Abstract
Riboswitches are naturally occurring RNA aptamers that control the expression of essential bacterial genes by binding to specific small molecules. The binding with both high affinity and specificity induces conformational changes. Thus, riboswitches were proposed as a possible molecular target for developing antibiotics and chemical tools. The adenine riboswitch can bind not only to purine analogues but also to pyrimidine analogues. Here, long molecular dynamics (MD) simulations and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) computational methodologies were carried out to show the differences in the binding model and the conformational changes upon five ligands binding. The binding free energies of the guanine riboswitch aptamer with C74U mutation complexes were compared to the binding free energies of the adenine riboswitch (AR) aptamer complexes. The calculated results are in agreement with the experimental data. The differences for the same ligand binding to two different aptamers are related to the electrostatic contribution. Binding dynamical analysis suggests a flexible binding pocket for the pyrimidine ligand in comparison with the purine ligand. The 18 μs of MD simulations in total indicate that both ligand-unbound and ligand-bound aptamers transfer their conformation between open and closed states. The ligand binding obviously affects the conformational change. The conformational states of the aptamer are associated with the distance between the mass center of two key nucleotides (U51 and A52) and the mass center of the other two key nucleotides (C74 and C75). The results suggest that the dynamical character of the binding pocket would affect its biofunction. To design new ligands of the adenine riboswitch, it is recommended to consider the binding affinities of the ligand and the conformational change of the ligand binding pocket.
Highlights
Riboswitches are noncoding RNAs that function as genetic switches and they are mostly found in bacteria [1,2]
They are located in the 5 untranslated region of messenger RNAs and consist of two domains: a conserved aptamer domain that forms a binding pocket to bind metabolite small molecules, and an expression platform that controls the expression of the downstream gene(s)
The ligand binding and conformational transition mechanisms were using by molecular dynamics (MD) simulations, as well as binding free energy calculations
Summary
Riboswitches are noncoding RNAs that function as genetic switches and they are mostly found in bacteria [1,2]. Aqvist et al analyzed the energetics of ligand binding to purine riboswitches by employing molecular dynamics simulations, free energy perturbation calculations, and the linear interaction energy method, explaining how the functional groups of ligands affect the binding model and affinity [3]. The inhibitor binding affinities for protein and ligand complexes [35,36,37,38] and RNA and ligand complexes [3,39,40,41,42] were successfully estimated via many computational methods with varying levels of computational expense and accuracy These methods include free energy perturbation (FEP) [43], thermodynamic integration, umbrella sampling (US) [44], and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) [45]. The results provide valuable information for understanding the conformational changes caused by ligand binding
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