Minimum Energy Pathway for Lesion Recognition and DNA Binding by RAD4/XPC.

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• UV radiation causes DNA damage, forming pyrimidine-pyrimidone (6-4) photoproducts (6-4PP).
• The XPC/RAD4 protein complex is essential for detecting 6-4PP and initiating nucleotide excision repair.
• Understanding the precise mechanism of XPC/RAD4-mediated lesion recognition and repair is critical for genomic integrity.

Purpose of the Study:

• To elucidate the molecular mechanism by which XPC/RAD4 initiates repair of UV-induced DNA lesions.
• To map the energy landscape and conformational changes involved in XPC/RAD4 binding to damaged DNA.

Main Methods:

• Molecular dynamics (MD) simulations
• Umbrella sampling
• Nudged elastic band (NEB) method to determine the minimum energy path (MEP).

Main Results:

• The initial DNA interrogation involves partial unwinding and opening, with partial lesion extrusion.
• A rate-limiting step, characterized by 5' base flipping, was identified as a bottleneck.
• Sequential base flipping (lesion, 5' base, 3' bases) and β-hairpin insertion stabilize the final XPC/RAD4-DNA complex.

Conclusions:

• The study reveals key conformational intermediates and energetics governing XPC/RAD4's DNA repair initiation.
• Insights into the base-flipping mechanism provide a deeper understanding of nucleotide excision repair.
• This work advances knowledge of DNA damage response pathways relevant to skin disorders and cancer.