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J Biomol NMR (2011) 50:263266 DOI 10.1007/s10858-011-9514-4
ARTICLE
Proteinprotein HADDocking using exclusively pseudocontact shifts
Christophe Schmitz Alexandre M. J. J. Bonvin
Received: 18 January 2011 / Accepted: 9 May 2011 / Published online: 29 May 2011 The Author(s) 2011. This article is published with open access at Springerlink.com
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 efciency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal e domain of the E. coli DNA polymerase III (e186) 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 3.13.9 range for the ten lowest energy complexes). Finally, using exclusively PCS as experimental information, we determine the structure of e186 in complex with the HOT-homologue h subunit of the
E. coli DNA polymerase III.
Keywords HADDOCK Pseudocontact shift Protein
docking Paramagnetic NMR DNA polymerase III
Introduction
Pseudocontact shifts (PCS) are measured as the difference in chemical shifts between two NMR spectra, one of which is
recorded with a paramagnetic center attached to the protein of interest. The presence of the paramagnetic center (usually a paramagnetic lanthanide; for a review on paramagnetic labeling techniques, see (Su and Otting 2010) changes the reference spectrum in several ways: Mainly, observed cross peaks are shifted, while active spins close to the paramagnetic probes (typically less than 510) are no longer detected. The amount and direction of the shift in each dimension of the spectrum depends on multiple factors, including the vicinity of the spin to the lanthanide, and its position with respect to the anisotropic Dv-tensor. The Dv-tensors axial and rhombic components, as well as the relative orientation of the tensor frame to the protein, depend on the type of lanthanide used and on the surrounding electronic environment of the paramagnetic center (Bertini et al. 2002). This allows the measurement of several spectra by varying the lanthanide, which provides non-redundant information. Importantly, PCS can be...