Proteomics

&

Nanobody Bioengineering

 

Shi Lab

Welcome! Our lab is interested in developing cutting-edge biotechnologies with a focus on mass spectrometry based proteomic techniques. Our lab is also interested in antibody bioengineering and translational science.

Research

Fascinated by the exciting biomedical and therapeutic potentials of camelid single-chain VHH antibodies (so-called nanobodies), we have begun to develop proteomics methods and informatics tools, such as machine-learning to enable high-throughout identification and characterization of drug-quality nanobodies.

 

In parallel, we are interested in harnessing and bioengineering nanobodies for disease diagnosis and treatment. Through collaborations with structure and computational biologists , we are keen to unravel the mechanisms by which nanobodies uniquely target antigens of interest with high specificity and affinity.  Finally, we are exploring new ways to screen for new drug targets against challenging diseases for future pharmacological interventions.

Publications

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

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.

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Huge thank you to our supports!

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