Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network

Area of Science:

• Molecular Biology
• Biophysics
• Computational Biology

Background:

• Riboswitches are critical genetic elements in bacteria, regulating gene expression.
• Their role in bacterial gene regulation makes them promising targets for novel antibacterial drugs.
• Tetrahydrofolate (THF) is an essential cofactor that downregulates gene expression via riboswitches, but its precise regulatory mechanism remains unclear.

Purpose of the Study:

• To elucidate the molecular mechanism by which Tetrahydrofolate (THF) binding to a riboswitch leads to gene regulation.
• To identify the specific allosteric pathway involved in THF-mediated riboswitch function.

Main Methods:

• All-atom molecular dynamic simulations were employed to construct a nucleotide dynamics correlation network.
• Shortest pathway analysis was performed on the network to identify allosteric communication routes.
• Experimental validation using THF binding and pseudoknot weakening assays confirmed the proposed mechanism.

Main Results:

• A nucleotide/nucleotide dynamics correlation network revealed an allosteric pathway from the THF binding site through the P2 helix, pseudoknot, and to the P1 helix.
• The hypothesis of THF-binding induced allosteric switching was supported by experimental evidence.
• A specific allosteric pathway (C30-C31-G33-A34-G35-G36-G37-A38-G48-G47-U46-A90-U91-C92-G93-C94-G95-C96) was identified and experimentally confirmed.

Conclusions:

• The study proposes a novel allosteric mechanism for THF-sensing riboswitches, detailing the pathway of signal transmission.
• This detailed understanding of the allosteric pathway provides fundamental insights into riboswitch regulation.
• The findings contribute to the development of new antibacterial strategies targeting essential bacterial pathways.