B Cells Break the Structure Rule: Recognition of Intrinsically Disordered Epitopes in the SARS-CoV-2 Spike Model 2259769

Abstract

Abstract Introduction Antibody recognition has long been defined by order–a stable, well-folded epitope that fits its antibody like a key in a lock. Yet many viral proteins contain intrinsically disordered regions (IDRs): dynamic, shape-shifting segments that defy this rule. Whether antibodies can recognize such flexible regions–and by what mechanism–remains largely untested. The SARS-CoV-2 Spike furin-cleavage loop (PRRAR↓S) is one such IDR, essential for viral activation yet conformationally fluid. We asked whether murine B cells can mount specific antibody responses to structural disorder itself. Methods A panel of eight peptide probes was designed–five structured Spike epitopes and three disordered furin-loop peptides preserving the PRRAR motif. Using the 10x Genomics BEAM-Ab platform, we profiled splenic B cells from mice immunized with full-length Omicron BA.1 Spike and recovered over one hundred paired heavy- and light-chain sequences binding the barcoded probes. Antibody—peptide interactions were modeled with IgFold, docked using ClusPro, and evaluated by ΔG analyses; molecular dynamics assessed complex stability. Results BEAM-Ab identified productive clonotypes recognizing both structured and disordered Spike epitopes at comparable frequencies (∼46% vs 54%). Several antibodies bound directly to the PRRAR motif–a region previously considered too mobile for precise recognition. Docking and ΔG analyses supported formation of energetically favorable antibody—peptide complexes localized to the furin-loop region, with predicted affinities comparable to structured epitopes. Structural modeling further indicated that antibody engagement can stabilize the disordered loop through induced ordering upon binding to paratopes of matched flexibility Conclusion These findings show that B cells can generate specific antibodies against intrinsically disordered viral epitopes, redefining the structural limits of immune recognition and highlighting flexibility as an antigenic feature exploitable for antibody and vaccine design. Funding Source NIAID/NIH Topic Categories Computational and Systems Immunology (COMP)