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Computational and experimental approaches to quantify protein binding interactions under confinement.

Deborah Leckband1, Daniel K Schwartz2, Yinghao Wu3

  • 1Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.

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New methods quantify protein interactions in crowded environments, revealing cadherin clustering and cooperativity that enhance cell adhesion. These approaches bridge binding kinetics across scales for adhesion proteins.

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Area of Science:

  • Biophysics
  • Cell Biology
  • Biochemistry

Background:

  • Crowded environments and confinement significantly alter adhesion protein interactions at cellular contacts.
  • Existing experimental and theoretical methods struggle to accurately quantify protein binding constants in these complex settings.

Purpose of the Study:

  • To introduce novel methodologies for quantifying protein binding kinetics in crowded membrane environments.
  • To investigate the role of cis (lateral) and trans (adhesive) cadherin interactions in intercellular adhesion.

Main Methods:

  • Development and application of single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule tracking.
  • Utilizing Kinetic Monte Carlo (KMC) simulations with a realistic model of cis cadherin interactions.
  • Extending smFRET measurements to analyze cis and trans cadherin interactions at membrane junctions.

Main Results:

  • Direct imaging of binding/unbinding rates for membrane-tethered cadherins.
  • Detection of cis cadherin interactions crucial for membrane clustering, which were previously unobserved in solution.
  • Identification of unexpected cooperativity between cis and trans cadherin binding, enhancing intercellular adhesion kinetics.

Conclusions:

  • The developed methods successfully quantify protein binding kinetics in complex, crowded environments.
  • A strategy is proposed to bridge protein binding kinetics across different length scales.
  • The methodologies are applicable beyond cadherins to other intercellular adhesion proteins.