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We are part of the Department of Structural Biology and Chemistry in Institut Pasteur, Paris.
We use biophysical experimental techniques such as crystallography and cryo-electron microscopy to visualize at the atomic level the structure of molecules essential to life, especially
We complement them with computational approaches such as molecular dynamics (atomic models), normal modes dynamics (coarse-grained models) and statistical thermodynamics, in order to go beyond the essentially static pictures given by these methods.
Our main goal is to understand how these molecular machines work at the atomic level so as to design structure-inspired drugs (pharmacology) and re-design their active site(s) to make them accept other substrates (synthetic biology).
Publications by year (2009-2019)
-New article on the cryo-EM structure of archaeal polD + DNA + PCNA
by Madru et al. (Nature Commun.) in Bioarxiv.
-With main authors Patrice Koehl (UC Davis) and Henri Orland (CEA, Saclay), a new look at
Optimal Transport theory using the tools of statistical mechanics, just published in Physical Review Letters
(PRL) and E (PRE).
-A structural model for human Pol mu interacting with an NHEJ junction containing a DNA double-strand-break,
based on crystal structures of a TdT chimera
that recapitulates all properties of Pol mu, published in JBC, see .
-Cryo-EM structure of the polD DNA polymerase (DP1+DP2) complex, with or without DNA, in PLoS Biol.
-An updated structure-based classification of all extant DNA polymerases (Here).
-Fifth DNA Polymerases Meeting in Leiden, NL (Program here).
-CECAM Meeting on Normal Modes in IHP, Paris, September (Program here).
-New and faster calculations of Normal Modes with Patrice Koehl (Ref).
-Design of a polymerase that generates libraries of random RNA in Nucleic Acids Res.
2017-Simulating the transition path between two known forms of a macromolecule using mixed ENMs,
in J. Chem. Phys. This is a follow up of our previous MAP method (see also P. Koehl in J. Chem. Phys.)
-Organisation with Y.H. Sanejouand of a one day meeting in Normal Mode analysis and Conformational Transitions in Pasteur (30 May 2017)
DNA Polymerases and DNA Repair
-X-ray structure of Archaeal polD DNA polymerase reveals a catalytic site similar to multi-subunit RNA polymerases that are found in all domains of life,
by L. Sauguet, P. Raia, G. Henneke and M. Delarue (Nature Commun).
-Structural basis for an unexpected "in trans" templated activity by TdT: implications for V(D)J recombination and DNA double-strand-breaks repair in eukaryotes,
J. Loc'h, S. Rosario and M. Delarue (Structure).
Pentameric Ligand-gated ion channels (pentaLGICs): drug binding sites in different conformational states
-TdT structures in complex with a DNA synapsis shed new light on DNA Double-Strand-Break Repair by NHEJ (EMBO J., Mar 2015).
-Structural basis for ion permeation in GLIC (EMBO Journal, Jan 2013) at 2.4 Angstrom
-Snapshots of Terminal deoxynucleotidyl transferase caught in action: dynamical aspects of the two-metal-ion mechanism (J. Gouge et al., J. Mol. Biol., Jul 2013)
-Structure of Archaeal DNA polymerase (polB) from P. abyssi in editing mode by J. Gouge et al. (JMB)
The following web sites provide online servers for algorithms such as normal mode
calculation, structural refinement, solvation, mutation and (later) transition path calculation.
a web-based software to calculate SAXS spectra from PDB coordinates,
including the solvent density predicted by AquaSol, see Ref. here.
MinActionPath (MAP) web server can be used to generate the most probable trajectory between two known structural forms
of the same macromolecule (see Ref. here).
The algorithm was greatly accelerated by P. Koehl, as described here.
Go to Older web site for more details on the group activities before 2009.