Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands

Abstract

Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulates the gene expression by undergoing a conformational change in response to the binding of a free guanidinium ion and thereby plays a potentially important role in alleviating guanidinium toxicity in cells. An experimental crystal structure of the guanidinium-bound aptamer domain of the riboswitch from Thermobifida Fusca revealed the overall RNA architecture and mapped the specific noncovalent interactions that stabilize the ligand within the binding pocket aptamer. However, details of how the aptamer domain discriminates the cognate ligand from its closest structurally analogous physiological metabolites (arginine and urea), and how the binding of cognate ligand arrays information from the aptamer domain to the expression platform for regulating the gene expression, are not well understood. To fill this void, we perform a cumulative of 2 μs all-atom explicit-solvent molecular dynamics (MD) simulations on the full aptamer domain, augmented with quantum-chemical calculations on the ligand-binding pocket, to compare the structural and dynamical details of the guanidinium-bound state with the arginine or urea bound states, as well as the unbound (open) state. Analysis of the ligand-binding pocket reveals that due to unfavorable interactions with the binding-pocket residues, urea cannot bind the aptamer domain and thereby cannot alter the gene expression. Although interaction of the guanidyl moiety of arginine within the binding pocket is either comparable or stronger than the guanidinium ion, additional non-native hydrogen-bonding networks, as well as differences in the dynamical details of the argininebound state, explain why arginine cannot transmit the information from the aptamer domain to the expression platform. Based on our simulations, we propose a mechanism of how the aptamer domain communicates with the expression platform. Overall, our work provides interesting insights into the ligand recognition by a specific class of riboswitches and may hopefully inspire future studies to further understand the gene regulation by riboswitches.

Towards the development of better therapeutic agents for Mycobacterium Tuberculosis: Computational design and evaluation of pyrazinone derivatives as inhibitors of enoyl acyl carrier protein reductase

“…MD simulations were performed on the docked complexes, as well as the apo form of the InhA protein, using the AMBER 20 suite of programs [39]. In accordance with previous studies [40,41], partial atomic charges for each ligand were calculated at the HF/6-31G(d) level using the RESP ESP Charge Derive (RED version 2.0) server [42]. These calculations were initiated using the stable conformation of each ligand obtained from B3LYP/6-31G(d,p) gas-phase geometry optimizations using Gaussian 09 [43].…”

“…The values of pairwise cross correlations range from -1 to 1, where positive values indicate that the motions of the two residues are correlated (i.e., move in the same direction) and the negative values represent the anti-correlated (i.e., opposing) motions. The occupancy of each protein:ligand hydrogen bond was calculated using the 'hbond' command of cpptraj, using the donor-acceptor cut-off distance of 3.4 Å and a donor-hydrogen-acceptor cut-off angle of 120˚ [40,41].…”

Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms

“…74 The study proposed a mechanism by which Gdm + binding leads to the dimerization of the two stem-loops of the guanidine-II AD through loop stabilization upon Gdm + binding. A similar combined quantum mechanics/MD (QM/ MD) study on the Thermobif ida f usca ykkC-III AD examined the role of bound urea, guanidine, and substituted guanidines on the stability of the AD 75 and proposed a mechanism by which the AD can transmit the ligand binding signal to the EP via the dynamics of the third strand of the TH in the AD. However, the exact mechanism by which the AD senses a free Gdm + from the solution and the role of the apo-state excited states in the ligand sensing mechanism are yet to be deciphered.…”

Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State

“…Multiple MD simulations started from different initial conditions (conformations or velocities) would greatly improve the sampling compared with a single trajectory, especially from a thermodynamics standpoint. The importance of multiple independent simulations and its application to obtain better statistics on simulation results is gaining recognition. − When multiple independent simulations show reproducible results and convergence of a structural and dynamic process, complete sampling of the thermally accessible conformational ensemble of a biomolecule is considered to be achieved.…”

“…The importance of multiple independent simulations and its application to obtain better statistics on simulation results is gaining recognition. 34 − 37 When multiple independent simulations show reproducible results and convergence of a structural and dynamic process, complete sampling of the thermally accessible conformational ensemble of a biomolecule is considered to be achieved.…”