ArticleBiophysical journal2004
Brownian adhesive dynamics (BRAD) for simulating the receptor-mediated binding of viruses.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- The Future of the COVID-19 Pandemic: How Good (or Bad) Can the SARS-CoV2 Spike Protein Get?Cells · 2022Review
- Computational methods to study enveloped viral entry.Biochemical Society transactions · 2021Review
- Quantifying and controlling bond multivalency for advanced nanoparticle targeting to cells.Nano convergence · 2021Review
- Shear-driven rolling of DNA-adhesive microspheres.Biophysical journal · 2021Article
- A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.PLoS computational biology · 2020Article
- A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness: A multiscale model of viral infection in epithelial tissues.bioRxiv : the preprint server for biology · 2020Article
- Probability of Immobilization on Host Cell Surface Regulates Viral Infectivity.Physical review letters · 2020Article
- Article
- The auxiliary region method: a hybrid method for coupling PDE- and Brownian-based dynamics for reaction-diffusion systems.Royal Society open science · 2018Article
- Kinetic Modeling of Virus Growth in Cells.Microbiology and molecular biology reviews : MMBR · 2018Review
- Evolution of Multivalent Nanoparticle Adhesion via Specific Molecular Interactions.Langmuir : the ACS journal of surfaces and colloids · 2016Article
- Modeling Nanoparticle Targeting to a Vascular Surface in Shear Flow Through Diffusive Particle Dynamics.Nanoscale research letters · 2015Article
- Probing the effect of force on HIV-1 receptor CD4.ACS nano · 2014Article
- Adhesive dynamics.Journal of biomechanical engineering · 2014Review
- Multiscale perspectives of virus entry via endocytosis.Virology journal · 2013Review
- Receptor concentration and diffusivity control multivalent binding of Sv40 to membrane bilayers.PLoS computational biology · 2013Article
- Kinetics of nanoparticle targeting by dissipative particle dynamics simulations.Biomacromolecules · 2009Article
- Platelet adhesive dynamics. Part II: high shear-induced transient aggregation via GPIbalpha-vWF-GPIbalpha bridging.Biophysical journal · 2008Article
- Role of gp120 trimerization on HIV binding elucidated with Brownian adhesive dynamics.Biophysical journal · 2008Article
- The role of flexible tethers in multiple ligand-receptor bond formation between curved surfaces.Biophysical journal · 2006Article
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2 authors.
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Abstract
Current viral docking models have relied upon the assumption that bond formation and breakage are independent of viral and docking surface geometry, as well as the forces exerted on the bonds. This assumption, known as the equivalent site hypothesis (ESH), is examined in detail using a newly developed simulation technique-Brownian adhesive dynamics (BRAD). The simulation couples the thermal motion of viral particles with adhesive dynamics models to characterize the effect of bonding on viral motion. We use the binding of HIV-like particles to CD4 expressing cells as a model system to illustrate the utility of BRAD. Comparison of the transition rates between bound states predicted by ESH and the rates resulting from BRAD simulations show dramatic differences; at values of the equilibrium crosslinking constant, K(x)R(T), where ESH suggests all virus adhesion proteins will be bound (K(x)R(T) = 10(6)), BRAD predicts not all virus adhesion proteins will be bound. At values of the equilibrium crosslinking constant used in typical ESH calculations of virus docking (K(x)R(T) = 1) we find BRAD simulations predict no binding. The mean bond density from BRAD models is often much lower than that predicted by ESH for equivalent parameter values. BRAD suggests that the viruses are much less well bound than ESH predicts. The differences suggest that binding models for viruses need to be reexamined closely. BRAD is a simulation technique that will be useful for quantifying the receptor-mediated binding of a wide variety of viruses to cells.
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