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Visualization of transient encounter complexes in protein–protein association

Abstract

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 complex1. Site-directed mutagenesis2,3,4 and brownian dynamics simulations5,6,7 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 dimensionality8 or the presence of a short-range, non-specific attractive potential9. 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 complex10 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.

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Figure 1: Observed and calculated intermolecular PREs for the EIN–HPr complex.
Figure 2: Ensemble refinement and intermolecular PRE Q -factor.
Figure 3: Characterization of non-specific EIN–HPr encounter complexes.
Figure 4: Observed and calculated PRE 1HN-Γ2 values for the IIAMannitol–HPr complex.

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Acknowledgements

We thank C. Schwieters, A. Szabo and C. Bewley for discussions; and C. Byeon for assistance with initial sample preparation. This work was supported by funds from the Intramural Program of the NIH, NIDDK and the AIDS Targeted Antiviral program of the Office of the Director of the NIH (to G.M.C.).

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Correspondence to G. Marius Clore.

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Supplementary Notes

This file contains Supplementary Figures 1–6, Supplementary Methods, Supplementary Table and additional references. (PDF 453 kb)

Supplementary Movie 1

Movie representation of left-hand panels of Supplementary Figure 4a. (MOV 105070 kb)

Supplementary Movie 2

Movie representation of right-hand panels of Supplementary Figure 4a. (MOV 91291 kb)

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Tang, C., Iwahara, J. & Clore, G. Visualization of transient encounter complexes in protein–protein association. Nature 444, 383–386 (2006). https://doi.org/10.1038/nature05201

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