Download MendeleyProtein-Protein Haddocking Using Exclusively Pseudocontact Shifts.
Schmitz, C., Bonvin, A.M.J.J.(2011) J Biomol NMR 50: 263-266
- PubMed: 21626213
- DOI: https://doi.org/10.1007/s10858-011-9514-4
- Primary Citation of Related Structures:
2XY8 - PubMed 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.
Organizational Affiliation:
Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan, The Netherlands.
