Characterizing the APOBEC3B closed to open pathway with weighted ensemble.

Abstract

APOBEC enzymes deaminate single stranded DNA (ssDNA) cytosine into uracil and physiologically function in antiviral immunity. APOBEC signature mutations, defined as C-to-T transitions and C-to-G transversions on 5’-TCA/T trinucleotide motifs, have been implicated in breast cancer and other tumor types. In breast cancer specifically, the proportion of APOBEC mutations increases greatly from primary tumors (∼20%) to metastases (∼50%); the presence of two distinct APOBEC mutational hotspots that activate PIK3CA; and correlations between APOBEC mutational signatures and poor clinical outcomes such as drug resistance and metastases. Using state-of-the-art computational methods, we have developed an atomistic model of the APOBEC3B(A3B) enzyme as it transitions from the closed to open state to gain understanding of how A3Bctd accommodates its ssDNA substrate. Because A3Bctd spends about 85% of classical MD simulations in the closed state, we employed the Weighted Ensemble method to thoroughly characterize this opening mechanism and identify critical residue interactions along the pathway. Using these simulations, we also performed computational solvent mapping to detect binding hotspots along the opening pathway of A3Bctd. Taken together, these efforts will increase our understanding of the dynamics of A3B in order to develop better small molecule targets to eventually improve clinical outcomes.