ArticlePLoS computational biology2015
Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Efficient generation of epitope-targeted antibodies with Germinal.Nature biotechnology · 2026Article
- Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis.bioRxiv : the preprint server for biology · 2026Article
- Oligo DNA-based quantum dot (QD) single-particle tracking for multicolor single-molecule imaging.Biophysics and physicobiology · 2026Article
- Efficient generation of epitope-targetedbioRxiv : the preprint server for biology · 2025Article
- Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions.Nature machine intelligence · 2025Article
- A single-domain antibody library based on a stability-engineered human VH3 scaffold.Scientific reports · 2024Article
- "Redirecting an anti-IL-1β antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A".Communications biology · 2023Article
- Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes.Nanoscale · 2023Article
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- Prediction of the structural interface between fibroblast growth factor23 and Burosumab using alanine scanning and molecular docking.Scientific reports · 2022Article
- Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody.Biomolecules · 2022Article
- Antigen binding by conformational selection in near-germline antibodies.The Journal of biological chemistry · 2022Article
- Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes.Angewandte Chemie (International ed. in English) · 2022Review
- Communication pathways bridge local and global conformations in an IgG4 antibody.Scientific reports · 2021Article
- Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VScientific reports · 2021Article
- Parameters and determinants of responses to selection in antibody libraries.PLoS computational biology · 2021Article
- The Allosteric Effect in Antibody-Antigen Recognition.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Local and Global Rigidification Upon Antibody Affinity Maturation.Frontiers in molecular biosciences · 2020Article
- Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments.Frontiers in molecular biosciences · 2020Article
- Structure and Dynamics of Stacking Interactions in an Antibody Binding Site.Biochemistry · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assessed using a Distance Constraint Model (DCM). We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants. The DCM is an ensemble based statistical mechanical approach that accounts for enthalpy/entropy compensation due to network rigidity, which has been quite successful in elucidating conformational flexibility and Quantitative Stability/Flexibility Relationships (QSFR) in proteins. Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation. The increase in CDR H3 loop rigidity is consistent with other studies in the literature. The redistribution of conformational flexibility is largely controlled by nonspecific changes in the H-bond network, although certain Arg to Asp salt bridges create highly localized rigidity increases. Taken together, these results reveal an intricate flexibility/rigidity response that accompanies affinity maturation.
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