Conformational Transition and Recognition Mechanism of Eukaryotic Riboswitches Powered by Thiamine Pyrophosphate Analogues: An Elucidation through Multiple Short Molecular Dynamics Simulations and Markov Model

Understanding the ligand-mediated conformational changes in eukaryotic riboswitches is crucial for elucidating their functional roles. In this study, multiple short molecular dynamics simulations, followed by Markov model analysis, were conducted to investigate how the binding of ligands such as three thiamine pyrophosphate analogues (TPP, PYI, and D2X) influences the conformational transitions of eukaryotic riboswitches. Our findings indicate that the presence of these ligands induces a greater number of conformational states and alters the relative orientation of ligands to key nucleotides, thereby impacting ligand-riboswitch recognition. The ligands TPP, PYI, and D2X were found to exert distinct effects on the conformations of specific structural regions, including P1, P4, P5, and L3 and junctions J23 and J45. This suggests that the dynamic nature of the riboswitch of eukaryotic riboswitches is highly dependent on the conformational responses within these regions, also supported by our principal component analysis. Additionally, changes in π-π interactions of ligands with nucleotides G30 and A31, hydrogen bonds formed between ligands and nucleotide, as well as those of a magnesium ion (Mg²⁺) with nucleotides G48, G66, and ligands, may play a significant role in mediating the conformational transitions of eukaryotic riboswitches. Overall, this research is expected to provide valuable theoretical insights into the functions and target roles of riboswitches.