Title
Comparative molecular dynamics simulation analysis of G20 and C92 mutations in c-di-GMP I riboswitch and the wild type with docked c-di-GMP ligand
Authors
Priyanka Kumari & Anup Som*
Affiliation
Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj – 211002, India;
PK - E-mail:priyanka.iids@gmail.com; AS – E-mail: som.anup@gmail.com; *Corresponding author
Article Type
Research Article
Date
Received April 4, 2021; Revised August 30, 2021; Accepted August 30, 2021, Published August 31, 2021
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 (cdi-GMP I) riboswitch using molecular dynamics simulation. The result shows that the binding energy of wild/native type riboswitchligand 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.
Keywords
Molecular docking; MD simulation; Riboswitch-ligand complexes; Binding free energy; hydrogen bonding
Citation
Kumari & Som, Bioinformation 17(8): 721-726 (2021)
Edited by
P Kangueane
ISSN
0973-2063
Publisher
License
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
