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bioRxiv · 10.1101/2024.03.19.585766

Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural and conformational properties.

Prakash, P.·Khodke, P.·Balasubramaniam, M.·Davids, B.-O.·Hollis, T.·Davis, J.·Pandhare, J.·Kumbhar, B.·Dash, C.
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Abstract

HIV-1 integration into the human genome is dependent on 3-processing of the reverse transcribed viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3-processed DNA remained resistant. Here, we describe the mechanism by which the 3-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3-processed DNA was significantly lower than the unprocessed HIV-1 DNA by TREX1. The efficiency of degradation (kcat/KM) of the 3-processed DNA was also significantly lower than the unprocessed DNA. Furthermore, the binding affinity (Kd) of TREX1 was markedly lower to the 3-processed DNA compared to the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3-processed DNA. These results pinpoint the biochemical mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3-processed HIV-1 DNA.

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Prakash, P., Khodke, P., Balasubramaniam, M., Davids, B.-O., Hollis, T., Davis, J., Pandhare, J., Kumbhar, B., Dash, C.. 2024-03-19. Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural and conformational properties.. https://doi.org/10.1101/2024.03.19.585766

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