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 ? domain of the E. coli DNA polymerase III (?186) 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 ?186 in complex with the HOT-homologue ? subunit of the E. coli DNA polymerase III.

SUBMITTER: Schmitz C 

PROVIDER: S-EPMC3133697 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature