Using the Voronoi tesselation for the modeling of protein-protein complexes
The function of a protein is often subordinated to its interaction with one or many partners. Yet, the tridimensional structure study of this complexes, that can't be done experimentally, would permit the understanding of many cellular processes. This work contains two parts. The first part concerns the setting up of a scoring function for protein-protein docking and the second part concerns the crystallographic structure study of a tetrameric protein : the Paramecium Bursaria Chlorella Virus thymidylate synthase X, a potential antibacterial target. Docking of protein-protein complexes consists in two successive steps : first a large number of putative conformations are generated, then a scoring function is applied to rank them. This scoring function has to take into account both geometric complementarity of the two molecules and physico-chemical properties of surfaces in interaction. We addressed the second step of this problem through the development of a quick and reliable scoring function. This was done using Voronoi tessellation of the tridimensional structure of the proteins. Voronoi or Laguerre tessellations were shown to be good mathematical models of protein structure. In particular, this formalization leads to a good description of structural properties of the residues. This modeling illustrates the packing of the residues at the interface between two proteins. Thus, it is possible to measure a set of parameters, on protein-protein complexes whose structure is known, and on decoys. These parameters are frequencies of residues and pair frequencies of the residues at the interface, volumes of Voronoi cells, distances between residues at the interface, interface area and number of residues at the interface. They were used as input in statistical machine learning procedures (logistic learning, support vector machines (SVM) and genetic algorithms). These led to efficient scoring functions, able to separate native structures from decoys. In the second part, I describe the experimental determination of thymidylate synthase X tridimensionnal structure, an interesting antibacterial target. Thymidylate synthase X is a flavoprotein discovered recently. It plays a key role in the synthesis of dTMP in most of the prokaryotic organisms, but does not exist in superior eukaryotic organisms. This protein catalyses the methyl transfer from tetrahydrofolate to dUMP using FAD as a cofactor and NADPH as substrate. The tridimensional structure of ThyX homotetramer with its cofactor, FAD, was solved at 2.4Å by molecular replacement. As shown in the Thermotoga maritima and Mycobacterium tuberculosis ThyX structures, the monomer contains a core of β sheets and two α helices at its extremity. The active site is at the interface between three monomers, the isoalloxazine part of FAD being accessible to the solvent and close to a long flexible loop. FAD binding in this structure is a little different from those already observed, especially its the adenine part. This structure, in association with directed mutagenesis experiments made by our collabora- tors, revealed residues playing a key role during the catalysis.