Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations
Customization of proteins to undertake temperature-specific functions would expand their scope of use in medical treatment, food processing, and bioelectronic devices. To customize papain for temperature-specific peptide binding, the dynamic structure of papain was modified by repeatedly mutating V1...
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| Format: | Article |
| Language: | English |
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AIP Publishing LLC
2025-03-01
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| Series: | AIP Advances |
| Online Access: | http://dx.doi.org/10.1063/5.0216782 |
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| _version_ | 1850259639061446656 |
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| author | Katsuhiko Nishiyama |
| author_facet | Katsuhiko Nishiyama |
| author_sort | Katsuhiko Nishiyama |
| collection | DOAJ |
| description | Customization of proteins to undertake temperature-specific functions would expand their scope of use in medical treatment, food processing, and bioelectronic devices. To customize papain for temperature-specific peptide binding, the dynamic structure of papain was modified by repeatedly mutating V110, R111, and Q112 through the complementary use of deep neural network methods and molecular dynamics simulations. Overall, 18 mutation patterns were discovered to customize papain for temperature-specific peptide binding. The decision tree indicated that the binding energy changed rapidly, with the 112th residue and carbon atoms of the 110 to 112th residue as the main influencing factors. |
| format | Article |
| id | doaj-art-e37fb238e6cf4f05b7224c0bcf47f80e |
| institution | OA Journals |
| issn | 2158-3226 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | AIP Publishing LLC |
| record_format | Article |
| series | AIP Advances |
| spelling | doaj-art-e37fb238e6cf4f05b7224c0bcf47f80e2025-08-20T01:55:49ZengAIP Publishing LLCAIP Advances2158-32262025-03-01153035111035111-610.1063/5.0216782Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulationsKatsuhiko Nishiyama0National Institute of Technology (KOSEN), Gunma College, 580 Toba-cho, Maebashi, Gunma 371-8530, JapanCustomization of proteins to undertake temperature-specific functions would expand their scope of use in medical treatment, food processing, and bioelectronic devices. To customize papain for temperature-specific peptide binding, the dynamic structure of papain was modified by repeatedly mutating V110, R111, and Q112 through the complementary use of deep neural network methods and molecular dynamics simulations. Overall, 18 mutation patterns were discovered to customize papain for temperature-specific peptide binding. The decision tree indicated that the binding energy changed rapidly, with the 112th residue and carbon atoms of the 110 to 112th residue as the main influencing factors.http://dx.doi.org/10.1063/5.0216782 |
| spellingShingle | Katsuhiko Nishiyama Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations AIP Advances |
| title | Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations |
| title_full | Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations |
| title_fullStr | Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations |
| title_full_unstemmed | Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations |
| title_short | Investigation of mutations to customize structurally dynamic papain proteins for temperature-specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations |
| title_sort | investigation of mutations to customize structurally dynamic papain proteins for temperature specific peptide binding by complementary use of two different artificial intelligence methods and molecular simulations |
| url | http://dx.doi.org/10.1063/5.0216782 |
| work_keys_str_mv | AT katsuhikonishiyama investigationofmutationstocustomizestructurallydynamicpapainproteinsfortemperaturespecificpeptidebindingbycomplementaryuseoftwodifferentartificialintelligencemethodsandmolecularsimulations |