Structure and specificity of several triclocarban-binding single domain camelid antibody fragments
Abstract
The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. Here, a high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed “CDR4”. A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In additionmore »
- Authors:
-
- Univ. of the Republic (UDELAR), Montevideo (Uruguay)
- Univ. of California, Davis, CA (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Univ. of California; National Science Foundation (NSF)
- OSTI Identifier:
- 1569914
- Alternate Identifier(s):
- OSTI ID: 1461214
- Grant/Contract Number:
- AC02-06CH11357; AC02-76SF00515; AC02-05CH11231; P41GM103393; GM105404; GM073210; GM082250; GM094625; P41GM103403; S10OD021527; MR-15-328599; 1330685
- Resource Type:
- Accepted Manuscript
- Journal Name:
- JMR. Journal of Molecular Recognition
- Additional Journal Information:
- Journal Volume: 32; Journal Issue: 1; Journal ID: ISSN 0952-3499
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Tabares-da Rosa, Sofia, Wogulis, Linda A., Wogulis, Mark D., González-Sapienza, Gualberto, and Wilson, David K. Structure and specificity of several triclocarban-binding single domain camelid antibody fragments. United States: N. p., 2018.
Web. doi:10.1002/jmr.2755.
Tabares-da Rosa, Sofia, Wogulis, Linda A., Wogulis, Mark D., González-Sapienza, Gualberto, & Wilson, David K. Structure and specificity of several triclocarban-binding single domain camelid antibody fragments. United States. https://doi.org/10.1002/jmr.2755
Tabares-da Rosa, Sofia, Wogulis, Linda A., Wogulis, Mark D., González-Sapienza, Gualberto, and Wilson, David K. Mon .
"Structure and specificity of several triclocarban-binding single domain camelid antibody fragments". United States. https://doi.org/10.1002/jmr.2755. https://www.osti.gov/servlets/purl/1569914.
@article{osti_1569914,
title = {Structure and specificity of several triclocarban-binding single domain camelid antibody fragments},
author = {Tabares-da Rosa, Sofia and Wogulis, Linda A. and Wogulis, Mark D. and González-Sapienza, Gualberto and Wilson, David K.},
abstractNote = {The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. Here, a high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed “CDR4”. A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In addition to methotrexate, this is the second report of haptens binding in a tunnel formed by CDR1, suggesting that compounds with similar hydrophobicity and shape could be recognized by nanobodies in analogous fashion. Structure-guided mutations failed to improve binding affinity for T4 and T9 underscoring the high degree of natural optimization.},
doi = {10.1002/jmr.2755},
journal = {JMR. Journal of Molecular Recognition},
number = 1,
volume = 32,
place = {United States},
year = {Mon Jul 23 00:00:00 EDT 2018},
month = {Mon Jul 23 00:00:00 EDT 2018}
}
Web of Science
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Works referencing / citing this record:
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