Antibodies, crucial in adaptive immunity, recognize antigens through specific interactions facilitated by Complementarity Determining Regions (CDRs), diversified via Variable-Diversity-Joining (VDJ) recombination. Traditional antibody development, limited by the scope of animal models and phage display libraries, captures a fraction of the potential antibody-antigen interactions. This underscores a gap in understanding antibody specificity and the relationship between antibody sequence and binding affinity. We have been developing an approach using the Single-Protein Interaction Detection (SPID) platform, repurposed to systematically map local landscapes of antibody-antigen interactions with unprecedented depth and speed, aiming to rival the precision of methods like Surface Plasmon Resonance (SPR) and Bio-Layer Interferometry (BLI) while significantly boosting throughput. By editing CDR sequences and measuring effects on dissociation constants, we are elucidating pathways for optimizing antibody affinity, enhancing predictive models for interactions. Our results demonstrate the capability of the SPID platform to characterize thousands of variants weekly, offering a deeper insight into antibody-antigen interactions and advancing antibody development with finely-tuned affinities.

Our research focuses on uncovering the molecular mechanisms of membrane proteins, a class of biomolecules often overlooked despite their critical biological and therapeutic significance. We utilize a diverse array of single-molecule techniques to observe both the conformational changes and functional dynamics of these proteins. As part of this effort, we are pioneering an innovative approach using single-molecule magnetic tweezers to monitor the folding of complex alpha-helical membrane proteins. This allows us to map the energy landscape that governs the complete folding process of polytopic alpha-helical membrane proteins (Nat. Comm. 2013, 2014, Nat. Chem. Biol. 2015, 2023, and Science 2019).

We have also applied similar techniques to explore the single-molecule mechanics of SNARE assembly, recently uncovering the disassembly mechanism of the SNARE complex by the proteasome system (20S complex). This work has shed light on how AAA+ ATPases tightly couple ATP hydrolysis with the unfolding of protein substrates (JACS 2013, Science 2015, and Nat. Comm. 2022).