Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution
Although the 20S core particle (CP) of the proteasome is an important component of the 26S holoenzyme, the stand-alone 20S CP acts directly on intrinsically disordered and oxidized/damaged proteins to degrade them in a ubiquitin-independent manner. It has been postulated that some structural feature...
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/24/17486 |
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| author | Yunhao Zhu Kaishin Shigeyoshi Yumiko Hayakawa Sae Fujiwara Masamichi Kishida Hitoshi Ohki Tomohisa Horibe Masafumi Shionyu Tamio Mizukami Makoto Hasegawa |
| author_facet | Yunhao Zhu Kaishin Shigeyoshi Yumiko Hayakawa Sae Fujiwara Masamichi Kishida Hitoshi Ohki Tomohisa Horibe Masafumi Shionyu Tamio Mizukami Makoto Hasegawa |
| author_sort | Yunhao Zhu |
| collection | DOAJ |
| description | Although the 20S core particle (CP) of the proteasome is an important component of the 26S holoenzyme, the stand-alone 20S CP acts directly on intrinsically disordered and oxidized/damaged proteins to degrade them in a ubiquitin-independent manner. It has been postulated that some structural features of substrate proteins are recognized by the 20S CP to promote substrate uptake, but the mechanism of substrate recognition has not been fully elucidated. In this study, we screened peptides that bind to the 20S CP from a random eight-residue pool of amino acid sequences using complementary DNA display an in vitro molecular evolution technique. The identified 20S CP-binding amino acid sequence was chemically synthesized and its effects on the 20S CP were investigated. The 20S CP-binding peptide stimulated the proteolytic activity of the inactive form of 20S CP. The peptide bound directly to one of the α-subunits, opening a gate for substrate entry on the α-ring. Furthermore, the attachment of this peptide sequence to α-synuclein enhanced its degradation by the 20S CP in vitro. In addition to these results, docking simulations indicated that this peptide binds to the top surface of the α-ring. These peptides could function as a key to control the opening of the α-ring gate. |
| first_indexed | 2024-03-08T20:40:34Z |
| format | Article |
| id | doaj.art-1e3a3e2661d54fa8b525b05f93ec044d |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T20:40:34Z |
| publishDate | 2023-12-01 |
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| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1e3a3e2661d54fa8b525b05f93ec044d2023-12-22T14:14:45ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0124241748610.3390/ijms242417486Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial EvolutionYunhao Zhu0Kaishin Shigeyoshi1Yumiko Hayakawa2Sae Fujiwara3Masamichi Kishida4Hitoshi Ohki5Tomohisa Horibe6Masafumi Shionyu7Tamio Mizukami8Makoto Hasegawa9Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanModality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, JapanModality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanGraduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, JapanAlthough the 20S core particle (CP) of the proteasome is an important component of the 26S holoenzyme, the stand-alone 20S CP acts directly on intrinsically disordered and oxidized/damaged proteins to degrade them in a ubiquitin-independent manner. It has been postulated that some structural features of substrate proteins are recognized by the 20S CP to promote substrate uptake, but the mechanism of substrate recognition has not been fully elucidated. In this study, we screened peptides that bind to the 20S CP from a random eight-residue pool of amino acid sequences using complementary DNA display an in vitro molecular evolution technique. The identified 20S CP-binding amino acid sequence was chemically synthesized and its effects on the 20S CP were investigated. The 20S CP-binding peptide stimulated the proteolytic activity of the inactive form of 20S CP. The peptide bound directly to one of the α-subunits, opening a gate for substrate entry on the α-ring. Furthermore, the attachment of this peptide sequence to α-synuclein enhanced its degradation by the 20S CP in vitro. In addition to these results, docking simulations indicated that this peptide binds to the top surface of the α-ring. These peptides could function as a key to control the opening of the α-ring gate.https://www.mdpi.com/1422-0067/24/24/17486directed evolutionpeptidesphotoaffinity labelingproteasomeprotein degradation |
| spellingShingle | Yunhao Zhu Kaishin Shigeyoshi Yumiko Hayakawa Sae Fujiwara Masamichi Kishida Hitoshi Ohki Tomohisa Horibe Masafumi Shionyu Tamio Mizukami Makoto Hasegawa Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution International Journal of Molecular Sciences directed evolution peptides photoaffinity labeling proteasome protein degradation |
| title | Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution |
| title_full | Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution |
| title_fullStr | Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution |
| title_full_unstemmed | Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution |
| title_short | Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution |
| title_sort | acceleration of protein degradation by 20s proteasome binding peptides generated by in vitro artificial evolution |
| topic | directed evolution peptides photoaffinity labeling proteasome protein degradation |
| url | https://www.mdpi.com/1422-0067/24/24/17486 |
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