Computational and experimental approaches to quantify protein binding interactions under confinement

Deborah Leckband, Daniel K. Schwartz, Yinghao Wu

Research output: Contribution to journalReview articlepeer-review


Crowded environments and confinement alter the interactions of adhesion proteins confined to membranes or narrow, crowded gaps at adhesive contacts. Experimental approaches and theoretical frameworks were developed to quantify protein binding constants in these environments. However, recent predictions and the complexity of some protein interactions proved challenging to address with prior experimental or theoretical approaches. This perspective highlights new methods developed by these authors that address these challenges. Specifically, single-molecule fluorescence resonance energy transfer and single-molecule tracking measurements were developed to directly image the binding/unbinding rates of membrane-tethered cadherins. Results identified predicted cis (lateral) interactions, which control cadherin clustering on membranes but were not detected in solution. Kinetic Monte Carlo simulations, based on a realistic model of cis cadherin interactions, were developed to extract binding/unbinding rate constants from heterogeneous single-molecule data. The extension of single-molecule fluorescence measurements to cis and trans (adhesive) cadherin interactions at membrane junctions identified unexpected cooperativity between cis and trans binding that appears to enhance intercellular binding kinetics. Comparisons of intercellular binding kinetics, kinetic Monte Carlo simulations, and single-molecule fluorescence data suggest a strategy to bridge protein binding kinetics across length scales. Although cadherin is the focus of these studies, the approaches can be extended to other intercellular adhesion proteins.

Original languageEnglish (US)
Pages (from-to)424-434
Number of pages11
JournalBiophysical journal
Issue number4
StatePublished - Feb 20 2024

ASJC Scopus subject areas

  • Biophysics


Dive into the research topics of 'Computational and experimental approaches to quantify protein binding interactions under confinement'. Together they form a unique fingerprint.

Cite this