Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation.

Chaoqun Li, Xiaojia Zhao, Xiaomin Zhu, Pengtao Xie, Guangju Chen

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Article in International journal of molecular sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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RNA language model and graph attention network for RNA and small molecule binding sites prediction.Bioinformatics (Oxford, England) · 2025
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5 authors.

Chaoqun LiCollege of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China. lichaoqun@hdc.edu.cn.ORCID 0000-0002-5888-4182

Xiaojia ZhaoCollege of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China. zhaoxiaoya@hdc.edu.cn.

Xiaomin ZhuCollege of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China. libin@hdc.edu.cn.

Pengtao XieCollege of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China. hdxyxpt@gmail.com.

Guangju ChenCollege of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China. gjchen@bnu.edu.cn.

Funding

Major Scientific Research Program of Handan University 15103National Natural Science Foundation of China 21573020Natural Science Foundation of Hebei Province B2016109022"Seedling Engineering" of Handan University 2017308

6 · The paper itself

Abstract

Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3',3'-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3',3'-cGAMP riboswitch induced by the 3',3'-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3',3'-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively compact structure versus that in the 3',3'-cGAMP-bound state. The binding of the 3',3'-cGAMP molecule to the 3',3'-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communication from the binding sites pocket containing the J1/2, J1/3 and J2/3 junction to the P1 helix. Simultaneously, these simulations also revealed that the preferential binding of the 3',3'-cGAMP riboswitch to its cognate ligand, 3',3'-cGAMP, over its noncognate ligand, c-di-GMP and c-di-AMP. The J1/2 junction in the 3',3'-cGAMP riboswitch contributing to the specificity of ligand recognition have also been found.

Indexed as

Molecular Dynamics SimulationRiboswitchAllosteric RegulationBinding SitesCyclic GMPHydrogen BondingLigandsNucleic Acid ConformationNucleotides, CyclicPrincipal Component AnalysisThermodynamicsTime Factorsbis(3',5')-cyclic diguanylic acidCyclic GMPcyclic guanosine monophosphate-adenosine monophosphateLigandsNucleotides, CyclicRiboswitch3′,3′-cGAMP riboswitchallosteric communicationligand recognitionmolecular dynamics simulation

Identifiers

PMID30423927

DOI10.3390/ijms19113527

PMCPMC6274999

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