Insights into the ligand-free structure of cyclic diguanosine monophosphate I riboswitch of Vibrio cholerae using molecular dynamics simulation

Abstract

Riboswitches are key cis regulatory elements present at 5 UTRs of mRNAs. They play a critical role in gene expression regulation at transcriptional and translational level by binding selectively to specific ligands followed by conformational changes. Ligands bind to the aptamer of riboswitches and their complex structures have been solved, but ligand-free riboswitches structures are not available which is important to understand specific ligand binding mechanism. In this paper, an all atom 150 nano-second (ns) molecular dynamics (MD) simulations of cyclic diguanosine monophosphate (c-di-GMP I) riboswitch aptamer domain from Vibrio cholerae were carried out to study ligand-free c-di-GMP I riboswitch aptamer structure and the binding mechanism. The Principle component analysis, cross correlation dynamics analysis and trajectory analyses revealed that the ligand-free structure has stable conformation with folded P2, P3 and an open P1 helix which opens the ligand binding helix-join-helix while the ligand-bound structure shows less deviation and remains as closed structure compared to the ligand-free structure. The junction residues significantly showed anti-correlated motions with each other elucidating the open conformation of the ligand-free aptamer of riboswitch. The identified key residues involved in binding are A18, G20, C46, A47 and C92. HighlightsO_LIThe c-di-GMP I riboswitch regulates the essential genes involved in the virulence of human bacterial pathogen V. Cholera. C_LIO_LIA 150 ns molecular dynamics run was performed to find a ligand-free stable structure of c-di-GMP I riboswitch aptamer. C_LIO_LIThe trajectory analysis resulted in stable conformation of ligand-free structure with folded P2, slightly open P3 and an unwind P1 helix. C_LIO_LIThe atomic level analyses through cross correlation dynamics and RMSF values showed the opening of catalytic pocket and unwinding P1 helix. C_LIO_LIThe identified key residues involved in binding are A18, G20, C46, A47 and C92 at the catalytic pocket. C_LI