Computer simulation of the molecular structure and interaction of the IscB protein with its guide RNA

The IscB-ωRNA-DNA complex is overall stable, but its core HNH(IscB)-DNA region shows increased separation.

• The HNH domain's dynamics and metal-ion selection may influence the gene-editing efficiency of the CRISPR-Cas9 system.
• Molecular dynamics simulations indicate that the IscB-ωRNA-DNA complex maintains overall stability.
• Increased separation in the core HNH(IscB)-DNA region aligns with findings of a connection between HNH movement and activation.
• Mutations analogous to Cas9 could reduce the motion of the HNH domain.
• Higher binding energy for three specific ions (Mg2+, Mn2+, Co2+) in the mutated HNH(IscB)-DNA region suggests a potential impact on catalytic efficiency.

Simplified