1):e3000122.
2019An updated structural classification of replicative DNA polymerases, Biochem. Soc. Trans. 2019 02;47(1):239-249.
2018Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments, Molecules 2018 Dec;24(1).
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Marie de Tarragon Phone: Ext. 86 96 Email: email@example.com Address Unite de Dynamique Structurales des Macromolecules Biologiques 25-28 Rue du Docteur Roux 75015, Paris France