Visualization of transient encounter complexes in protein-protein association

Kinetic data on a number of protein - protein associations have provided evidence for the initial formation of a pre- equilibrium encounter complex that subsequently relaxes to the final stereospecific complex (1). Site- directed mutagenesis(2 - 4) and brownian dynamics simulations(5 - 7) have suggested that the rate of association can be modulated by perturbations in charge distribution outside the direct interaction surfaces. Furthermore, rate enhancement through non- specific binding may occur by either a reduction in dimensionality(8) or the presence of a short- range, non- specific attractive potential(9). Here, using paramagnetic relaxation enhancement, we directly demonstrate the existence and visualize the distribution of an ensemble of transient, non- specific encounter complexes under equilibrium conditions for a relatively weak protein - protein complex between the amino- terminal domain of enzyme I and the phosphocarrier protein HPr. Neither the stereospecific complex(10) alone nor any single alternative conformation can account fully for the intermolecular paramagnetic relaxation enhancement data. Restrained rigid- body simulated annealing refinement against the paramagnetic relaxation enhancement data enables us to obtain an atomic probability distribution map of the non- specific encounter complex ensemble that qualitatively correlates with the electrostatic surface potentials on the interacting proteins. Qualitatively similar results are presented for two other protein - protein complexes.