Dynamic of the ligand release
We have studied the dynamic of ligand release after reaction on xylosetriose from GH-11 xylanase, a highly substrate specific enzyme. GH-11 xylanase possesses a thumb shaped loop, characterized by an opening and closing position that can modify the shape of the catalytic site.
/o gain insight into this mecanism, we have run molecular dynamics (MD) simulations. We have performed 10*10 ns MD runs on GH-11 xylanase / xylosetriose with Gromacs software using an explicit representation of solvent. We have observed a complete product release and a large opening loop motion. Identical simulaton ran over mutant on the thumb-loop had showed that our new approach can help in understanding how mutations in enzymes can modify the efficiency of product release. Experimental results reinforce our predictions.
Model of the 3DL1*015 structure and model for the interaction of KIR3DL1*015 with HLA-A*2402.
Have a look to abstract and supplementary material of Sharma et al., 2009 here...
The studies mentioned below have been carried under the supervision of Chantal Prevost and Richard Lavery, Laboratoire de Biochimie Theorique, IBPC, Paris:
[Download the PDF of my PhD thesis (in french)]
Key words : macromolecular assemblies, flexible docking methods, flexible loop, mean-field theory, RecA nucleo-protein filament.
Development of proteins docking software that account for loop flexibilty:
Docking methods aim to predict the structure of a macromolecular complex starting from the atomic coordinates of its individual components. Most of these methods do not consider the internal deformations that may occur during association. We proposed a novel algorithm to introduce loop flexibility into docking methods. In this algorithm, each flexible loop is represented by an ensemble of rigid conformations, generated prior to the docking. Following the principle of the mean-field theory, each conformation is caracterized by a weight, roughly corresponding to the probability that the loop adopts such conformation for a given position of the partner. We have introduced this strategy into two docking programs, in each case coupling the mean-field theory with the exploration methods used by the programs:
- The first one, called ATTRACT, performs an exhaustive search of all possible partner combinations, based on energy minimization, and allowed by the use of a simplified protein representation. This work has been carried out in collaboration with Martin Zacharias from the International University Bremen and has been published in Proteins. Pubmed | PDF
- The second program, called MC2, allows to predict the details of interaction between the two macromolecules with a Monte-Carlo process bearing on the partner positions within a restricted space. This work has been published in Journal Of Computational Chemistry. Pubmed | PDF.
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Modeling the RecA nucleo-protein filament:
RecA is a central protein for homologous recombination in prokaryotes. This process is important for both DNA repair and DNA segregation. It involves the formation of long helical nucleoprotein filaments of the RecA protein on single-stranded DNA. These filaments incorporate double-stranded DNA from the cell's genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. This process is accompanied by ATP hydrolysis and modification of the geometry of RecA filament. The speed of the reaction and its dynamic propagation make it difficult to isolate and characterize the intermediate products of the reaction. However, for a better understanding of the homologous recombination process, it is necessary to determine how the protein interacts with DNA at atomic level during the different steps of the reaction. We built structures for the complex issued from docking of a model of DNA R-type triple helix on the crystal filament of RecA/ADP. We proposed several conformations and positions of the L1 and L2 loops, missing in the crystal structure, with respect to the DNA. This work will be the purpose of an incoming publication.