Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes

Abstract

Oxidative stress mediated clustering of membrane protein band 3 plays an essential role in the clearance of damaged and aged red blood cells (RBCs) from the circulation. While a number of previous experimental studies have observed changes in band 3 distribution after oxidative treatment, the details of how these clusters are formed and how their properties change under different conditions have remained poorly understood. To address these issues, a framework that enables the simultaneous monitoring of the temporal and spatial changes following oxidation is needed. In this study, we established a novel simulation strategy that incorporates deterministic and stochastic reactions with particle reaction-diffusion processes, to model band 3 cluster formation at single molecule resolution. By integrating a kinetic model of RBC antioxidant metabolism with a model of band 3 diffusion, we developed a model that reproduces the time-dependent changes of glutathione and clustered band 3 levels, as well as band 3 distribution during oxidative treatment, observed in prior studies. We predicted that cluster formation is largely dependent on fast reverse reaction rates, strong affinity between clustering molecules, and irreversible hemichrome binding. We further predicted that under repeated oxidative perturbations, clusters tended to progressively grow and shift towards an irreversible state. Application of our model to simulate oxidation in RBCs with cytoskeletal deficiency also suggested that oxidation leads to more enhanced clustering compared to healthy RBCs. Taken together, our model enables the prediction of band 3 spatio-temporal profiles under various situations, thus providing valuable insights to potentially aid understanding mechanisms for removing senescent and premature RBCs.

Multi-algorithm particle simulations with Spatiocyte

“…These predictions were later supported experimentally [29][30]. Recently, we built a multi-algorithm simulation model of erythrocyte band 3 membrane cluster formation with Spatiocyte [31]. The model showed that strong affinity between the clustering molecules and irreversibly binding hemichromes aid the generation of oxidation induced clusters as observed in experiments.…”

Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator

“…5b–d ). Oxidative stress impairs erythrocyte membrane integrity through initial oxidation of hemoglobin, leading to the precipitation of Heinz bodies and band 3 (a major erythrocyte membrane protein) clustering; thus, band 3 clustering serves as an essential molecular marker of erythrocyte removal 40 . Using erythrocytes isolated from 9 to 11 individual whole blood samples, we confirmed that band 3 protein is aggregated with either chloroquine (CQ) or diamide treatment, which was alleviated by AG1 treatment (Fig.…”

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.…”

“…The run time of Spatiocyte is also comparable to Smoldyn in the benchmark enzymatic reaction model [56]. The reduced computational cost and the simplicity of MLM implementation have promoted its applications in both biological [57][58][59][60][61][62] and chemical [63][64][65] surface reactions. Nonetheless, biological surfaces such the cell and nuclear membranes are not arranged as fixed lattice structures.…”