| Large-scale atomic molecular dynamics simulations enable detailed analysis of transition states,kinetic intermediates and multiple folding pathways for specific sequences of interest.However,molecular dynamics studies are limited to very short sequences.Monte Carlo simulation has also been used by several researchers to simulate the RNA folding process.However,the above two methods,the conformation and kinetic sampling may be incomplete,and the method cannot give the analysis results of stable prediction of long-term dynamics.In order to solve the above problems,we used the master equation and the transition node approximation method to theoretically study the co-transcription folding behavior of the lysC riboswitch in the Gram-positive bacteria Bacillus subtilis in the presence/absence of ligand lysine.Thereby a complete and comprehensive physical image of the regulation mechanism and characteristics of the lysC riboswitch is obtained.The 5'-UTR of the B.Subtilis lysC gene carries a conserved RNA motif that acts as a Lys-sensitive riboswitch that regulates gene expression of intracellular Lys-sensitive aspartate kinase II(AK).We used the master equation and transition node approximation method to theoretically study the co-transcriptional folding behavior of the lysC riboswitch in the presence or absence of ligand lysine in Gram-positive bacterium B.Subtilis,and obtained lysC riboswitch regulation mechanism.We found that in the presence of the ligand Lys,the ligand Lys binds to the ligand-inducing pocket to form a terminator hairpin,causing transcriptional attenuation.When the Lys concentration is low,the termination efficiency of the lysC riboswitch decreases with the increase of the transcription rate.On the contrary,when the Lys concentration increases,the increase of the transcription rate will leads to an increase in the termination efficiency of the lysC riboswitch.The lysC riboswitch is regulated by a combination of thermodynamic and kinetic mechanisms. |
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