Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq

Under the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation...

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Autores principales:	Mengxin Li, Yalong Cong, Yifei Qi, John Z. H. Zhang
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	small RNA OxyS RNA chaperone Hfq protein gene expression regulator molecular dynamics simulations binding free energy interaction entropy Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c3b78333201347af86bd12e751a86bec
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spelling	oai:doaj.org-article:c3b78333201347af86bd12e751a86bec2021-11-25T16:53:24ZComputational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq10.3390/biom111116532218-273Xhttps://doaj.org/article/c3b78333201347af86bd12e751a86bec2021-11-01T00:00:00Zhttps://www.mdpi.com/2218-273X/11/11/1653https://doaj.org/toc/2218-273XUnder the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in the defection of gene regulation. However, how the Hfq protein interacts with sRNA OxyS and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result was correlated with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly came from the increased van der Waals interactions (vdW). This research explored the binding mechanism between Oxys and chaperone protein Hfq and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights into the mechanism of gene expression regulation affected by protein mutations.Mengxin LiYalong CongYifei QiJohn Z. H. ZhangMDPI AGarticlesmall RNA OxySRNA chaperone Hfq proteingene expression regulatormolecular dynamics simulationsbinding free energyinteraction entropyMicrobiologyQR1-502ENBiomolecules, Vol 11, Iss 1653, p 1653 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	small RNA OxyS RNA chaperone Hfq protein gene expression regulator molecular dynamics simulations binding free energy interaction entropy Microbiology QR1-502
spellingShingle	small RNA OxyS RNA chaperone Hfq protein gene expression regulator molecular dynamics simulations binding free energy interaction entropy Microbiology QR1-502 Mengxin Li Yalong Cong Yifei Qi John Z. H. Zhang Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq
description	Under the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in the defection of gene regulation. However, how the Hfq protein interacts with sRNA OxyS and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result was correlated with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly came from the increased van der Waals interactions (vdW). This research explored the binding mechanism between Oxys and chaperone protein Hfq and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights into the mechanism of gene expression regulation affected by protein mutations.
format	article
author	Mengxin Li Yalong Cong Yifei Qi John Z. H. Zhang
author_facet	Mengxin Li Yalong Cong Yifei Qi John Z. H. Zhang
author_sort	Mengxin Li
title	Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq
title_short	Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq
title_full	Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq
title_fullStr	Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq
title_full_unstemmed	Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq
title_sort	computational insights into the binding mechanism of oxys srna with chaperone protein hfq
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/c3b78333201347af86bd12e751a86bec
work_keys_str_mv	AT mengxinli computationalinsightsintothebindingmechanismofoxyssrnawithchaperoneproteinhfq AT yalongcong computationalinsightsintothebindingmechanismofoxyssrnawithchaperoneproteinhfq AT yifeiqi computationalinsightsintothebindingmechanismofoxyssrnawithchaperoneproteinhfq AT johnzhzhang computationalinsightsintothebindingmechanismofoxyssrnawithchaperoneproteinhfq
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Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq

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