Protein structure modeling using backbone chemical shifts

Abstract

The knowledge of the tridimensional structure of a protein is essential to study its interactions and understand its mode of action. The Purpose of our work is to quickly and easily determine the structure of proteins using the backbone chemical shifts. Backbone chemical shifts data are NMR parameters that can be rapidly, easily and accurately measured. This parameter is very sensitive to the conformation of amino acids and is used to deduct the secondary structure (TALOS, RCI,...). We therefore plan to use backbone chemical shifts as constraints on dihedral angles to quickly and easily determine protein structure. Several « de novo » methods like CS-Rosetta , CS23D et CHESHIRE have been recently developed in this purpose. We will use proteins of different sizes for which, the structure (X-ray or NMR structure) and chemical shifts backbone are available for testing the three softwares. Knowing that each of these softwares predicted a large number of low energy models on the one hand, and that the deployment and use of these tools constitutes obstacles for users who are not experts in computer science on the other hand, our goal will be to develop a platform that can easily compare these three methods based on quality of the structure produced