ArticlemAbs
Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations.Journal of chemical information and modeling · 2023Article
- Non-covalent Fc-Fab interactions significantly alter internal dynamics of an IgG1 antibody.Scientific reports · 2022Article
- A universal in silico V(D)J recombination strategy for developing humanized monoclonal antibodies.Journal of nanobiotechnology · 2022Article
- IgG1 conformational behavior: elucidation of the N-glycosylation role via molecular dynamics.Biophysical journal · 2021Article
- Communication pathways bridge local and global conformations in an IgG4 antibody.Scientific reports · 2021Article
- Modeling and Molecular Dynamic Simulation of F(ab')Bioinformatics and biology insights · 2021Article
- Comparison of the pH- and thermally-induced fluctuations of a therapeutic antibody Fab fragment by molecular dynamics simulation.Computational and structural biotechnology journal · 2021Article
- Article
- Thinking outside the Laboratory: Analyses of Antibody Structure and Dynamics within Different Solvent Environments in Molecular Dynamics (MD) Simulations.Antibodies (Basel, Switzerland) · 2018Article
- Fast antibody fragment motion: flexible linkers act as entropic spring.Scientific reports · 2016Article
- Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.PLoS computational biology · 2016Article
- Review
- Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.PLoS computational biology · 2015Article
- Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage.Proteins · 2015Article
- Article
- Fluorescence anisotropy (polarization): from drug screening to precision medicine.Expert opinion on drug discovery · 2015Review
- In silico selection of therapeutic antibodies for development: viscosity, clearance, and chemical stability.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Molecular dynamics simulation of the crystallizable fragment of IgG1-insights for the design of Fcabs.International journal of molecular sciences · 2014Article
- Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with F(ab) and F(c) domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.