Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29

Area of Science:

• Structural biology
• Virology
• Biochemistry

Background:

• The genome-organizing protein p6 is crucial for Bacillus subtilis bacteriophage φ29 development.
• Protein p6 activates DNA replication initiation and regulates transcriptional switching.
• p6 forms a nucleoprotein complex with viral DNA, essential for genome compaction and supercoiling management.

Purpose of the Study:

• To determine the three-dimensional structure of bacteriophage φ29 protein p6.
• To elucidate the self-association mechanism and DNA-binding interactions of p6.
• To develop a comprehensive structural model of the p6-DNA nucleoprotein complex.

Main Methods:

• Utilized AlphaFold2 to design p6 constructs for crystallization and structure determination.
• Employed protein-DNA docking and molecular dynamics simulations for model building.
• Performed analytical ultracentrifugation to validate nucleoprotein complex properties in solution.

Main Results:

• Revealed a novel fold for protein p6, explaining its self-association and DNA interaction.
• Generated a detailed structural model of the p6-DNA nucleoprotein complex consistent with biochemical data.
• Confirmed the hydrodynamic properties of the nucleocomplex, validating the model in solution.

Conclusions:

• The determined p6 structure provides a mechanistic explanation for its functions in viral development.
• The study enhances the understanding of the structural and functional roles of p6 in bacteriophage φ29 infection.
• The findings reconcile decades of experimental data with a validated structural model.