Abstract
Riboswitch, a bacterial regulatory RNA consists of an aptamer (specific ligand binding unit) and an expression platform (gene expression modulation unit), which act as a potential drug target as it regulates critical genes. Therefore, it is of interest to glean information on the binding of c-di-GMP ligand to mutated conserved G20 and C92 residues of cyclic diguanosine monophosphate I (c-di-GMP I) riboswitch using molecular dynamics simulation. The result shows that the binding energy of wild/native type riboswitch-ligand complex (3IRW) is lower than the mutant complexes suggesting that the binding affinity for c-di-GMP ligand decreases in case of mutant riboswitches. The hydrogen bonding interactions analysis also showed a high number of hydrogen bonds formation in the wild type riboswitch-ligand complex as compared to the mutant complexes illustrating stronger interaction of ligand to wild type riboswitch than the mutants. The simulation result shows that the mutations affected riboswitch-ligand interactions. The residues G14, G21, C46, A47, and U92 were identified as the key residues which contributed effectively to the binding of c-di-GMP I riboswitch with the natural ligand.
Highlights
The role of c-di-GMP riboswitch attracts the ligand/metabolite and bring about the conformational changes researchers to explore and modulate its mechanism of action at resulting in modulated gene expression according to changes in molecular and dynamical level for the development of the physiology of the bacterial system [1, 2]
Mutation studies have became essential to are considered as potential drug target against pathogenic evaluate significance of each residue and their role in the binding bacteria [3, 4]
One such riboswitch is c-di-GMP I riboswitch that pocket, here we study the effect of mutated residues on binding binds to c-di-GMP ligand and is pivotal in regulation of gene energy of ligand and receptor and changes in their interactions expression and maintenance of cellular homeostasis caused by in order to find the
Summary
Declaration on Publication Ethics: The author’s state that they adhere with COPE guidelines on publishing ethics as described elsewhere at https://publicationethics.org/. The authors undertake that they are not associated with any other third party (governmental or non-governmental agencies) linking with any form of unethical issues connecting to this publication. The authors declare that they are not withholding any information that is misleading to the publisher in regard to this article. Author responsibility: The authors are responsible for the content of this article. The editorial and the publisher have taken reasonable steps to check the content of the article in accordance to publishing ethics with adequate peer reviews deposited at PUBLONS. Declaration on official E-mail: The corresponding author declares that official e-mail from their institution is not available for all authors
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