Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes
Publication Date
June 05, 2015
Journal
PLOS Computational Biology
Authors
Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, et al
Volume
11
Issue
6
Pages
e1004210
DOI
https://dx.plos.org/10.1371/journal.pcbi.1004210
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004210
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26046580
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457884
Europe PMC
http://europepmc.org/abstract/MED/26046580
Web of Science
000357340100007
Scopus
84953261487
Mendeley
http://www.mendeley.com/research/particle-simulation-oxidation-induced-band-3-clustering-human-erythrocytes
Events
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Mendeley | Further Information

{"title"=>"Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes", "type"=>"journal", "authors"=>[{"first_name"=>"Hanae", "last_name"=>"Shimo", "scopus_author_id"=>"36453117000"}, {"first_name"=>"Satya Nanda Vel", "last_name"=>"Arjunan", "scopus_author_id"=>"35202946200"}, {"first_name"=>"Hiroaki", "last_name"=>"Machiyama", "scopus_author_id"=>"35170513500"}, {"first_name"=>"Taiko", "last_name"=>"Nishino", "scopus_author_id"=>"35741388400"}, {"first_name"=>"Makoto", "last_name"=>"Suematsu", "scopus_author_id"=>"7006480591"}, {"first_name"=>"Hideaki", "last_name"=>"Fujita", "scopus_author_id"=>"55315497900"}, {"first_name"=>"Masaru", "last_name"=>"Tomita", "scopus_author_id"=>"55552897900"}, {"first_name"=>"Koichi", "last_name"=>"Takahashi", "scopus_author_id"=>"56956009900"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"84953261487", "pmid"=>"26046580", "pui"=>"607497659", "issn"=>"15537358", "scopus"=>"2-s2.0-84953261487", "doi"=>"10.1371/journal.pcbi.1004210"}, "id"=>"fea83c48-86a0-3c85-9f74-e3be691bbef1", "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.", "link"=>"http://www.mendeley.com/research/particle-simulation-oxidation-induced-band-3-clustering-human-erythrocytes", "reader_count"=>21, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>3, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Physics and Astronomy"=>3, "Chemistry"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Japan"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2097892"], "description"=>"<p>We developed a particle model to represent the spatial and temporal changes that occur during RBC oxidation, which result in the clustering of band 3 and opsonization by naturally occurring antibodies (NAbs). (1) Major reactions from a prior kinetic model of RBC metabolism [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004210#pcbi.1004210.ref039\" target=\"_blank\">39</a>], and experimentally validated diffusion related parameters for band 3 were integrated into a single-particle simulation model. (2) Time-course data and visual data resulting from simulations under 0.25 mM diamide treatment were compared with those of past experiments. (3) The model was optimized by testing various reaction schemes, including specification of cluster dissociation rates and the addition of an irreversible clustering reaction. (4) The model was simulated under multiple diamide additions for varying concentrations and time intervals. (5) An extended model including physical confinement by spectrin cytoskeletal components was developed. (6) The spectrin model was applied to assess band 3 clustering in spectrin deficient RBCs.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438413, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Workflow_diagram_of_present_study_/1438413", "title"=>"Workflow diagram of present study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097893"], "description"=>"<p>(A) A representative image of band 3 distribution in control and diamide treated mouse RBCs obtained by epifluorescence microscopy. Scale bar is 10 μm, inset represents a higher magnification of the portion of the cell indicated. Arrows indicate dense cluster-like dense regions of band 3 on the membrane. (B) Schematic representation of the band 3 clustering model. Nodes and edges in the cytoplasm represent metabolites/hemoglobin states and enzymatic reactions, respectively. Nodes in the membrane indicate diffusion-reaction processes. Bold arrows represent diamide-mediated reactions. Abbreviations: Glucose; GLC, Glucose-6-phosphate; G6P, Glucose-6-phosphatase; GL6P, Reduced nicotinamide adenine dinucleotide phosphate; NADPH, Nicotinamide adenine dinucleotide phosphate; NADP, Reduced glutathione; GSH, Oxidized glutathione; GSSG, Adenosine triphosphate; MgATP, Adenosine diphosphate; MgADP, Phosphate group; P, Oxygenated hemoglobin; HbO<sub>2</sub>, Methemoglobin; metHb, Denatured hemoglobin; hemichrome, Hexokinase; HK, Glucose-6-phosphate dehydrogenase; G6PDH, glutathione reductase; GSSGR, Glutathione turnover; OX, Oxidized band 3; Band3oxi, Phosphorylated band 3; Band3phos, Clustered band 3; Band3cluster.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438414, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Remodeling_of_diamide_induced_band_3_cluster_formation_in_RBCs_/1438414", "title"=>"Remodeling of diamide induced band 3 cluster formation in RBCs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097894"], "description"=>"<p>(A) Comparison between measured levels of GSH (top) and clustered band 3 (bottom) published by Pantaleo et al. ([<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004210#pcbi.1004210.ref003\" target=\"_blank\">3</a>]) and corresponding simulated values, in healthy (left) and G6PD deficient (right) RBCs during diamide treatment. All simulations were performed using E-Cell System Environment Version 3.2.3pre2 installed with Spatiocyte, and the average for stochastic simulations of 100 runs was computed. (B) Visualization of simulation results showing inhomogeneous distribution of band 3. Each molecule represents a single band 3 dimer. The membrane is represented by the surface of a cuboid shape compartment with one-thousandth actual RBC volume. Error bars (indicated in grey) represent the standard deviation. The mean for the percentage of clustered molecules at t = 15, 30, 60, and 120 min are 7.61 (standard deviation, SD: 0.44), 10.2 (SD: 0.52), 7.42 (SD: 0.48), and 2.47 (SD: 0.25) for the control, and 15.3 (SD: 0.59), 32.4 (SD: 0.72), 41.0 (SD: 0.75), and 41.3 (SD: 0.77) for the G6PD deficient RBC, respectively. (C) Visual results of simulation on biconcave shape compartment one-hundredth actual RBC size (t = 30 min).</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438415, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Measured_and_predicted_biochemical_changes_in_diamide_treated_RBCs_/1438415", "title"=>"Measured and predicted biochemical changes in diamide treated RBCs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097895"], "description"=>"<p>(A) Scheme of cluster disassembly in the developed model. In the Spatiocyte model, space is discretized into a hexagonal close-packed lattice, with each surface voxel having 6 adjoining neighbors. Here we modified the model to have binding site number dependent dissociation rates, thus allowing molecules bound to fewer molecules, to dissociate from the cluster faster than those bound to many molecules. (B) Histograms of the number of neighboring cluster-associated band 3 for reaction scheme with equal rates for cluster dissociation (left) and binding site number dependent dissociation rates (right) at t = 30 min. Insets represent the visual output of the simulation, and close-ups of the clustered regions. Cluster associated band 3 are represented in yellow, remaining band 3 species are represented in green. In this analysis, a large number of molecules with a large number of neighbors represent a large cluster with densely packed molecules.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438416, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_cluster_dissociation_reaction_scheme_on_cluster_morphology_/1438416", "title"=>"Effect of cluster dissociation reaction scheme on cluster morphology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097896"], "description"=>"<p>(A) Schematic representation of a scheme where band 3 only reversibly undergoes transitions into oxidized, phosphorylated, and clustered state (top), and the full scheme of the developed model (bottom) including irreversible formation and attachment of denatured hemoglobin, known as hemichrome, to band 3. (B) Comparison of predicted clustered band 3 levels in using the scheme with only reversible reactions (grey), the developed model (solid black), and experimental results (dotted black, [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004210#pcbi.1004210.ref003\" target=\"_blank\">3</a>]) for control and G6PD deficient RBCs. The graphs for the developed model and experimental results are the same as those of <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004210#pcbi.1004210.g003\" target=\"_blank\">Fig 3</a>, but have been reprinted for comparison.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438417, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Addition_of_an_irreversible_hemichrome_attachment_scheme_prolongs_cluster_lifetimes_/1438417", "title"=>"Addition of an irreversible hemichrome attachment scheme prolongs cluster lifetimes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097897"], "description"=>"<p>(A) Clustered band 3 levels during addition of 0.25 μM diamide at 10s intervals for 1 week. (B) Clustered band 3 levels during single pulse and repeated perturbations by 0.125 mM diamide at 30 and 60 min intervals (left), and corresponding visual output (right). (C) Heatmap of clustered band 3 levels with the x-axis as pulse intervals, and y-axis as diamide concentration, and z-axis as percentage of clustered band 3 at t = 60 min.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438418, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g006", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Repeated_oxidation_triggers_irreversible_clustering_in_healthy_RBCs_/1438418", "title"=>"Repeated oxidation triggers irreversible clustering in healthy RBCs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097898"], "description"=>"<p>(A) The erythrocyte membrane skeleton is organized as a polygonal network formed by spectrin molecules linked to ankyrin, which is bound to the cytoplasmic domain of band 3 (right). This spectrin-based RBC membrane cytoskeletal network was reproduced in Spatiocyte (right) where light grey molecules represent spectrin, and orange molecules represent spectrin bound band 3. (B) A typical simulated trajectory of band 3 undergoing confined diffusion observed with a time resolution of 0.22 ms for total observation time of 700 ms. (C) Comparison of the clustered band 3 levels in the spectrin network band 3 membrane model, for control (red), half of spectrin present (green), and one third of spectrin present (blue). (D) Corresponding visual output of simulation results. Spectrin and band 3 molecules are shown in yellow and green, respectively.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438419, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.g007", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spectrin_deficiency_enhances_band_3_cluster_formation_in_the_spectrin_network_compartment_model_/1438419", "title"=>"Spectrin deficiency enhances band 3 cluster formation in the spectrin network compartment model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097899"], "description"=>"<p>Model reactions.</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438420, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.t001", "stats"=>{"downloads"=>10, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_reactions_/1438420", "title"=>"Model reactions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097900"], "description"=>"<p>Model parameters for the healthy and G6PD deficient RBC (from [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004210#pcbi.1004210.ref047\" target=\"_blank\">47</a>]).</p>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438421, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004210.t002", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_parameters_for_the_healthy_and_G6PD_deficient_RBC_from_47_/1438421", "title"=>"Model parameters for the healthy and G6PD deficient RBC (from [47]).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-05 03:30:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2097901", "https://ndownloader.figshare.com/files/2097902", "https://ndownloader.figshare.com/files/2097903", "https://ndownloader.figshare.com/files/2097904", "https://ndownloader.figshare.com/files/2097905", "https://ndownloader.figshare.com/files/2097906", "https://ndownloader.figshare.com/files/2097907"], "description"=>"<div><p>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.</p></div>", "links"=>[], "tags"=>["aid understanding mechanisms", "band 3 distribution", "Human Erythrocytes Oxidative stress", "band 3 levels", "oxidation", "band 3 diffusion", "Oxidation Induced Band 3 Clustering", "novel simulation strategy", "oxidative treatment", "RBC antioxidant metabolism", "membrane protein band 3", "model band 3 cluster formation"], "article_id"=>1438422, "categories"=>["Biological Sciences"], "users"=>["Hanae Shimo", "Satya Nanda Vel Arjunan", "Hiroaki Machiyama", "Taiko Nishino", "Makoto Suematsu", "Hideaki Fujita", "Masaru Tomita", "Koichi Takahashi"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004210.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004210.s002", "https://dx.doi.org/10.1371/journal.pcbi.1004210.s003", "https://dx.doi.org/10.1371/journal.pcbi.1004210.s004", "https://dx.doi.org/10.1371/journal.pcbi.1004210.s005", "https://dx.doi.org/10.1371/journal.pcbi.1004210.s006", "https://dx.doi.org/10.1371/journal.pcbi.1004210.s007"], "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Particle_Simulation_of_Oxidation_Induced_Band_3_Clustering_in_Human_Erythrocytes_/1438422", "title"=>"Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-05 03:30:18"}

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  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"1", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"11", "full-text"=>"5", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"2", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"12", "full-text"=>"10", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"21", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"4", "full-text"=>"31", "pdf"=>"14", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"6", "full-text"=>"3", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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