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• W2598982774 abstract "Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA’s secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches. The snapshots used in MM-PBSA calculation were extracted from ten 50 ns MD simulation trajectories for each complex. These free energy results are in consistent with the experimental data and rationalize the selectivity of the riboswitches for different ligands. In particular, it is found that the loss in binding free energy upon mutation is mainly electrostatic in guanine (GUA) and riboswitch complex. Furthermore, new hydrogen bonds are found in mutated complexes. To reveal the conformational properties of guanine riboswitch, we performed a total of 6 μs MD simulations in both the presence and the absence of the ligand GUA. The MD simulations suggest that the conformation of guanine riboswitch depends on the distance of two groups in the binding pocket of ligand. The conformation is in a close conformation when U51-A52 is close to C74-U75." @default.
• W2598982774 created "2017-04-07" @default.
• W2598982774 creator A5005397465 @default.
• W2598982774 creator A5010501969 @default.
• W2598982774 creator A5052509900 @default.
• W2598982774 date "2017-04-06" @default.
• W2598982774 modified "2023-10-17" @default.
• W2598982774 title "Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations" @default.
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• W2598982774 doi "https://doi.org/10.1021/acs.jcim.7b00139" @default.
• W2598982774 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/28345904" @default.
• W2598982774 hasPublicationYear "2017" @default.
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