Phage empty set 29 protein p6 is in a monomer-dimer equilibrium that shifts to higher association states at the millimolar concentrations found in vivo

Protein p6 from Bacillus subtilis phage empty set29 (M-r = 11 800) binds in vitro to DNA forming a large nucleoprotein complex in which the :DNA wraps a multimeric protein core. The high intracellular abundance of protein p6 together with its ability to bind the whole empty set29 DNA in vitro strongly suggests that it plays a role in viral genome organization. We have determined by sedimentation equilibrium analysis that protein p6 (1-100 mu M range), in the absence of DNA, is in a monomer-dimer equilibrium, with an association constant (K-2) of similar to 2 x 10(5) M-1. The intracellular concentration of protein p6 (similar to 1 mM) was estimated measuring the number of copies per cell (7 x 10(5)) and the cell volume (1 x 10(-15) L), At concentrations around 1 mM, protein p6 associates into oligomers. This self-association behavior is compatible with a dimer-hexamer model (K-2,K-6 = 3.2 x 10(8) M-2) or with an isodesmic association of the dimer (K = 950 M-1), because the apparent weight-average molecular mass (M-w,M-a) does not reach saturation at the highest protein concentrations. The sedimentation coefficients of protein p6 monomer and dimer were 1.4 and 2.0, respectively, compatible with translational frictional ratios (f/f(0)) of 1.15 and 1.30, which slightly deviate from the hydrodynamics of a rigid globular protein. Taking together these results and considering the structure of the nucleoprotein complex, we speculate that the observed oligomers of protein p6 could mimic a scaffold on which DNA folds to form the nucleoprotein complex in vivo.