Small-angle x-ray scattering models of apobec3b catalytic domain in a complex with a single-stranded dna inhibitor

Fareeda M. Barzak; Timothy M. Ryan; Maksim V. Kvach; Harikrishnan M. Kurup; Hideki Aihara; Reuben S. Harris; Vyacheslav V. Filichev; Elena Harjes; Geoffrey B. Jameson

doi:10.3390/v13020290

Small-angle x-ray scattering models of apobec3b catalytic domain in a complex with a single-stranded dna inhibitor

Fareeda M. Barzak, Timothy M. Ryan, Maksim V. Kvach, Harikrishnan M. Kurup, Hideki Aihara, Reuben S. Harris, Vyacheslav V. Filichev, Elena Harjes, Geoffrey B. Jameson

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroele-ments. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.

Original language	English (US)
Article number	290
Journal	Viruses
Volume	13
Issue number	2
DOIs	https://doi.org/10.3390/v13020290
State	Published - Feb 2021

Bibliographical note

Funding Information:
V.V.F., E.H., G.B.J., and M.V.K. are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Palmerston North Medical Research Foundation, Massey University Research Fund (MURF 2015, 7003 and RM20734) and School of Fundamental Sciences, Massey University. F.M.B. was a recipient of Massey University graduate PhD scholarship. We gratefully acknowledge the support of the New Zealand Synchrotron Group Ltd. for facilitating access to the Australian Synchrotron. The labs of H.A. and R.S.H. are supported in part by NCI P01 CA234228. RH 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funding Information:
Funding: V.V.F., E.H., G.B.J., and M.V.K. are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Palmerston North Medical Research Foundation, Massey University Research Fund (MURF 2015, 7003 and RM20734) and School of Fundamental Sciences, Massey University. F.M.B. was a recipient of Massey University graduate PhD scholarship. We gratefully acknowledge the support of the New Zealand Synchrotron Group Ltd. for facilitating access to the Australian Synchrotron. The labs of H.A. and R.S.H. are supported in part by NCI P01 CA234228. RH 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

APOBEC
APOBEC inhibitors
APOBEC3
APOBEC3B
Cancer evolution
Dimer
Drug resistance
SAXS
Virus restriction

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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title = "Small-angle x-ray scattering models of apobec3b catalytic domain in a complex with a single-stranded dna inhibitor",

abstract = "In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroele-ments. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.",

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author = "Barzak, {Fareeda M.} and Ryan, {Timothy M.} and Kvach, {Maksim V.} and Kurup, {Harikrishnan M.} and Hideki Aihara and Harris, {Reuben S.} and Filichev, {Vyacheslav V.} and Elena Harjes and Jameson, {Geoffrey B.}",

note = "Funding Information: V.V.F., E.H., G.B.J., and M.V.K. are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Palmerston North Medical Research Foundation, Massey University Research Fund (MURF 2015, 7003 and RM20734) and School of Fundamental Sciences, Massey University. F.M.B. was a recipient of Massey University graduate PhD scholarship. We gratefully acknowledge the support of the New Zealand Synchrotron Group Ltd. for facilitating access to the Australian Synchrotron. The labs of H.A. and R.S.H. are supported in part by NCI P01 CA234228. RH 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding Information: Funding: V.V.F., E.H., G.B.J., and M.V.K. are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Palmerston North Medical Research Foundation, Massey University Research Fund (MURF 2015, 7003 and RM20734) and School of Fundamental Sciences, Massey University. F.M.B. was a recipient of Massey University graduate PhD scholarship. We gratefully acknowledge the support of the New Zealand Synchrotron Group Ltd. for facilitating access to the Australian Synchrotron. The labs of H.A. and R.S.H. are supported in part by NCI P01 CA234228. RH 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

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AU - Barzak, Fareeda M.

AU - Ryan, Timothy M.

AU - Kvach, Maksim V.

AU - Kurup, Harikrishnan M.

AU - Aihara, Hideki

AU - Harris, Reuben S.

AU - Filichev, Vyacheslav V.

AU - Harjes, Elena

AU - Jameson, Geoffrey B.

N1 - Funding Information: V.V.F., E.H., G.B.J., and M.V.K. are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Palmerston North Medical Research Foundation, Massey University Research Fund (MURF 2015, 7003 and RM20734) and School of Fundamental Sciences, Massey University. F.M.B. was a recipient of Massey University graduate PhD scholarship. We gratefully acknowledge the support of the New Zealand Synchrotron Group Ltd. for facilitating access to the Australian Synchrotron. The labs of H.A. and R.S.H. are supported in part by NCI P01 CA234228. RH 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding Information: Funding: V.V.F., E.H., G.B.J., and M.V.K. are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Palmerston North Medical Research Foundation, Massey University Research Fund (MURF 2015, 7003 and RM20734) and School of Fundamental Sciences, Massey University. F.M.B. was a recipient of Massey University graduate PhD scholarship. We gratefully acknowledge the support of the New Zealand Synchrotron Group Ltd. for facilitating access to the Australian Synchrotron. The labs of H.A. and R.S.H. are supported in part by NCI P01 CA234228. RH 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

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N2 - In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroele-ments. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.

AB - In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroele-ments. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.

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KW - APOBEC3

KW - APOBEC3B

KW - Cancer evolution

KW - Dimer

KW - Drug resistance

KW - SAXS

KW - Virus restriction

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JF - Viruses

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ER -

Small-angle x-ray scattering models of apobec3b catalytic domain in a complex with a single-stranded dna inhibitor

Abstract

Bibliographical note

Keywords

UN SDGs

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