Structural characterization of a minimal antibody against human apobec3b

Heng Tang, Özlem Demir, Fredy Kurniawan, William L. Brown, Ke Shi, Nicholas H. Moeller, Michael A. Carpenter, Christopher Belica, Kayo Orellana, Guocheng Du, Aaron M. Lebeau, Rommie E. Amaro, Reuben S. Harris, Hideki Aihara

Research output: Contribution to journalArticlepeer-review

Abstract

APOBEC3B (A3B) is one of seven human APOBEC3 DNA cytosine deaminases that restrict viral infections as part of the overall innate immune response, but it also plays a major role in tumor evolution by mutating genomic DNA. Given the importance of A3B as a restriction factor of viral infections and as a driver of multiple human cancers, selective antibodies against A3B are highly desirable for its specific detection in various research and possibly diagnostic applications. Here, we describe a high-affinity minimal antibody, designated 5G7, obtained via a phage display screening against the C-terminal catalytic domain (ctd) of A3B. 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. The crystal structure of 5G7 shows a canonical arrangement of the heavy and light chain variable domains, with their complementarity-determining region (CDR) loops lining an antigen-binding cleft that accommodates a pair of α-helices. To understand the mechanism of A3Bctd recognition by 5G7, we used the crystal structures of A3Bctd and 5G7 as templates and computationally predicted the A3B-5G7 complex structure. Stable binding poses obtained by the simulation were further tested by site-directed mutagenesis and in vitro binding analyses. These studies mapped the epitope for 5G7 to a portion of C-terminal α6 helix of A3Bctd, with Arg374 playing an essential role. The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. Our studies provide a platform for the development of selective antibodies against A3B and other APOBEC3 family enzymes.

Original languageEnglish (US)
Article number663
JournalViruses
Volume13
Issue number4
DOIs
StatePublished - Apr 2021
Externally publishedYes

Bibliographical note

Funding Information:
Funding: This work was supported by grants from the NIH (NIGMS R35-GM118047 to HA, NCI P01-CA234228 to RSH, REA, and HA, NCI R01-CA237272 to AML), a 2013 Prostate Cancer Foundation Young Investigator Award to AML, NSF XSEDE CHE060063 to REA, and a China Scholarship Council fund to HT. This work is based upon research conducted at the NE-CAT beamlines, which are funded by NIH (P30 GM124165). The Pilatus 6M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. R.S.H. is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished University McKnight Professor, and an Investigator of the Howard Hughes Medical Institute.

Funding Information:
This work was supported by grants from the NIH (NIGMS R35-GM118047 to HA, NCI P01-CA234228 to RSH, REA, and HA, NCI R01-CA237272 to AML), a 2013 Prostate Cancer Foundation Young Investigator Award to AML, NSF XSEDE CHE060063 to REA, and a China Scholarship Council fund to HT. This work is based upon research conducted at the NE-CAT beamlines, which are funded by NIH (P30 GM124165). The Pilatus 6M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. R.S.H. is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished University McKnight Professor, and an Investigator of the Howard Hughes Medical Institute.

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

Keywords

  • APOBEC3B
  • Antiviral innate immunity
  • Cancer mutagenesis
  • Crystal structure
  • DNA cytosine deaminase
  • Molecular dynamics simulation
  • Monoclonal antibody
  • Protein-protein docking
  • ScFv
  • Tumor evolution

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