Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding
Open accessAbstract
Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo.
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The increasing number of structural, sequence and experimental data on antibodies being deposited in the public domain provides the necessary foundation for improving data-driven methods.
“The increasing number of structural [16], sequence [17] and experimental data [18–21] on antibodies being deposited in the public domain provides the necessary foundation for improving such data-driven methods.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [20]
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- Authors
- Koenig, P., Lee, C. V., Walters, B. T., Janakiraman, V., Stinson, J., Patapoff, T. W., & Fuh, G.
- Affiliations
- Genentech (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2017-01-05
- Volume
- 114
- Issue
- 4
- Pages
- E486-E495
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC5278476
- OpenAlex
- W2570949719
- Cited by
- 107
- References
- 73
- Citations by year
- 2026: 16 · 2025: 12 · 2024: 15 · 2023: 11 · 2022: 9 · 2021: 8 · 2020: 6 · 2019: 13 · 2018: 13 · 2017: 3
- FWCI
- 7.25
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- antibody variable domains, somatic hypermutation, deep mutational scanning, antigen binding affinity, thermal stability, antibody maturation, human antibody repertoire
- MeSH terms
- Antibodies, Antibody Affinity, Antigens, Binding Sites, Antibody, Humans, Immunoglobulin Fab Fragments, Mutation, Protein Conformation
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