Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies

Yufei Xiang, Zhe Sang, Lirane Bitton, Jianquan Xu, Yang Liu, Dina Schneidman-Duhovny, Yi Shi

Research output: Contribution to journalArticlepeer-review


The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.

Original languageEnglish
Pages (from-to)220-234
JournalCell Systems
Issue number3
StatePublished - 17 Mar 2021


  • antibody immune response
  • antibody technology
  • nanobody
  • structural modeling
  • structural proteomics

All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Histology
  • Cell Biology


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