ALL-ATOM MOLECULAR DYNAMICS SIMULATIONS OF S-ADENOSYL METHIONINE (SAM) ASSISTED

Carnegie-Mellon University, Pittsburgh PA

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We aim to investigate the complicated molecular mechanism of a SAM-I riboswitch RNA element with all-atom Molecular Dynamics (MD) simulations. The riboswitch RNA is a regulatory RNA element residing on 5'-untransrated region (UTR) of a target mRNA and regulate relevant genes in transcriptional or translational levels. Riboswitch RNAs are cis-acting regulatory RNA that comprises the aptamer domain and the expression domain. The complicated interplay between these two domains regulate a downstream gene in a mRNA, but the detailed molecular mechanisms remain elusive that are potentially affected by metabolite binding, roles of Mg2+, competing secondary structure elements, and dynamical distribution of secondary structures before binding a SAM. Therefore, examining the folded state stability as well as unfolding pathways with long time trajectories is beneficial for understanding molecular level information, which is further utilized to rationalize the molecular mechanism of the SAM-I riboswitch.