Format

Send to

Choose Destination
J Biomol NMR. 2011 Jul;50(3):263-6. doi: 10.1007/s10858-011-9514-4. Epub 2011 May 29.

Protein-protein HADDocking using exclusively pseudocontact shifts.

Author information

1
Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan, The Netherlands.

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.

PMID:
21626213
PMCID:
PMC3133697
DOI:
10.1007/s10858-011-9514-4
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Springer Icon for PubMed Central
Loading ...
Support Center