Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction

Despite the high specificity between antigen and antibody binding, similar epitopes can be recognized or cross-neutralized by paratopes of antibody with different binding affinities. How to accurately characterize this slight variation which may or may not change the antigen-antibody binding affinit...

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Autores principales: Qiu, Tianyi, Xiao, Han, Zhang, Qingchen, Qiu, Jingxuan, Yang, Yiyan, Wu, Dingfeng, Cao, Zhiwei, Zhu, Ruixin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406442/
https://www.ncbi.nlm.nih.gov/pubmed/25901362
http://dx.doi.org/10.1371/journal.pone.0122416
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author Qiu, Tianyi
Xiao, Han
Zhang, Qingchen
Qiu, Jingxuan
Yang, Yiyan
Wu, Dingfeng
Cao, Zhiwei
Zhu, Ruixin
author_facet Qiu, Tianyi
Xiao, Han
Zhang, Qingchen
Qiu, Jingxuan
Yang, Yiyan
Wu, Dingfeng
Cao, Zhiwei
Zhu, Ruixin
author_sort Qiu, Tianyi
collection PubMed
description Despite the high specificity between antigen and antibody binding, similar epitopes can be recognized or cross-neutralized by paratopes of antibody with different binding affinities. How to accurately characterize this slight variation which may or may not change the antigen-antibody binding affinity is a key issue in this area. In this report, by combining cylinder model with shell structure model, a new fingerprint was introduced to describe both the structural and physical-chemical features of the antigen and antibody protein. Furthermore, beside the description of individual protein, the specific epitope-paratope interaction fingerprint (EPIF) was developed to reflect the bond and the environment of the antigen-antibody interface. Finally, Proteochemometric Modeling of the antigen-antibody interaction was established and evaluated on 429 antigen-antibody complexes. By using only protein descriptors, our model achieved the best performance ([Image: see text] ) among peers. Further, together with EPIF as a new cross-term, our model ([Image: see text] ) can significantly outperform peers with multiplication of ligand and protein descriptors as a cross-term ([Image: see text] ). Results illustrated that: 1) our newly designed protein fingerprints and EPIF can better describe the antigen-antibody interaction; 2) EPIF is a better and specific cross-term in Proteochemometric Modeling for antigen-antibody interaction. The fingerprints designed in this study will provide assistance to the description of antigen-antibody binding, and in future, it may be valuable help for the high-throughput antibody screening. The algorithm is freely available on request.
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spelling pubmed-44064422015-05-07 Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction Qiu, Tianyi Xiao, Han Zhang, Qingchen Qiu, Jingxuan Yang, Yiyan Wu, Dingfeng Cao, Zhiwei Zhu, Ruixin PLoS One Research Article Despite the high specificity between antigen and antibody binding, similar epitopes can be recognized or cross-neutralized by paratopes of antibody with different binding affinities. How to accurately characterize this slight variation which may or may not change the antigen-antibody binding affinity is a key issue in this area. In this report, by combining cylinder model with shell structure model, a new fingerprint was introduced to describe both the structural and physical-chemical features of the antigen and antibody protein. Furthermore, beside the description of individual protein, the specific epitope-paratope interaction fingerprint (EPIF) was developed to reflect the bond and the environment of the antigen-antibody interface. Finally, Proteochemometric Modeling of the antigen-antibody interaction was established and evaluated on 429 antigen-antibody complexes. By using only protein descriptors, our model achieved the best performance ([Image: see text] ) among peers. Further, together with EPIF as a new cross-term, our model ([Image: see text] ) can significantly outperform peers with multiplication of ligand and protein descriptors as a cross-term ([Image: see text] ). Results illustrated that: 1) our newly designed protein fingerprints and EPIF can better describe the antigen-antibody interaction; 2) EPIF is a better and specific cross-term in Proteochemometric Modeling for antigen-antibody interaction. The fingerprints designed in this study will provide assistance to the description of antigen-antibody binding, and in future, it may be valuable help for the high-throughput antibody screening. The algorithm is freely available on request. Public Library of Science 2015-04-22 /pmc/articles/PMC4406442/ /pubmed/25901362 http://dx.doi.org/10.1371/journal.pone.0122416 Text en © 2015 Qiu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Qiu, Tianyi
Xiao, Han
Zhang, Qingchen
Qiu, Jingxuan
Yang, Yiyan
Wu, Dingfeng
Cao, Zhiwei
Zhu, Ruixin
Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction
title Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction
title_full Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction
title_fullStr Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction
title_full_unstemmed Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction
title_short Proteochemometric Modeling of the Antigen-Antibody Interaction: New Fingerprints for Antigen, Antibody and Epitope-Paratope Interaction
title_sort proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406442/
https://www.ncbi.nlm.nih.gov/pubmed/25901362
http://dx.doi.org/10.1371/journal.pone.0122416
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