Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes

Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, Makoto Suematsu, Hideaki Fujita, Masaru Tomita, Koichi Takahashi

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Article numbere1004210
JournalPLoS Computational Biology
Volume11
Issue number6
DOIs
Publication statusPublished - 2015 Jun 5

Fingerprint

Erythrocyte
Oxidation
Cluster Analysis
Red Blood Cells
erythrocytes
Erythrocytes
Clustering
oxidation
Blood
blood
simulation
Simulation
Cluster Formation
Erythrocyte Anion Exchange Protein 1
Cells
Blood Circulation
Enzyme kinetics
Molecules
Oxidative stress
Oxidative Stress

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Modelling and Simulation
  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology
  • Ecology
  • Cellular and Molecular Neuroscience

Cite this

Shimo, H., Arjunan, S. N. V., Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., ... Takahashi, K. (2015). Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS Computational Biology, 11(6), [e1004210]. https://doi.org/10.1371/journal.pcbi.1004210

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. / Shimo, Hanae; Arjunan, Satya Nanda Vel; Machiyama, Hiroaki; Nishino, Taiko; Suematsu, Makoto; Fujita, Hideaki; Tomita, Masaru; Takahashi, Koichi.

In: PLoS Computational Biology, Vol. 11, No. 6, e1004210, 05.06.2015.

Research output: Contribution to journalArticle

Shimo, H, Arjunan, SNV, Machiyama, H, Nishino, T, Suematsu, M, Fujita, H, Tomita, M & Takahashi, K 2015, 'Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes', PLoS Computational Biology, vol. 11, no. 6, e1004210. https://doi.org/10.1371/journal.pcbi.1004210
Shimo H, Arjunan SNV, Machiyama H, Nishino T, Suematsu M, Fujita H et al. Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS Computational Biology. 2015 Jun 5;11(6). e1004210. https://doi.org/10.1371/journal.pcbi.1004210
Shimo, Hanae ; Arjunan, Satya Nanda Vel ; Machiyama, Hiroaki ; Nishino, Taiko ; Suematsu, Makoto ; Fujita, Hideaki ; Tomita, Masaru ; Takahashi, Koichi. / Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. In: PLoS Computational Biology. 2015 ; Vol. 11, No. 6.
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