Mutation-Induced Conformational Changes and Energetics for Binding of FMN Ligand in Flavin Mononucleotide Riboswitch by Molecular Dynamics Simulations

Padmaja D Wakchaure,Bishwajit Ganguly

doi:10.5562/cca3550

Abstract

Riboswitches are the type of regulatory elements present in the untranslated region of mRNA and specifically bind to the natural ligand to regulate gene expression. This binding specificity can be affected by even single point mutation incorporated in the core of the riboswitch. In this work, we have examined the mutations at the binding site residue in Flavin Mononucleotide (FMN) riboswitch structure with 30ns molecular dynamics simulations. The interaction of ligand (FMN) with riboswitch has been characterized using root mean square deviation, hydrogen bonding analysis, and the calculated binding affinities. Mutation at A48G and G62U show the enhanced binding energy however, the mutation at A85G, are energetically unfavorable compared to the wild type. This work gives valuable insight into the structures and energetics of the mutated FMN riboswitch to design new hits for biological applications.

Highlights

R IBOSWITCHES are RNA elements present in 5’ untranslated regions in mRNA that regulates the expression of downstream genes in response to specific metabolites.[1]
To study the preferential binding of Flavin mononucleotide (FMN) to wild type FMN riboswitch and mutated FMN riboswitch structure, we have performed the structural analysis with calculating root mean square deviation (RMSD), root means square fluctuations (RMSF), the radius of gyration and hydrogen bond interactions
We have examined the effect of a single mutation on the structural stability of FMN riboswitch with molecular dynamics (MD) simulations

Summary

Introduction

R IBOSWITCHES are RNA elements present in 5’ untranslated regions in mRNA that regulates the expression of downstream genes in response to specific metabolites.[1]. One of the three hydroxyl groups in the ribitylphosphate chain in FMN forms hydrogen bonds with Guanine (G) 11 and phosphate group forms magnesium (Mg) bridged interaction with G33. In addition to these interactions, the phosphate group in FMN forms hydrogen bonds with G10, G11, G32, G62, and G84. It is reported that the non G:C base-pairing composition in riboswitch sequence affects the FMN dissociation rate constant.[9] Gene expression in downstream genes can be tuned by mutating the base pairings in the binding site. All these experimental studies show that base pair composition, as well as a single base mutation in the binding site, has a direct influence on ligand binding

Methods

Results

Conclusion