Group of Marc Delarue
Projects
 1. X-Ray crystallography |
All these structures have benefitted from excellent X-ray data collection facilities in ESRF, Grenoble.
1.1 X-Ray crystallography and Drug Design
TMP kinase from M. tuberculosis.
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The structure of thymidylate kinase TMPK which is essential for nucleotide metabolism has been solved at 1.95 Å resolution in the presence of TMP. We use this structural information to design potent new inhibitors of this target. The enzyme is active in the crystal state (see D. Bourgeois web site). |
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The Trypanosoma brucei 6-phosphogluconolactonase
has been crystallized and solved at 2.1 Angstrom resolution. It is a member of the Pentose-Phosphate-Pathway
(PPP) and is a good
candidate for drug design against T. brucei.
This work is a collaboration with Veronique Stoven (Unite de BioInformatique Structurale) and was made possible
thanks to both PT5 (P. Beguin) and PT6 (A. Haouz). |
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1.2 Structural Molecular Biology and DNA polymerases
Terminal desoxynucleotidyl transferase.
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Tdt is a member of the pol X family; it is responsible for the random addition of nucleotides at the N regions of immunoglobulins and T-cell receptors genes at the V(D)J junctions, during somatic recombination, thereby contributing to the generation of the diversity of the immune response (Tdt). Crystals of the catalytic domain of TdT have been obtained in the lab and the structure has been solved by MIR methods at 2.35 Å resolution. Binary complexes with either the incoming dNTP or the oligonucleotide primer have also been solved and analysed. A number of important biological implications of the structure have been found.
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Pol &mu: see here for our latest results published in Nucleic Acids Res. (2009).
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We have performed extensive site-directed mutagenesis in the Loop1 region and beyond and finally managed to transform a template-independent Tdt into a template-dependent DNA polymerase by just a single-point mutation. |
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DNA Pol B from Archaea: this is a collaboration with G. Hennike (IFREMER, Brest).
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In construction... |
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1.3 Bacterial homologues of pentameric Ligand-gated Ion channels, in collaboration with P.J. Corringer: in construction.
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In construction... |
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| 2. Mean-Field Optimization techniques in molecular modelling and crystallography |
2.1 Side chain prediction, homology modelling and sequence design.
Mean Field optimization can be used to "decorate" very rapidly a given protein backbone with any desired protein sequence. Compared to other similar techniques, MF optimization is very fast ; it was originally developed together with P. Koehl. The output of the program are the coordinates of all the atoms of the model.
Four main applications are available :
2.2 Phase Refinement in Crystallography (Methodology)
Mean Field theory has been used to recast
in a single formalism the problem of phase optimization and phase combination, generalizing the approach
of Blow and Crick (1959) and Sim (1960) to treat rigourously density modification techniques in the
presence of an experimentally derived phase probability distribution function
in the same unifying theoretical framework.
In effect, a new statistical thermodynamics theory of
crystallographic refinement has been set up.
Because structure factors are complex numbers, field theoretic methods
had to be used to write down the partition function Z of the system, from which the free energy can
easily be derived. It bears strong resemble to maximum likelihood formalism but there are subtle differences.
The "best" maps are those that minimize the free energy.
Their use should increase the efficiency of automatic model building programs (Arp/wArp)
in structural genomics projects.
Click here to find out more about the derived formula giving the generalized figure-of-merit and mean-phase
FOM and mean-phase for different cases of density modification
(use of a partial model, solvent flattening and Sayre formula) which are imposed as energy functions in reciprocal space:
definitions of Yk for these three different cases.
The formalism bears strong resemblance with maximum likelihood, but can be readily interpreted in terms of
usual thermodynamic functions such as free energy, entropy etc...
2.3 Variations on Poisson-Boltzmann equation
We use Mean Field formalism to write down and solve variations of the Poisson-Boltzmann equation
applied to proteins in different situations (finite size of the free ions...).
We are especially interested in the case where the solvent is represented as an assembly of dipoles of variable density.
Go to PDB_Hydro web site for a recent implementation of our Poisson-Boltzmann-Langevin model which treats the solvent as an assembly of self-optimised orientable dipoles of variable density.
N.B. This site also contains a number of programs to handle, repair and refine protein coordinates (PDB) files.
This is our web site for our own computational structural biology on-line tools.
Eventually, this should have applications in drug design methodology, because it gives the solvation energy that is needed to estimate the free energy of binding of a ligand onto a macromolecule (protein).
| 3. Normal Modes and the Elastic Network Model: a simplified
approach to structural transitions in macromolecules |
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We discovered that Normal Modes are extremely good to describe structural transitions in polymerases. |
