A divalent metal-mediated switch controlling protein-induced DNA bending

Area of Science:

• Molecular Biology
• Structural Biology
• Genetics

Background:

• Architectural proteins are crucial for DNA transactions by reconfiguring DNA segments.
• Integration host factor (IHF) is a key DNA architectural protein involved in various genomic processes.
• Understanding protein-DNA interactions is vital for deciphering gene regulation and genome stability.

Purpose of the Study:

• To engineer a single-chain derivative of IHF capable of adopting distinct conformational states.
• To investigate the mechanism of metal-ion-controlled conformational switching in IHF.
• To explore the application of this switch in controlling DNA bending and site-specific recombination.

Main Methods:

• Protein engineering: Lysine-to-glutamate substitutions were introduced into IHF.
• Structural analysis: Characterization of protein-DNA complexes in different conformational states.
• Biochemical assays: Assessed DNA bending and site-specific recombination efficiency.

Main Results:

• The engineered IHF derivative exists in two stable states: open and closed, with altered DNA bending.
• Divalent metal ion binding triggers the conformational switch between the open and closed states.
• The conformational switch effectively modulates the efficiency of lambda integrase-catalyzed site-specific recombination.

Conclusions:

• Metal-ion-mediated conformational switching of architectural proteins can be engineered.
• This engineered switch provides a novel mechanism to control DNA architecture and function.
• Acidic residue introduction at protein-DNA interfaces offers a strategy for designing responsive molecular tools for genomic studies.