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Publications by theme (2006-2016)

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. L. Sauguet, P. Raia, G. Henneke and M. Delarue, Nature Comms. (Sept 2016). See F1000.

-Structural basis for a new "in trans" templated activity by TdT: implications for V(D)J recombination,
by J. Loc'h, S. Rosario and M. Delarue, in Structure (Sep 2016). See F1000.

-TdT structures in complex with a DNA synapsis shed new light on DNA Double-Strand-Break Repair in NHEJ by J. Gouge et al., EMBO J. (Mar 2015).

-Snapshots of Terminal deoxynucleotidyl transferase (TdT) caught in action: dynamical aspects of the two-metal-ion mechanism by J. Gouge et al., J. Mol. Biol. (Jul 2013).

-Co-crystal structures of inhibitors of Tdt, with G. Maga (Milan) and R. di Santo (Roma), J. Med. Chem. (Sep 2013).

-Structures of DNA pol B from P. abyssi in the editing mode, by J. Gouge et al., JMB (2012)

-Transforming Tdt into an "in cis" templated polymerase by a single mutation, by F. Romain et al., NAR (2009)

Pentameric Ligand-gated ion channels

-X-ray structures of GLIC with Barbiturates, with Pr. Trevor Smart (UCL, UK), 2017 (JBC).
-X-ray structures of GLIC with Xenon, in the open and pre-activation states, 2016 (PLoS One).
-X-ray structures of GLIC with Bromoform with MD studies by M. Baaden and coll., 2016 (Structure).

-Structure of a GLIC-GlyR chimera (PNAS, Feb 2015)
-Structural characterization of allosteric binding sites in GLIC (Acta D, March 2015) see F1000.

-Structural basis for the gating mechanism in GLIC (PNAS, Jan 2014), see F1000.
-A structural perspective in the pharmacology of pLGICs (BBA, May 2014)

-Structural basis for ion permeation in GLIC (EMBO Journal, Jan 2013) at 2.4 Angstrom.
-Structural basis for alcohol potentiation in a mutant of GLIC (Nature Comms, April 2013), see F1000.

-A review on cys-loop receptors in Structure, 2012
-The locally-closed form for GLIC in 2012, see F1000.

-The structure of the binding site of general anesthetics on GLIC in 2011, see F1000.

-One microsecond-long Molecular dynamics simulations on GLIC in 2010

-The structure of the open form of GLIC in 2009, see F1000.

-The structure of the ECD alone of GLIC in 2008

Software/Web services

-AquaSAXS, a web-based software to calculate SAXS spectra from PDB coordinates, including the solvent density predicted by AquaSol, is now available on-line (Ref. Poitevin et al., 2011).

-The Dipolar Solvent Model which forms the basis of AquaSol (Ref. Azuara et al., 2008).

-MinActionPath (MAP) web server: (Ref. Franklin et al., 2007).

-Nomad_Ref software (Ref. Lindahl et al., 2006).

-PDB_Hydro software (Ref. Azuara et al., 2006).

Macromolecular Electrostatics: Earlier papers

-Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations. Poitevin F, Delarue M, Orland H. J Phys Chem B. 2016 Jul 7;120(26):6270-7. PDF

-Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. Smaoui MR, Poitevin F, Delarue M, Koehl P, Orland H, Waldispuhl J. Biophys J. 2013 Feb 5;104(3):683-93. Ref

-Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling. Koehl P, Orland H, Delarue M. J Chem Phys. 2011 Aug 7;135(5):055104. Ref

-AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. Koehl P, Delarue M. J Chem Phys. 2010 Feb 14;132(6):064101. Ref

-Computing ion solvation free energies using the dipolar Poisson model. Koehl P, Orland H, Delarue M. J Phys Chem B. 2009 Apr 30;113(17):5694-7. Ref

-Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Koehl P, Orland H, Delarue M. Phys Rev Lett. 2009 Feb 27;102(8):087801. PDF and See F1000.

Crystallography and Modelling (older papers): Methods/Mean Field Optimisation

Normal Modes and Structure-encoded dynamics (older papers): Structural Dynamics

NOMAD-Ref web server
Normal Mode Analysis
NOMAD-Ref web server
Normal Mode Refinement
PDB_Hydro web server
Mutation & Solvation: Dipolar solvent
PDB_Hydro web server
AquaSaxs web server

  Marc Delarue http://lorentz.dynstr.pasteur.fr