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Int. J. Mol. Sci. 2018, 19(11), 3527; https://doi.org/10.3390/ijms19113527

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

1
College of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China
2
College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China
*
Author to whom correspondence should be addressed.
Received: 26 September 2018 / Revised: 3 November 2018 / Accepted: 4 November 2018 / Published: 9 November 2018
(This article belongs to the Collection Proteins and Protein-Ligand Interactions)
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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. View Full-Text
Keywords: molecular dynamics simulation; 3′,3′-cGAMP riboswitch; allosteric communication; ligand recognition molecular dynamics simulation; 3′,3′-cGAMP riboswitch; allosteric communication; ligand recognition
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Li, C.; Zhao, X.; Zhu, X.; Xie, P.; Chen, G. Structural Studies of the 3′,3′-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation. Int. J. Mol. Sci. 2018, 19, 3527.

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