Abstract A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 Ã?) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure determination of the p62 PB1-PB1 complex, which forms a front-to-back 20 kDa homo-oligomer. As p62 PB1 does not intrinsically bind metal ions, the lanthanide binding peptide tag was attached to one subunit of the dimer at two anchoring points. Each monomer was treated as a rigid body and was docked based on the backbone PCS and backbone chemical shift perturbation data. Unlike NOE-based structural determination, this method only requires resonance assignments of the backbone 1HN/15N signals and the PCS data obtained from several sets of two-dimensional 15N-heteronuclear single quantum coherence spectra, thus facilitating rapid structure determination of the proteinâ??protein complex.
- Content Type Journal Article
- DOI 10.1007/s10858-010-9401-4
- Authors
- Tomohide Saio, Hokkaido University Graduate School of Life Science Sapporo 001-0021 Japan
- Masashi Yokochi, Hokkaido University Graduate School of Pharmaceutical Sciences Sapporo 001-0021 Japan
- Hiroyuki Kumeta, Hokkaido University Graduate School of Pharmaceutical Sciences Sapporo 001-0021 Japan
- Fuyuhiko Inagaki, Hokkaido University Graduate School of Pharmaceutical Sciences Sapporo 001-0021 Japan
Source: Journal of Biomolecular NMR