We present here an experimental and theoretical mixed approach designed to determine the quaternary structure of protein-peptide complexes.NMR spectroscopy is known to have difficulties of resolving the 3D structure of large macromolecules. However, for protein-peptide complexes, within specific experimental conditions, NMR STD experiments can identify the peptide atoms and residues that interact with or are located near the protein and TR-NOESY data allow to determine the peptide bound conformation. The question that remains is where the peptide binds on the protein ?To tackle this issue, a coarse-grained protein docking procedure can be used to quasi-exhaustively search and provide the most probable quaternary structures of protein-peptide complexes. The presented protein model describes each amino-acid by one to three beads. Inter-grains effective van-der-Waals and Coulomb potentials were parameterized from an atomic force field, thus preserving the specificity of protein-protein interactions.This mixed approach was used to study the association of FtsZ or tubulin with small peptides having pharmaceutical potentials.

Combining  NMR experiments with coarse-grained proteins docking to characterize protein-peptide complexes

243rd National Meeting (2012)

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