In eukaryotic global genomic nucleotide excision repair (NER), the initial step of recognition of DNA lesions involves the XPC-RAD23B protein. A crystal structure of the yeast ortholog Rad4-Rad23 heterodimer bound to DNA containing a cis-syn cyclobutane pyrimidine dimer (CPD) lesion, shows that for productive binding a beta-hairpin from domain BHD3 is inserted between the two strands of the DNA at the lesion site, and two lesion partner bases are flipped out of the double helix and interact with amino acids in the protein. The energetics of this process have not been explored yet. To gain insights into the free energy required for this recognition process in the presence of different lesions, we are performing free energy computations using umbrella sampling with the weighted histogram analysis method (WHAM). The objective is to gain understanding of how productive binding of Rad4-Rad23 contributes to the overall NER efficiency, which varies by more than two orders of magnitude for different DNA lesions. Our hypothesis is that the local thermodynamic stabilization/destabilization imposed by the lesion on the DNA duplex is an important contributor to the free energy profile of productive binding. Our simulation results, complementary to experimental studies, provide insights into the important and complex process of lesion recognition in NER.

Free energy profile of Rad4 productive binding to damaged DNA provides insight on lesion recognition in nucleotide excision repair

248th National Meeting (2014)

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