MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch

Abstract

Riboswitches are structural cis-acting genetic regulatory elements in 59 UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

“…The sample structures in the absence of the ligand are some of the possible conformations accessible to the system. However, after the removal of the ligand, the rootmean-square fluctuation of the residues in the junction area increases by 20% (data not shown), in agreement with previous MD studies (Sharma et al 2009;Villa et al 2009;Priyakumar and MacKerell 2010). The bases A21 and A19 (helix P1) and U74 (ligand recognition residue located in junction area J3-1) and U75 (helix P1) become more exposed to solvent than in the complex with adenine.…”

“…The simulations in the absence of the cognate ligand allow us to identify which interactions are stabilized by the presence of the ligand. MD simulations together with a classical force field have previously been successfully used to investigate the structure of the purine-aptamer in the presence and absence of the cognate ligands (Sharma et al 2009;Villa et al 2009;Priyakumar and MacKerell 2010). Here, we apply umbrella sampling techniques to induce the breaking of the tertiary interaction between the L2 and L3 loops.…”

Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics

“…More specifically, MD has elucidated chemical features that stabilize ligand binding, the interactions that stabilize conformational endpoints, and features that facilitate conformational switching. Studies have been conducted on the SAM-I riboswitch (Huang et al 2009;Stoddard et al 2010;Doshi et al 2012;Hayes et al 2012;Huang et al 2013;Xue et al 2015), the SAM-II riboswitch (Kelley and Hamelberg 2010;Doshi et al 2012), the guanine riboswitch (Villa et al 2009;Sund et al 2014), the adenine riboswitch (Sharma et al 2009;Priyakumar and MacKerell 2010;Nozinovic et al 2014;Sund et al 2014), the GlmS riboswitch (Banáš et al 2010;Xin and Hamelberg 2010), and the preQ 1 -I and preQ 1 -III riboswitches (Petrone et al 2011;Banáš et al 2012;Eichhorn et al 2012;Gong et al 2014;Liberman et al 2015). Overall, these studies show the feasibility of using MD to understand riboswitch function and provide an opportunity to look for common themes in ligand binding and conformational dynamics.…”

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

“…12,15 Therefore, we did not specifically examine the unfolding behavior induced by Mg 2+ release. Here, the contacts mediated by Mg 2+ are not treated specially and the unfolding process is simulated purely in a fluctuation-dependent manner.…”

“…8 The adenosine deaminase (add) A-riboswitch is one of the structurally simplest riboswitches and has been widely studied. [9][10][11][12] The folded aptamer domain of the add A-riboswitch bound with the ligand adenine was structurally characterized by X-ray crystallography with a) Authors to whom correspondence should be addressed. Electronic addresses: jiguosu@ysu.edu.cn and zhng@umich.edu Protein Data Bank (PDB) code 1Y26 ( Fig.…”