Hydrodynamic bead modelling of the 2:1 p50–IκBγ complex Original Research Article

NFκB is an important and ubiquitous transcription factor formed by various homo- and heterodimers of the NFκB family. The active transcription factor regulates genes involved in immune, inflammatory and survival responses. Specificity in gene regulation is achieved, at least in part, by the distinct DNA binding preferences of the various homo- and heterodimers and by the complex pathways that lead to signal-induced degradation of the IκB inhibitors. Analytical ultracentrifugation and hydrodynamic bead modelling were used to model the solution structures of the NFκB family member p50, its inhibitor IκBγ and their complex. Sedimentation equilibrium (SE) and sedimentation velocity (SV) data show that p50 is a dimer in solution with a sedimentation coefficient consistent with a conformation intermediate between the closed conformation observed in the crystal structure of the p50 (N-terminal domain)–p65 heterodimer complexed with IκBα and the open conformation adopted by p50 when bound to DNA. SE and SV data show that IκBγ is a monomer in solution and is prone to aggregation over time. p50 forms a 2:1 stoichiometric complex with IκBγ in solution with a sedimentation coefficient consistent with a closed conformation for the p50 dimer.