Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves.


Abstract

Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody's amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems.

Submission Details

ID: pfN5Rjzn

Submitter: Paul Chang

Submission Date: Nov. 1, 2018, 5:25 p.m.

Version: 3

Publication Details
Adams RM;Mora T;Walczak AM;Kinney JB,Elife (2016) Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. PMID:28035901
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1CFN 1999-03-19T00:00:00+0000 2.65 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-RELATED PEPTIDE
1HH6 2000-12-21T00:00:00+0000 2.6 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE
1FRG 1994-01-17T00:00:00+0000 2.8 CRYSTAL STRUCTURE, SEQUENCE, AND EPITOPE MAPPING OF A PEPTIDE COMPLEX OF AN ANTI-INFLUENZA HA PEPTIDE ANTIBODY FAB 26(SLASH)9: FINE-TUNING ANTIBODY SPECIFICITY
1CFQ 1999-03-19T00:00:00+0000 2.8 ANTI-P24 (HIV-1) FAB FRAGMENT CB41
1CFT 1999-03-19T00:00:00+0000 2.8 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-UNRELATED D-PEPTIDE
1CFS 1999-03-19T00:00:00+0000 2.75 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-UNRELATED PEPTIDE
1HH9 2000-12-21T00:00:00+0000 2.7 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE
1HI6 2001-01-02T00:00:00+0000 2.55 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE
1BOG 1998-08-04T00:00:00+0000 2.6 ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-HOMOLOGOUS PEPTIDE
1SVZ 2004-03-30T00:00:00+0000 1.89 Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 L 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT P01837 IGKC_MOUSE
94.7 L 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT P01631 KV2A7_MOUSE
94.0 H 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT P01864 GCAB_MOUSE
100.0 H 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT P01865 GCAM_MOUSE
100.0 H 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT P01863 GCAA_MOUSE