Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Flavin mononucleotide (FMN) riboswitches are prevalent in pathogenic bacteria, making them promising antibiotic targets.
• The FMN riboswitch binds riboflavin (vitamin B2), but its precise binding mechanism remains elusive despite solved complex structures.

Purpose of the Study:

• To elucidate the dynamic binding mechanism of riboflavin to the FMN riboswitch aptamer domain.
• To identify the key steps and conformational changes involved in ligand entry and stabilization within the riboswitch.

Main Methods:

• Utilized a Multicanonical Molecular Dynamics (McMD)-based dynamic docking protocol.
• Simulated the binding process starting from the apo state of the FMN riboswitch aptamer.
• Employed a refinement stage to distinguish the native binding configuration from transient interactions.

Main Results:

• Identified an initial binding event at the P4-P6 interface, involving nucleotides U61 and G62, acting as a ligand gateway.
• Observed riboflavin (RBF) lingering at this gateway before conformational changes allowed passage.
• Determined the final binding site within the RNA, involving nucleotides A48, A49, and A85, after the gateway opens.

Conclusions:

• The binding mechanism involves a dynamic process with an initial gateway interaction followed by entry into a deep, hidden binding pocket.
• This detailed understanding of the FMN riboswitch-riboflavin interaction is crucial for rational antibiotic design targeting bacterial pathogens.