ArticlePLoS computational biology2016
Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Streptavidin-DisplayingSensors (Basel, Switzerland) · 2026Article
- Impact of N-terminal dimerization on formin homology 1 domain polymer dynamics and actin assembly.Biophysical journal · 2026Article
- Affinity Enhancement in Discrete Multivalent MegaMolecules.Chembiochem : a European journal of chemical biology · 2026Article
- Antigen flexibility supports the avidity of hemagglutinin-specific antibodies at low antigen densities.PLoS pathogens · 2026Article
- Impact of N-terminal dimerization on formin homology 1 domain polymer dynamics and actin assembly.bioRxiv : the preprint server for biology · 2025Article
- Elemental mass spectrometry imaging of biomolecules using metal-conjugated probes.Nature reviews. Chemistry · 2025Review
- A Kinetic Model of Antigen-Dependent IgG Oligomerization and Complement Binding.Small science · 2025Article
- Doubling multiplexed imaging capability via spatial expression pattern-guided protein pairing and computational unmixing.Communications biology · 2025Article
- The molecular reach of antibodies crucially underpins their viral neutralisation capacity.Nature communications · 2025Article
- High-throughput antibody screening with high-quality factor nanophotonics and bioprinting.ArXiv · 2024Article
- Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors.PLoS computational biology · 2024Article
- Serum immunoglobulin and the threshold of Fc receptor-mediated immune activation.Biochimica et biophysica acta. General subjects · 2023Review
- Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding.The journal of physical chemistry. B · 2023Article
- Rational nanoparticle design: Optimization using insights from experiments and mathematical models.Journal of controlled release : official journal of the Controlled Release Society · 2023Review
- Engineered molecular sensors for quantifying cell surface crowding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Antibody binding reports spatial heterogeneities in cell membrane organization.Nature communications · 2023Article
- Non-covalent Fc-Fab interactions significantly alter internal dynamics of an IgG1 antibody.Scientific reports · 2022Article
- From affinity selection to kinetic selection in Germinal Centre modelling.PLoS computational biology · 2022Article
- Absolute Quantitation of Serum Antibody Reactivity Using the Richards Growth Model for Antigen Microspot Titration.Sensors (Basel, Switzerland) · 2022Article
- Stochastic modeling of antibody binding predicts programmable migration on antigen patterns.Nature computational science · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, we work out a theoretical model that allows to explain all the features observed in the simulations. Our combined computational and theoretical framework is in excellent agreement with surface-plasmon resonance data and allows us to establish a number of important results. (i) Internal flexibility is key to maximize bivalent binding, flexible IgGs being able to explore the surface with their second arm in search for an available hapten. This is made clear by the strongly reduced ability to bind with both arms displayed by artificial IgGs designed to rigidly keep a prescribed shape. (ii) The large size of IgGs is instrumental to keep neighboring molecules at a certain distance (surface repulsion), which essentially makes antigens within reach of the second Fab always unoccupied on average. (iii) One needs to account independently for the thermodynamic and geometric factors that regulate the binding equilibrium. The key geometrical parameters, besides excluded-volume repulsion, describe the screening of free haptens by neighboring bound antibodies. We prove that the thermodynamic parameters govern the low-antigen-concentration regime, while the surface screening and repulsion only affect the binding at high hapten densities. Importantly, we prove that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies. Overall, our model provides a valuable, accurate theoretical paradigm beyond existing frameworks to interpret experimental profiles of antibodies binding to multi-valent surfaces of different sorts in many contexts.
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