Prediction of protein corona on nanomaterials by machine learning using novel descriptors
© 2020 Elsevier B.V. Effective in silico methods to predict protein corona compositions on engineered nanomaterials (ENMs) could help elucidate the biological outcomes of ENMs in biosystems without the need for conducting lengthy experiments for corona characterization. However, the physicochemical...
| Main Authors: | , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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Elsevier BV
2021
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| Online Access: | https://hdl.handle.net/1721.1/136307 |
| _version_ | 1826211037552050176 |
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| author | Duan, Yaokai Coreas, Roxana Liu, Yang Bitounis, Dimitrios Zhang, Zhenyuan Parviz, Dorsa Strano, Michael Demokritou, Philip Zhong, Wenwan |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Duan, Yaokai Coreas, Roxana Liu, Yang Bitounis, Dimitrios Zhang, Zhenyuan Parviz, Dorsa Strano, Michael Demokritou, Philip Zhong, Wenwan |
| author_sort | Duan, Yaokai |
| collection | MIT |
| description | © 2020 Elsevier B.V. Effective in silico methods to predict protein corona compositions on engineered nanomaterials (ENMs) could help elucidate the biological outcomes of ENMs in biosystems without the need for conducting lengthy experiments for corona characterization. However, the physicochemical properties of ENMs, used as the descriptors in current modeling methods, are insufficient to represent the complex interactions between ENMs and proteins. Herein, we utilized the fluorescence change (FC) from fluorescamine labeling on a protein, with or without the presence of the ENM, as a novel descriptor of the ENM to build machine learning models for corona formation. FCs were significantly correlated with the abundance of the corresponding proteins in the corona on diverse classes of ENMs, including metal and metal oxides, nanocellulose, and 2D ENMs. Prediction models established by the random forest algorithm using FCs as the ENM descriptors showed better performance than the conventional descriptors, such as ENM size and surface charge, in the prediction of corona formation. Moreover, they were able to predict protein corona formation on ENMs with very heterogeneous properties. We believe this novel descriptor can improve in silico studies of corona formation, leading to a better understanding on the protein adsorption behaviors of diverse ENMs in different biological matrices. Such information is essential for gaining a comprehensive view of how ENMs interact with biological systems in ENM safety and sustainability assessments. |
| first_indexed | 2024-09-23T14:59:34Z |
| format | Article |
| id | mit-1721.1/136307 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:59:34Z |
| publishDate | 2021 |
| publisher | Elsevier BV |
| record_format | dspace |
| spelling | mit-1721.1/1363072023-10-06T20:25:39Z Prediction of protein corona on nanomaterials by machine learning using novel descriptors Duan, Yaokai Coreas, Roxana Liu, Yang Bitounis, Dimitrios Zhang, Zhenyuan Parviz, Dorsa Strano, Michael Demokritou, Philip Zhong, Wenwan Massachusetts Institute of Technology. Department of Chemical Engineering © 2020 Elsevier B.V. Effective in silico methods to predict protein corona compositions on engineered nanomaterials (ENMs) could help elucidate the biological outcomes of ENMs in biosystems without the need for conducting lengthy experiments for corona characterization. However, the physicochemical properties of ENMs, used as the descriptors in current modeling methods, are insufficient to represent the complex interactions between ENMs and proteins. Herein, we utilized the fluorescence change (FC) from fluorescamine labeling on a protein, with or without the presence of the ENM, as a novel descriptor of the ENM to build machine learning models for corona formation. FCs were significantly correlated with the abundance of the corresponding proteins in the corona on diverse classes of ENMs, including metal and metal oxides, nanocellulose, and 2D ENMs. Prediction models established by the random forest algorithm using FCs as the ENM descriptors showed better performance than the conventional descriptors, such as ENM size and surface charge, in the prediction of corona formation. Moreover, they were able to predict protein corona formation on ENMs with very heterogeneous properties. We believe this novel descriptor can improve in silico studies of corona formation, leading to a better understanding on the protein adsorption behaviors of diverse ENMs in different biological matrices. Such information is essential for gaining a comprehensive view of how ENMs interact with biological systems in ENM safety and sustainability assessments. 2021-10-27T20:34:48Z 2021-10-27T20:34:48Z 2020 2021-06-15T17:11:45Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136307 en 10.1016/J.IMPACT.2020.100207 NanoImpact Creative Commons Attribution-NonCommercial-NoDerivs License http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier BV PMC |
| spellingShingle | Duan, Yaokai Coreas, Roxana Liu, Yang Bitounis, Dimitrios Zhang, Zhenyuan Parviz, Dorsa Strano, Michael Demokritou, Philip Zhong, Wenwan Prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| title | Prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| title_full | Prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| title_fullStr | Prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| title_full_unstemmed | Prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| title_short | Prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| title_sort | prediction of protein corona on nanomaterials by machine learning using novel descriptors |
| url | https://hdl.handle.net/1721.1/136307 |
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