Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements

Abstract

We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring biological cooperativity of molecular binding networks: in particular, ligand molecules binding to cell surface receptor proteins. Our results show how the non-statistical uncertainties lead to invalid identification of the measured cooperativity. Through this computational scheme, the biological interpretation can be more objectively evaluated and understood under a specific experimental configuration of interest.

G-Quadruplex-Proximized Aptamers (G4PA) Efficiently Targeting Cell-Surface Transferrin Receptors for Targeted Cargo Delivery

“…To address it, we conducted a fluorescence titration using FACS (Figure S3) to compare the binding affinity of the dimeric G4PA and monomeric control (Figure e), of which the Scatchard plot shows a TfR is attached by two TfR aptamers with a synergistic effect reflected by the downward concavity (Figure S4). − The dimerization of G4PA holds the two aptamers close, and such a proximity effect contributes to their effective corporation in binding TfR, just as other proximity-enhanced aptamer–ligand interactions. − …”

Surface reaction-diffusion kinetics on lattice at the microscopic scale

“…It has been successfully used to capture the influence of microscopic effects on the behavior of cells at the macroscopic scale. These include the formation of a high density ring over the entire bacterium cell membrane as a result of transient membrane association and rebinding of proteins [57], the clustering of proteins on the red blood cell membrane from oxidative stress [62] and the oligomerization of receptors and its influence on ligand binding kinetics [86]. As the spatiotemporal resolution of imaging techniques continue to advance [87], time-dependent reaction kinetics and molecular trajectories will become more accessible.…”