Open Access
International Journal of Molecular Sciences, volume 23, issue 3, pages 1129
Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry
Publication type: Journal Article
Publication date: 2022-01-20
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 5.6
ISSN: 16616596, 14220067
PubMed ID:
35163047
Catalysis
Organic Chemistry
Inorganic Chemistry
Physical and Theoretical Chemistry
Computer Science Applications
Spectroscopy
Molecular Biology
General Medicine
Abstract
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 S. pyogenes 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.
Citations by journals
|
1
2
|
|
|
International Journal of Molecular Sciences
|
International Journal of Molecular Sciences
2 publications, 100%
|
|
1
2
|
Citations by publishers
|
1
2
|
|
|
Multidisciplinary Digital Publishing Institute (MDPI)
|
Multidisciplinary Digital Publishing Institute (MDPI)
2 publications, 100%
|
|
1
2
|
- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2022],"ids":[0],"codes":[0],"imageUrls":[""],"datasets":[{"label":"Citations number","data":[2],"backgroundColor":["#3B82F6"],"percentage":["100"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["International Journal of Molecular Sciences"],"ids":[14627],"codes":[0],"imageUrls":["\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp"],"datasets":[{"label":"","data":[2],"backgroundColor":["#3B82F6"],"percentage":[100],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Multidisciplinary Digital Publishing Institute (MDPI)"],"ids":[202],"codes":[0],"imageUrls":["\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp"],"datasets":[{"label":"","data":[2],"backgroundColor":["#3B82F6"],"percentage":[100],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}
Metrics
Cite this
GOST |
RIS |
BibTex |
MLA
Cite this
GOST
Copy
Zhdanova P. V. et al. Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry // International Journal of Molecular Sciences. 2022. Vol. 23. No. 3. p. 1129.
GOST all authors (up to 50)
Copy
Zhdanova P. V., Chernonosov A. A., Prokhorova D. V., Stepanov G. A., Kanazhevskaya L. Yu., Koval V. V. Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry // International Journal of Molecular Sciences. 2022. Vol. 23. No. 3. p. 1129.
Cite this
RIS
Copy
TY - JOUR
DO - 10.3390/ijms23031129
UR - https://doi.org/10.3390%2Fijms23031129
TI - Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry
T2 - International Journal of Molecular Sciences
AU - Zhdanova, Polina V
AU - Prokhorova, Daria V
AU - Chernonosov, Alexander Anatolievich
AU - Stepanov, Grigory A
AU - Kanazhevskaya, Lyubov Yu
AU - Koval, Vladimir V
PY - 2022
DA - 2022/01/20 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 1129
IS - 3
VL - 23
PMID - 35163047
SN - 1661-6596
SN - 1422-0067
ER -
Cite this
BibTex
Copy
@article{2022_Zhdanova,
author = {Polina V Zhdanova and Daria V Prokhorova and Alexander Anatolievich Chernonosov and Grigory A Stepanov and Lyubov Yu Kanazhevskaya and Vladimir V Koval},
title = {Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry},
journal = {International Journal of Molecular Sciences},
year = {2022},
volume = {23},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {jan},
url = {https://doi.org/10.3390%2Fijms23031129},
number = {3},
pages = {1129},
doi = {10.3390/ijms23031129}
}
Cite this
MLA
Copy
Zhdanova, Polina V., et al. “Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry.” International Journal of Molecular Sciences, vol. 23, no. 3, Jan. 2022, p. 1129. https://doi.org/10.3390%2Fijms23031129.