Conserved heavy/light contacts and germline preferences revealed by a large-scale analysis of natively paired human antibody sequences and structural data

Understanding the pairing preferences and structural interactions between antibody heavy and light chains can enhance our ability to design more effective and specific therapeutic antibodies. Insights from natural antibody repertoires and conserved contact sites help reduce autoreactivity and improve drug safety and efficacy. Current databases represent only a limited portion of the estimated diversity of unique paired antibody molecules. To address this, we introduce PairedAbNGS, a novel database with paired heavy/light antibody chains. To our knowledge, this is the largest resource for paired natural antibody sequences with 58 bioprojects and over 14 million assembled productive sequences. Using this dataset, we investigated heavy and light chain variable (V) gene pairing preferences and found significant biases beyond gene usage frequencies, possibly due to receptor editing favoring less autoreactive combinations. Analyzing the available antibody structures from the Protein Data Bank, we studied conserved contact residues between heavy and light chains, particularly interactions between the CDR3 region of one chain and the FWR2 region of the opposite chain. Examination of amino acid pairs at key contact sites revealed significant deviations of amino acids distributions compared to random pairings, in the heavy chain's CDR3 region contacting the opposite chain, indicating specific interactions might be crucial for proper chain pairing. This observation is further reinforced by preferential IGHV-IGLJ and IGLV-IGHJ pairing preferences. We hope that both our resources and the findings would contribute to improving the engineering of biological drugs. We make the database accessible at https://naturalantibody.com/paired-ab-ngs as a valuable tool for biological and machine-learning applications.