Protein-protein HADDocking using exclusively pseudocontact shifts

In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal epsilon domain of the E. coli DNA polymerase III (epsilon 186) in complex with the HOT domain. Docking from the bound form of the two partners is swiftly executed (interface RMSDs < 1 ) even with addition of very large amount of noise, while the conformational changes of the free form still present some challenges (interface RMSDs in a 3.1-3.9 range for the ten lowest energy complexes). Finally, using exclusively PCS as experimental information, we determine the structure of epsilon 186 in complex with the HOT-homologue theta subunit of the E. coli DNA polymerase III.