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The Allosteric Effect in Antibody-Antigen Recognition

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Allostery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2253))

Abstract

We studied the molecular details of the recognition of antigens by the variable domain of their cognate antibodies in as well as those elicited by the constant domains, which do not directly interact with antigens. Such effects are difficult to study experimentally; however, molecular dynamics simulations and subsequent residue interaction network analysis provide insight into the allosteric communication between the antigen-binding CDR region and the constant domain. We performed MD simulations of the complex of Fab and prion-associated peptide in the apo and bound forms and follow the conformational changes in the antibody and cross-talk between its subunits and with antigens. These protocols could be generally applied for studies of other antigens-antibody recognition systems.

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Acknowledgements

This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number HHSN261200800001E. This research was supported (in part) by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. JZ was supported in part by the Intramural Research Program of the NIH, NIDCD.

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Authors and Affiliations

  1. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA

    Jun Zhao

  2. Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA

    Ruth Nussinov & Buyong Ma

  3. Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel

    Ruth Nussinov

Authors
  1. Jun Zhao
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  2. Ruth Nussinov
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  3. Buyong Ma
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Corresponding author

Correspondence to Buyong Ma .

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Editors and Affiliations

  1. Unit of Chemical-Physics Fundamentals in Chemical Engineering Department of Engineering, Universitá Campus Bio-Medico di Rome, Rome, Italy

    Luisa Di Paola

  2. Environment and Health Department, Instituto Superiore di Sanità, Rome, Italy

    Alessandro Giuliani

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Zhao, J., Nussinov, R., Ma, B. (2021). The Allosteric Effect in Antibody-Antigen Recognition. In: Di Paola, L., Giuliani, A. (eds) Allostery. Methods in Molecular Biology, vol 2253. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1154-8_11

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  • DOI: https://doi.org/10.1007/978-1-0716-1154-8_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1153-1

  • Online ISBN: 978-1-0716-1154-8

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