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On the protein-protein diffusional encounter complex.

R R Gabdoulline1, R C Wade

  • 1European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.

Journal of Molecular Recognition : JMR
|August 10, 1999
PubMed
Summary
This summary is machine-generated.

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Researchers constructed protein-protein encounter complex structures using experimental data. The study reveals encounter complex formation involves partial protein contact and desolvation, influencing association rates.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Physical Chemistry

Background:

  • Protein-protein interactions are crucial for biological processes.
  • The encounter complex is a transient intermediate in protein association, but its structure is experimentally elusive.
  • Understanding encounter complexes is key to determining protein association rates.

Purpose of the Study:

  • To construct the ensemble of three-dimensional structures of protein-protein diffusional encounter complexes.
  • To utilize experimental data on association rates, mutation effects, and solvent properties to model encounter complexes.

Main Methods:

  • Fitting association rate data to various encounter complex definitions.
  • Analyzing the dependence of association rates on ionic strength, viscosity, and protein mutations.

Related Experiment Videos

  • Developing a model for the encounter complex based on experimental observations.

    • Main Results:

    • Encounter complexes were well-fitted when proteins were within approximately 17 Å root-mean-squared distance of their bound state.
    • Ionic strength dependence of association rates is primarily influenced by protein-ion interactions, not protein-protein charge separation.
    • Experimental data suggest encounter complexes involve partial contacts and significant desolvation of the interacting proteins.

    Conclusions:

    • The structure of the encounter complex can be inferred from experimental association rate data.
    • Ionic strength is a less reliable indicator of encounter complex geometry compared to mutation and viscosity data.
    • A model of the encounter complex featuring partial contacts and desolvation aligns with experimental findings.