Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry
The Cas9 endonuclease is an essential component of the CRISPR–Cas-based genome editing tools. The attainment of high specificity and efficiency of Cas9 during targetted DNA cleavage is the main problem that limits the clinical application of the CRISPR–Cas9 system. A deep understanding of the Cas9 m...
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MDPI AG
2022-01-01
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| Series: | International Journal of Molecular Sciences |
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| author | Polina V. Zhdanova Alexander A. Chernonosov Daria V. Prokhorova Grigory A. Stepanov Lyubov Yu. Kanazhevskaya Vladimir V. Koval |
| author_facet | Polina V. Zhdanova Alexander A. Chernonosov Daria V. Prokhorova Grigory A. Stepanov Lyubov Yu. Kanazhevskaya Vladimir V. Koval |
| author_sort | Polina V. Zhdanova |
| collection | DOAJ |
| description | The Cas9 endonuclease is an essential component of the CRISPR–Cas-based genome editing tools. The attainment of high specificity and efficiency of Cas9 during targetted DNA cleavage is the main problem that limits the clinical application of the CRISPR–Cas9 system. A deep understanding of the Cas9 mechanism and its structural-functional relationships is required to develop strategies for precise gene editing. Here, we present the first attempt to describe the solution structure of Cas9 from <i>S. pyogenes</i> using hydrogen-deuterium exchange mass spectrometry (HDX-MS) coupled to molecular dynamics simulations. HDX data revealed multiple protein regions with deuterium uptake levels varying from low to high. By analysing the difference in relative deuterium uptake by apoCas9 and its complex with sgRNA, we identified peptides involved in the complex formation and possible changes in the protein conformation. The REC3 domain was shown to undergo the most prominent conformational change upon enzyme-RNA interactions. Detection of the HDX in two forms of the enzyme provided detailed information about changes in the Cas9 structure induced by sgRNA binding and quantified the extent of the changes. The study demonstrates the practical utility of HDX-MS for the elucidation of mechanistic aspects of Cas9 functioning. |
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| format | Article |
| id | doaj.art-cbbe6a058f5045138a2c2af5aed7e9f4 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:51:03Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-cbbe6a058f5045138a2c2af5aed7e9f42023-11-23T16:35:22ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-01-01233112910.3390/ijms23031129Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass SpectrometryPolina V. Zhdanova0Alexander A. Chernonosov1Daria V. Prokhorova2Grigory A. Stepanov3Lyubov Yu. Kanazhevskaya4Vladimir V. Koval5Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, RussiaThe Cas9 endonuclease is an essential component of the CRISPR–Cas-based genome editing tools. The attainment of high specificity and efficiency of Cas9 during targetted DNA cleavage is the main problem that limits the clinical application of the CRISPR–Cas9 system. A deep understanding of the Cas9 mechanism and its structural-functional relationships is required to develop strategies for precise gene editing. Here, we present the first attempt to describe the solution structure of Cas9 from <i>S. pyogenes</i> using hydrogen-deuterium exchange mass spectrometry (HDX-MS) coupled to molecular dynamics simulations. HDX data revealed multiple protein regions with deuterium uptake levels varying from low to high. By analysing the difference in relative deuterium uptake by apoCas9 and its complex with sgRNA, we identified peptides involved in the complex formation and possible changes in the protein conformation. The REC3 domain was shown to undergo the most prominent conformational change upon enzyme-RNA interactions. Detection of the HDX in two forms of the enzyme provided detailed information about changes in the Cas9 structure induced by sgRNA binding and quantified the extent of the changes. The study demonstrates the practical utility of HDX-MS for the elucidation of mechanistic aspects of Cas9 functioning.https://www.mdpi.com/1422-0067/23/3/1129HDX-MShydrogen-deuterium exchange mass spectrometryCRISPR–Cas systemsCas9single guide RNAmolecular dynamics |
| spellingShingle | Polina V. Zhdanova Alexander A. Chernonosov Daria V. Prokhorova Grigory A. Stepanov Lyubov Yu. Kanazhevskaya Vladimir V. Koval Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry International Journal of Molecular Sciences HDX-MS hydrogen-deuterium exchange mass spectrometry CRISPR–Cas systems Cas9 single guide RNA molecular dynamics |
| title | Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry |
| title_full | Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry |
| title_fullStr | Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry |
| title_full_unstemmed | Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry |
| title_short | Probing the Dynamics of <i>Streptococcus pyogenes</i> Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry |
| title_sort | probing the dynamics of i streptococcus pyogenes i cas9 endonuclease bound to the sgrna complex using hydrogen deuterium exchange mass spectrometry |
| topic | HDX-MS hydrogen-deuterium exchange mass spectrometry CRISPR–Cas systems Cas9 single guide RNA molecular dynamics |
| url | https://www.mdpi.com/1422-0067/23/3/1129 |
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