- 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, […]
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 […]
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-binding mechanism and evolution of replication protein A
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of […]
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.
2023Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson–Boltzmann Theories, Viruses 2023, 15, 1366.
2023DNA-binding mechanism and evolution of replication protein A., Nat Commun 2023 Apr; 14(1): 2326.
2023Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features, Nucleic Acids Research.
2023Computing the Gromov-Wasserstein Distance between Two Surface Meshes Using Optimal Transport, Algorithms 2023, 16, 131.
2021Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8., Nucleic Acids Res 2021 Nov; 49(20): 11974-11985.
2021Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus., J Chem Inf Model 2021 Oct; 61(10): 4832-4838.
2021Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA., Nat Commun 2021 08; 12(1): 4710.
2021Parameterizing elastic network models to capture the dynamics of proteins., J Comput Chem. 2021 Jun 11..
2021Physics approach to the variable-mass optimal-transport problem, Phys Rev E . 2021 Jan;103(1-1):012113 .
2021Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach., J Phys Chem B. 2021 May 20;125(19):5052-5067..
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