Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

Hanlun Jiang; Lizhe Zhu; Amélie Héliou; Xin Gao; Julie Bernauer; Xuhui Huang

doi:10.1007/978-1-4939-6563-2_18

Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

Hanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao, Julie Bernauer, Xuhui Huang

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2 Scopus citations

Abstract

MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

Original language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Springer Nature
Pages	251-275
Number of pages	25
ISBN (Print)	9781493965618
DOIs	https://doi.org/10.1007/978-1-4939-6563-2_18
State	Published - Dec 7 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: This work is supported by the Hong Kong Research Grant Council [grant numbers 16302214, 609813, HKUST C6009-15G, AoE/ M-09/12, M-HKUST601/13, and T13-607/12R to X.H.] and the National Science Foundation of China [grant number 21273188 to X.H.]. The work is also supported by a grant from the PROCOREFrance/ Hong Kong Joint Research Scheme sponsored by the Research Grants Council and the Consulate General of France in Hong Kong (F-HK29/11T) (X.H. and J.B.). X.G. was supported by funding from King Abdullah University of Science and Technology. This research made use of the resources of the Supercomputing Laboratory at King Abdullah University of Science and Technology.

ASJC Scopus subject areas

Genetics
Molecular Biology

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10.1007/978-1-4939-6563-2_18

Cite this

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title = "Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches",

abstract = "MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.",

author = "Hanlun Jiang and Lizhe Zhu and Am{\'e}lie H{\'e}liou and Xin Gao and Julie Bernauer and Xuhui Huang",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: This work is supported by the Hong Kong Research Grant Council [grant numbers 16302214, 609813, HKUST C6009-15G, AoE/ M-09/12, M-HKUST601/13, and T13-607/12R to X.H.] and the National Science Foundation of China [grant number 21273188 to X.H.]. The work is also supported by a grant from the PROCOREFrance/ Hong Kong Joint Research Scheme sponsored by the Research Grants Council and the Consulate General of France in Hong Kong (F-HK29/11T) (X.H. and J.B.). X.G. was supported by funding from King Abdullah University of Science and Technology. This research made use of the resources of the Supercomputing Laboratory at King Abdullah University of Science and Technology.",

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N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: This work is supported by the Hong Kong Research Grant Council [grant numbers 16302214, 609813, HKUST C6009-15G, AoE/ M-09/12, M-HKUST601/13, and T13-607/12R to X.H.] and the National Science Foundation of China [grant number 21273188 to X.H.]. The work is also supported by a grant from the PROCOREFrance/ Hong Kong Joint Research Scheme sponsored by the Research Grants Council and the Consulate General of France in Hong Kong (F-HK29/11T) (X.H. and J.B.). X.G. was supported by funding from King Abdullah University of Science and Technology. This research made use of the resources of the Supercomputing Laboratory at King Abdullah University of Science and Technology.

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N2 - MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

AB - MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

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Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

Abstract

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