title: Protein-protein HADDocking using exclusively pseudocontact shifts.
abstract: 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 ε domain of the E. coli DNA polymerase III (ε186) in complex with the HOT domain. Docking from the bound form of the two partners is swiftly executed (interface RMSDs < 1 Å) 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 Å range for the ten lowest energy complexes). Finally, using exclusively PCS as experimental information, we determine the structure of ε186 in complex with the HOT-homologue θ subunit of the E. coli DNA polymerase III.
authors.affiliation: Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan, The Netherlands.
authors.forename: Christophe
authors.initials: C
authors.lastname: Schmitz
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D004258:DNA Polymerase III / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation
chemical_list: D029968:Escherichia coli Proteins; D004258:DNA Polymerase III