Cited by 125Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies ResearchEnzyme Structure and Function

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ABangle: characterising the VH-VL orientation in antibodies

Dunbar, J., Fuchs, A., Shi, J., Deane, C. M.·2013·Protein Engineering Design and Selection

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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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Authors: Dunbar, J., Fuchs, A., Shi, J., & Deane, C. M.
Affiliations: University of Oxford (GB)
UCB Pharma (United Kingdom) (GB)
ORCID: Shi, J.
Deane, C. M.
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
DOI: 10.1093/protein/gzt020
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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ABangle: characterising the VH-VL orientation in antibodies

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