APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.
Bibliographical noteFunding Information:
J.R.W. was supported by the NIH Molecular Biophysics Training Grant T32 GM008326. This work was funded in part by the Director’s New Innovator Award Program NIH DP2 OD007237 to R.E.A.; R01-GM110129 to D.A.H., R.S.H., and R.E.A.; R01-GM118000 to R.S.H., H.A., and D.A.H. Funding and support from the National Biomedical Computation Resource (NBCR) is provided through NIH P41 GM103426. R.S.H. is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a distinguished McKnight University professor, and an investigator of the Howard Hughes Medical Institute.