title: 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.
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, Japan; Department of Biochemistry, School of Medicine, Keio University, Shinjuku, Tokyo, Japan.
authors.forename: Hanae
authors.initials: H
authors.lastname: Shimo
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, Japan.
authors.forename: Satya Nanda Vel
authors.initials: SN
authors.lastname: Arjunan
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Osaka, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Machiyama
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
authors.forename: Taiko
authors.initials: T
authors.lastname: Nishino
authors.affiliation: Department of Biochemistry, School of Medicine, Keio University, Shinjuku, Tokyo, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Suematsu
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Osaka, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Fujita
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan; Department of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Takahashi
mesh_terms: D001457:Anion Exchange Protein 1, Erythrocyte / Q000737:chemistry* / Q000378:metabolism*; D019295:Computational Biology; D004910:Erythrocyte Membrane / Q000737:chemistry* / Q000378:metabolism*; D004912:Erythrocytes / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D010084:Oxidation-Reduction
chemical_list: D001457:Anion Exchange Protein 1, Erythrocyte