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Dynamical characterization and multiple unbinding paths of two PreQ1 ligands in one pocket.
- Source :
- Physical Chemistry Chemical Physics (PCCP); 9/21/2023, Vol. 25 Issue 35, p24004-24015, 12p
- Publication Year :
- 2023
-
Abstract
- Riboswitches naturally regulate gene expression in bacteria by binding to specific small molecules. Class 1 preQ<subscript>1</subscript> riboswitch aptamer is an important model not only for RNA folding but also as a target for designing small molecule antibiotics due to its well-known minimal aptamer domain. Here, we ran a total of 62.4 μs conventional and enhanced-sampling molecular dynamics (MD) simulations to characterize the determinants underlying the binding of the preQ<subscript>1</subscript>-I<subscript>I</subscript> riboswitch aptamer to two preQ<subscript>1</subscript> ligands in one binding pocket. Decomposition of binding free energy suggested that preQ<subscript>1</subscript> ligands at α and β sites interact with four nucleotides (G5, C17, C18, and A30) and two nucleotides (A12 and C31), respectively. Mg<superscript>2+</superscript> ions play a crucial role in both stabilizing the binding pocket and facilitating ligand binding. The flexible preQ<subscript>1</subscript> ligand at the β site leads to the top of the binding pocket loosening and thus pre-organizes the riboswitch for ligand entry. Enhanced sampling simulations further revealed that the preQ<subscript>1</subscript> ligand at the α site unbinds through two orthogonal pathways, which are dependent on whether or not a β site preQ<subscript>1</subscript> ligand is present. One of the two preQ<subscript>1</subscript> ligands has been identified in the binding pocket, which will aid to identify the second preQ<subscript>1</subscript> Ligand. Our work provides new information for designing robust ligands. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14639076
- Volume :
- 25
- Issue :
- 35
- Database :
- Complementary Index
- Journal :
- Physical Chemistry Chemical Physics (PCCP)
- Publication Type :
- Academic Journal
- Accession number :
- 171923641
- Full Text :
- https://doi.org/10.1039/d3cp03142j