Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.

Area of Science:

• Structural Biology
• Computational Biology
• Biochemistry

Background:

• Magnesium ions are essential for RNA structure, dynamics, and function.
• The precise microscopic effects of chelated magnesium on RNA are not fully understood.
• Magnesium interactions with RNA occur via diffuse clouds, outer-sphere, inner-sphere, and chelated ion-mediated pathways.

Purpose of the Study:

• To elucidate the mechanism of site-specific chelated magnesium ions on the conformational dynamics of SAM-I riboswitch aptamers.
• To investigate the role of chelated magnesium in bacterial SAM-I riboswitch function.
• To understand how magnesium ions control RNA folding and transcription switching.

Main Methods:

• Atomistic simulations in a physiological mixed salt environment at high temperature.
• Validation with phosphorothioate interference mapping experiments.
• Identification of crucial inner-sphere Mg2+ sites and ion distribution.

Main Results:

• A novel concerted mechanism involving two chelated magnesium ions was discovered, supporting pseudoknot formation.
• This interaction functions as a logical AND gate, where the absence of either ion disrupts the pseudoknot.
• A base triple serves as the epicenter for magnesium chelation, allosterically controlling RNA pseudoknot stability.

Conclusions:

• Chelated magnesium ions play a critical, allosteric role in stabilizing the functional fold of SAM-I riboswitch aptamers.
• The discovered mechanism explains how magnesium ions control transcription ON/OFF switching.
• This provides new insights into the molecular mechanisms of riboswitch regulation.