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Robust protein protein interactions in crowded cellular environments.

Eric J Deeds1, Orr Ashenberg, Jaline Gerardin

  • 1Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert #536, Boston, MA 02115, USA.

Proceedings of the National Academy of Sciences of the United States of America
|September 13, 2007
PubMed
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Specific protein interactions are crucial for life but challenging to study in crowded cells. Our model shows specific interactions are robust within a defined temperature range, requiring an energy gap for stability and evolution.

Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Systems Biology

Background:

  • Protein-protein interactions are fundamental to cellular function and biological processes.
  • The crowded and heterogeneous cellular environment poses challenges to specific protein interactions due to potential promiscuous binding.
  • Understanding specificity is key to comprehending protein function, evolution, and cellular system dynamics.

Purpose of the Study:

  • To investigate the robustness of specific protein-protein interactions in a crowded cellular environment using a computational model.
  • To identify the physical constraints governing the formation and stability of specific protein complexes.
  • To explore the implications for the evolution and design of protein interaction networks.

Main Methods:

Related Experiment Videos

  • Development of a simplified computational model simulating diffusion and interaction of designed model proteins within a mixture of unrelated proteins.
  • Analysis of interaction specificity across a range of temperatures to assess complex stability and promiscuity.
  • Inclusion of factors such as relative concentrations and binding energies to mimic cellular conditions.

    • Main Results:

    • Specific protein complexes exhibit robustness against promiscuous interactions within a defined temperature range: T(design) > T > T(rand).
    • Above T(design), specific complexes become unstable; below T(rand), their formation is suppressed by non-specific interactions.
    • The condition T(design) > T(rand) is necessary for specific interactions, implying an energy gap between specific and non-specific binding events.

    Conclusions:

    • A specific energy gap between binding energies is a critical physical constraint for the evolutionary selection or design of specific protein interfaces.
    • The findings provide insights into how protein interaction specificity is maintained and evolved within complex cellular systems.
    • This work contributes to a deeper understanding of protein repertoire function and evolution in vivo.