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ABangle: characterising the VH-VL orientation in antibodies
Abstract
The binding site of an antibody is formed between the two variable domains, VH and VL, of its antigen binding fragment (Fab). Understanding how VH and VL orientate with respect to one another is important both for studying the mechanisms of antigen specificity and affinity and improving antibody modelling, docking and engineering. Different VH-VL orientations are commonly described using relative measures such as root-mean-square deviation. Recently, the orientation has also been characterised using the absolute measure of a VH-VL packing angle. However, a single angle cannot fully describe all modes of orientation. Here, we present a method which fully characterises VH-VL orientation in a consistent and absolute sense using five angles (HL, HC1, LC1, HC2 and LC2) and a distance (dc). Additionally, we provide a computational tool, ABangle, to allow the VH-VL orientation for any antibody to be automatically calculated and compared with all other known structures. We compare previous studies and show how the modes of orientation being identified relate to movements of different angles. Thus, we are able to explain why different studies identify different structural clusters and different residues as important. Given this result, we then identify those positions and their residue identities which influence each of the angular measures of orientation. Finally, by analysing VH-VL orientation in bound and unbound forms, we find that antibodies specific for protein antigens are significantly more flexible in their unbound form than antibodies specific for hapten antigens. ABangle is freely available at http://opig.stats.ox.ac.uk/webapps/abangle.
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“The second step involves accurate determination of the relative orientation of the VH and VL domains, which is crucial to determine the correct shape of the paratope [107, 109].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [109]
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Metadata
- Authors
- Dunbar, J., Fuchs, A., Shi, J., & Deane, C. M.
- Affiliations
- University of Oxford (GB)
- UCB Pharma (United Kingdom) (GB)
- ORCID
- Venue
- Protein Engineering Design and Selection
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-05-24
- Volume
- 26
- Issue
- 10
- Pages
- 611-620
- ISSN
- 0269-2139 (ISSN-L)
- 1741-0126
- 1741-0134
- OpenAlex
- W2154135618
- Cited by
- 125
- References
- 40
- Citations by year
- 2026: 5 · 2025: 11 · 2024: 6 · 2023: 22 · 2022: 11 · 2021: 12 · 2020: 8 · 2019: 11 · 2018: 7 · 2017: 9 · 2016: 7 · 2015: 7 · 2014: 7 · 2013: 2
- FWCI
- 3.43
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Protein Engineering Design and Selection (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Engineering and Physical Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Immunology and Microbiology › Immunology › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- antibody structure, Fab fragment, antibody binding sites, structural clusters, antibody flexibility, antibody engineering
- MeSH terms
- Animals, Antibodies, Haptens, Humans, Immunoglobulin Variable Region, Immunoglobulin Light Chains, Models, Molecular, Protein Conformation, Consensus Sequence, Computational Biology, Mice, Rats
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