Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein–protein complex structure determination

• DOI: 10.1007/s10858-012-9623-8
• Publication Date: 2012-04-09T12:26:14Z
• Authors: Yoshihiro Kobashi...; Tomohide Saio; Masahiro Ushio; Mitsuhiro Sekiguchi; Masashi Yokochi; Kenji Ogura; Fuyuhiko Inagaki
• Keywords: Degeneracy (biology)

Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, are valuable for the structure determination of protein–protein protein–ligand complexes. We have been developing lanthanide-binding peptide tag (hereafter LBT) anchored at two points via bond disulfide to target proteins. However, magnetic susceptibility tensor displays symmetry, which can cause multiple degenerated solutions calculation based solely on PCSs. Here we show convenient method resolving this degeneracy changing spacer length between LBT protein. applied approach PCS-based rigid body docking FKBP12-rapamycin complex mTOR FRB domain, demonstrated that could be resolved using PCS restraints obtained from two-point with different lengths. The present strategy will markedly increase usefulness determination.