Determination of tertiary structure of human HMGB4 protein by two homology modeling-based methods

HMGB4 protein which was identified in 2008 is a member of mammalian non-histone HMGB protein family. All HMGB proteins bind to DNA through two tandem DNA-binding motifs named HMG-box A and HMG-box B. HMGB proteins are known to improve the anticancer properties of platinum-based drugs such as cisplatin by high affinity binding to the platinum-DNA adducts and retarding the process of DNA excision repair. The results from previous studies have revealed in comparison with full-length HMGB1, the full-length HMGB4 binds with higher affinity to platinum-DNA lesions and inhibits the excision repair of the lesions much more efficient. It seems the hypersensitivity of testicular germ cell tumors to cisplatin is originated from strong expression of HMGB4 in this tissue. In the present work, the tertiary structure of human HMGB4 was determined using two methods based on homology modeling (MODELLER software and I-TASSER server). The results show that models created by both methods have good quality and stability. Although I-TASSER model in comparison to the modeller better explain the differences between HMGB1 and HMGB4 binding to the platinated DNA. The results obtained from the work demonstrate that HMGB4 binds to DNA by intercalating of Valine17 and Phenylalanine38 from box A and Leucine101 and Valine120 from box B between base pairs of DNA minor groove. The results also show the C-terminal part of HMGB4 possesses disordered tertiary structure. In general, the results will be helpful to understand the structure-function relationship of the protein and to design new anticancer drugs.