Protein flexibility directs DNA recognition by the papillomavirus E2 proteins

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• DNA flexibility is crucial for DNA-protein interactions.
• The role of protein flexibility in these interactions remains less understood.
• The human papillomavirus (HPV) type 6 E2 protein is a well-characterized model system for studying DNA recognition.

Purpose of the Study:

• To investigate the impact of protein flexibility on DNA binding specificity.
• To elucidate the role of protein dynamics in DNA recognition using the HPV 6 E2 DNA binding domain (DBD).

Main Methods:

• Comparative analysis of wild-type HPV 6 E2 DBD and a mutant lacking two C-terminal leucine residues.
• (15)N NMR relaxation and hydrogen/deuterium exchange to assess protein flexibility.
• Stopped-flow kinetic studies to analyze DNA binding dynamics.

Main Results:

• The mutant E2 DBD exhibited increased specific and non-specific DNA binding.
• A decrease in overall DNA binding specificity was observed in the mutant.
• Increased flexibility in the mutant's hydrophobic core and loop regions was confirmed.
• Enhanced initial DNA interactions were noted, with minimal effect on subsequent structural rearrangements.

Conclusions:

• Subtle alterations in protein dynamics can profoundly influence protein-DNA interactions.
• Protein flexibility plays a significant role in the specificity and kinetics of DNA binding.
• The study underscores the importance of considering protein dynamics in understanding molecular recognition processes.