NMR-based Method of Small Changes Reveals How DNA Mutator APOBEC3A Interacts with Its Single-stranded DNA Substrate

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Apr 4

PMID 28369637

Citations 12

Authors

Stefan Harjes

Geoffrey B Jameson

Vyacheslav V Filichev

Patrick J B Edwards

Elena Harjes

Affiliations

Soon will be listed here.

Abstract

APOBEC3 proteins are double-edged swords. They deaminate cytosine to uracil in single-stranded DNA and provide protection, as part of our innate immune system, against viruses and retrotransposons, but they are also involved in cancer evolution and development of drug resistance. We report a solution-state model of APOBEC3A interaction with its single-stranded DNA substrate obtained with the 'method of small changes'. This method compares pairwise the 2D 15N-1H NMR spectra of APOBEC3A bearing a deactivating mutation E72A in the presence of 36 slightly different DNA substrates. From changes in chemical shifts of peptide N-H moieties, the positions of each nucleotide relative to the protein can be identified. This provided distance restraints for molecular-dynamic simulations to derive a 3-D molecular model of the APOBEC3A-ssDNA complex. The model reveals that loops 1 and 7 of APOBEC3A move to accommodate substrate binding, indicating an important role for protein-DNA dynamics. Overall, our method may prove useful to study other DNA-protein complexes where crystallographic techniques or full NMR structure calculations are hindered by weak binding or other problems. Subsequent to submission, an APOBEC3A structure with a bound DNA oligomer was published and coordinates released, which has provided an unbiased validation of the 'method of small changes'.

Citing Articles

Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes.

Sanchez A, Ortega P, Sakhtemani R, Manjunath L, Oh S, Bournique E Nat Commun. 2024; 15(1):2370.

PMID: 38499542 PMC: 10948877. DOI: 10.1038/s41467-024-45909-5.

Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.

Harjes S, Kurup H, Rieffer A, Bayarjargal M, Filitcheva J, Su Y Nat Commun. 2023; 14(1):6382.

PMID: 37821454 PMC: 10567711. DOI: 10.1038/s41467-023-42174-w.

Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.

Harjes S, Kurup H, Rieffer A, Bayaijargal M, Filitcheva J, Su Y bioRxiv. 2023; .

PMID: 36824964 PMC: 9949147. DOI: 10.1101/2023.02.17.528918.

Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A.

Kurup H, Kvach M, Harjes S, Barzak F, Jameson G, Harjes E Biochemistry. 2022; 61(22):2568-2578.

PMID: 36302365 PMC: 9724085. DOI: 10.1021/acs.biochem.2c00449.

The current toolbox for APOBEC drug discovery.

Grillo M, Jones K, Carpenter M, Harris R, Harki D Trends Pharmacol Sci. 2022; 43(5):362-377.

PMID: 35272863 PMC: 9018551. DOI: 10.1016/j.tips.2022.02.007.

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