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© Structural Dynamics Of Macromolecules
The structure of a bacterial analog of the nicotinic receptor (one color per subunit) inserted into the cell membrane (grey and orange). A representation of the volume accessible to ions is shown in yellow.

About

  • 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 
  • delarue.jpg

Former Members

2000
2000
Name
Position
2015
2020
Zeineb Fourati-Kammoun
Post-doc
2015
2020
Frédéric Poitevin
Post-doc
2015
2020
Filippo Romoli
Post-doc
2015
2020
Danièle Sinnaya
Administrative Staff
2015
2020
Irina Volahasina Randrianjatovo-Gbalou
Post-doc
2015
2020
Pierre Raia
PhD Student
2015
2020
Thomas Ybert
Post-doc
2015
2020
Jérôme Loc’h
Post-doc
2015
2020
Haidai Hu
PhD Student
2015
2020
Victoire PRAT
Undergraduate Student

Projects

Project
Ongoing
2 Members

DNA Replisome in Archaea

Ludovic Sauguet (PI)

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, […]
Project
Ongoing
2 Members

Development of methods in computational structural biology

Marc Delarue (PI)

  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.
Project
Ongoing
2 Members

DNA Polymerases Engineering and Synthetic Biology

Marc Delarue (PI)

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 […]
Project
Ongoing
2 Members

DNA Repair and Cancer

Marc Delarue (PI)

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
Project
Ongoing
2 Members

Ligand-gated Ion channels

Marc Delarue (PI)

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 […]

Transversal Project

Cancer Initiative

With more than 19.3 million new cases in 2020 worldwide, including nearly 400,000 in France, cancer is a common disease that affects or will affect us all one day, directly or indirectly. It is […]

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 […]

Software

Software
Ongoing
2 Members

MinActionPath

Marc Delarue (PI)

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
Software
Ongoing
2 Members

AquaSol

Marc Delarue (PI)

 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.
Software
Ongoing
2 Members

NOMAD-Ref

Marc Delarue (PI)

This software helps in understanding the dynamical properties of (very) large macromolecular assemblies, through Normal Modes. The software is co-developed with Patrice Kohl (UC Davis, USA). Please visit our older web page on Normal […]

Fundings

Publications

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Contact

Marie de Tarragon Phone: Ext. 86 96 Email: marie.de-tarragon@pasteur.fr Address
Architecture and Dynamics of Biologic Macromolecules
25-28 Rue du Docteur Roux 75015, Paris France