Recognition of platinum-DNA adducts by HMG-box proteins Public Deposited

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  • March 21, 2019
Creator
  • Ramachandran, Srinivas
    • Affiliation: School of Medicine, Department of Biochemistry and Biophysics
Abstract
  • Cisplatin (CP) and oxaliplatin (OX) are platinum (Pt) based drugs that are widely used in chemotherapy. The mode of action of Pt drugs is through the formation of Pt adducts on intrastrand guanines (5'GG) in genomic DNA. A class of proteins that bind specifically to Pt adducts contain the HMG-domain, which is found in both abundant housekeeping proteins like HMGB1 and also in low abundance transcription factors. The differential affinity of HMG-domain proteins to CP- and OX-DNA may play a role in the differential efficacies of CP- and OX-DNA. In this study, we aim to understand the molecular basis of the differential affinity of HMGB1a to CP- and OX-DNA, given that the only differences between these two species is their carrier ligand, which is not even involved in the Protein-DNA interface. We hypothesized that the differences in conformational dynamics rather than the major conformation of Pt-DNA determines the differential binding affinity to HMGB1a. To test this hypothesis, we performed molecular dynamics simulations of both free Pt-DNA and HMGB1a-Pt-DNA complexes. Our simulations of free Pt-DNA revealed that the conformational dynamics of CP- and OX-GG adducts are distinct and depend on the sequence context of the adduct. We found that the minor conformations sampled exclusively by the CP-GG adduct exhibit structural properties that favor binding by HMGB1a, while these conformations are not sampled by OX-GG adducts. Comparing the conformations of Pt-DNA in three sequence contexts revealed the sequence and carrier ligand dependent distortions induced by the Pt-GG adduct. Finally, simulations of HMGB1a-Pt-DNA revealed that the lack of flexibility of OX-DNA in the TGGA sequence context seen in free Pt-DNA translated to a much weaker binding interface compared to CP-DNA, thus explaining the experimentally observed low binding affinity of OX-DNA compared to CP-DNA. Based on these results, we postulate that the carrier ligand affects the DNA conformations explored by Pt-GG adduct, which influences the binding affinities of HMG-domain proteins for Pt-GG adducts, and that these conformations are further influenced by the DNA sequence context of the Pt-GG adduct.
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  • " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry and Biophysics."
Advisor
  • Dokholyan, Nikolay
Degree granting institution
  • University of North Carolina at Chapel Hill
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  • Chapel Hill, NC
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  • Open access
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