Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering
NCYM, a Homininae-specific oncoprotein, is the first de novo gene product experimentally shown to have oncogenic functions. NCYM stabilizes MYCN and β-catenin via direct binding and inhibition of GSK3β and promotes cancer progression in various tumors. Thus, the identification of compounds that bind...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2023.1213678/full |
| _version_ | 1797501620808843264 |
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| author | Seigi Yamamoto Fumiaki Kono Kazuma Nakatani Kazuma Nakatani Kazuma Nakatani Kazuma Nakatani Miwako Hirose Katsunori Horii Yoshitaka Hippo Yoshitaka Hippo Yoshitaka Hippo Taro Tamada Taro Tamada Yusuke Suenaga Tatsuhito Matsuo |
| author_facet | Seigi Yamamoto Fumiaki Kono Kazuma Nakatani Kazuma Nakatani Kazuma Nakatani Kazuma Nakatani Miwako Hirose Katsunori Horii Yoshitaka Hippo Yoshitaka Hippo Yoshitaka Hippo Taro Tamada Taro Tamada Yusuke Suenaga Tatsuhito Matsuo |
| author_sort | Seigi Yamamoto |
| collection | DOAJ |
| description | NCYM, a Homininae-specific oncoprotein, is the first de novo gene product experimentally shown to have oncogenic functions. NCYM stabilizes MYCN and β-catenin via direct binding and inhibition of GSK3β and promotes cancer progression in various tumors. Thus, the identification of compounds that binds to NCYM and structural characterization of the complex of such compounds with NCYM are required to deepen our understanding of the molecular mechanism of NCYM function and eventually to develop anticancer drugs against NCYM. In this study, the DNA aptamer that specifically binds to NCYM and enhances interaction between NCYM and GSK3β were identified for the first time using systematic evolution of ligands by exponential enrichment (SELEX). The structural properties of the complex of the aptamer and NCYM were investigated using atomic force microscopy (AFM) in combination with truncation and mutation of DNA sequence, pointing to the regions on the aptamer required for NCYM binding. Further analysis was carried out by small-angle X-ray scattering (SAXS). Structural modeling based on SAXS data revealed that when isolated, NCYM shows high flexibility, though not as a random coil, while the DNA aptamer exists as a dimer in solution. In the complex state, models in which NCYM was bound to a region close to an edge of the aptamer reproduced the SAXS data. Therefore, using a combination of SELEX, AFM, and SAXS, the present study revealed the structural properties of NCYM in its functionally active form, thus providing useful information for the possible future design of novel anti-cancer drugs targeting NCYM. |
| first_indexed | 2024-03-10T03:21:09Z |
| format | Article |
| id | doaj.art-19950001310f4a32898ccdef6c04184d |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-03-10T03:21:09Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-19950001310f4a32898ccdef6c04184d2023-11-23T10:02:17ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2023-11-011310.3389/fonc.2023.12136781213678Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scatteringSeigi Yamamoto0Fumiaki Kono1Kazuma Nakatani2Kazuma Nakatani3Kazuma Nakatani4Kazuma Nakatani5Miwako Hirose6Katsunori Horii7Yoshitaka Hippo8Yoshitaka Hippo9Yoshitaka Hippo10Taro Tamada11Taro Tamada12Yusuke Suenaga13Tatsuhito Matsuo14Laboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, JapanInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, JapanLaboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, JapanGraduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, JapanInnovative Medicine CHIBA Doctoral WISE Program, Chiba University, Chiba, JapanAll Directional Innovation Creator Ph.D. Project, Chiba University, Chiba, JapanDigital Healthcare Business Development Office, NEC Solution Innovators, Ltd., Tokyo, JapanDigital Healthcare Business Development Office, NEC Solution Innovators, Ltd., Tokyo, JapanLaboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, JapanGraduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, JapanLaboratory of Precision Tumor Model Systems, Chiba Cancer Center Research Institute, Chiba, JapanInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, JapanGraduate School of Science, Chiba University, Chiba, JapanLaboratory of Evolutionary Oncology, Chiba Cancer Center Research Institute, Chiba, JapanInstitute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, JapanNCYM, a Homininae-specific oncoprotein, is the first de novo gene product experimentally shown to have oncogenic functions. NCYM stabilizes MYCN and β-catenin via direct binding and inhibition of GSK3β and promotes cancer progression in various tumors. Thus, the identification of compounds that binds to NCYM and structural characterization of the complex of such compounds with NCYM are required to deepen our understanding of the molecular mechanism of NCYM function and eventually to develop anticancer drugs against NCYM. In this study, the DNA aptamer that specifically binds to NCYM and enhances interaction between NCYM and GSK3β were identified for the first time using systematic evolution of ligands by exponential enrichment (SELEX). The structural properties of the complex of the aptamer and NCYM were investigated using atomic force microscopy (AFM) in combination with truncation and mutation of DNA sequence, pointing to the regions on the aptamer required for NCYM binding. Further analysis was carried out by small-angle X-ray scattering (SAXS). Structural modeling based on SAXS data revealed that when isolated, NCYM shows high flexibility, though not as a random coil, while the DNA aptamer exists as a dimer in solution. In the complex state, models in which NCYM was bound to a region close to an edge of the aptamer reproduced the SAXS data. Therefore, using a combination of SELEX, AFM, and SAXS, the present study revealed the structural properties of NCYM in its functionally active form, thus providing useful information for the possible future design of novel anti-cancer drugs targeting NCYM.https://www.frontiersin.org/articles/10.3389/fonc.2023.1213678/fullde novo proteinNCYMDNA aptamersolution structureAFMSAXS |
| spellingShingle | Seigi Yamamoto Fumiaki Kono Kazuma Nakatani Kazuma Nakatani Kazuma Nakatani Kazuma Nakatani Miwako Hirose Katsunori Horii Yoshitaka Hippo Yoshitaka Hippo Yoshitaka Hippo Taro Tamada Taro Tamada Yusuke Suenaga Tatsuhito Matsuo Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering Frontiers in Oncology de novo protein NCYM DNA aptamer solution structure AFM SAXS |
| title | Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering |
| title_full | Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering |
| title_fullStr | Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering |
| title_full_unstemmed | Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering |
| title_short | Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering |
| title_sort | structural characterization of human de novo protein ncym and its complex with a newly identified dna aptamer using atomic force microscopy and small angle x ray scattering |
| topic | de novo protein NCYM DNA aptamer solution structure AFM SAXS |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2023.1213678/full |
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