Principles for computational design of binding antibodies


Abstract

Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called “ideal” folds rich in regular secondary structures and almost devoid of loops and destabilizing elements, such as cavities. Molecular function, such as binding and catalysis, however, often demands nonideal features, including large and irregular loops and buried polar interaction networks, which have remained challenging for fold design. Through five design/experiment cycles, we learned principles for designing stable and functional antibody variable fragments (Fvs). Specifically, we (i) used sequence-design constraints derived from antibody multiple-sequence alignments, and (ii) during backbone design, maintained stabilizing interactions observed in natural antibodies between the framework and loops of complementarity-determining regions (CDRs) 1 and 2. Designed Fvs bound their ligands with midnanomolar affinities and were as stable as natural antibodies, despite having >30 mutations from mammalian antibody germlines. Furthermore, crystallographic analysis demonstrated atomic accuracy throughout the framework and in four of six CDRs in one design and atomic accuracy in the entire Fv in another. The principles we learned are general, and can be implemented to design other nonideal folds, generating stable, specific, and precise antibodies and enzymes.

Submission Details

ID: WkyQPR9A

Submitter: Stephanie Contreras

Submission Date: June 22, 2020, 11:31 a.m.

Version: 1

Publication Details
Dror Baran, M. Gabriele Pszolla, Gideon D. Lapidoth, Christoffer Norn, Orly Dym, Tamar Unger, Shira Albeck, Michael D. Tyka, Sariel J. Fleishman,Proceedings of the National Academy of Sciences of the United States of America (2017) Principles for computational design of binding antibodies
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
5W38 2017-06-07T00:00:00+0000 1.8 1.80A resolution structure of human IgG3 Fc (N392K)
6D58 2018-04-19T00:00:00+0000 2.39 Crystal structure of a Fc fragment of Human IgG3
4ZNC 2015-05-04T00:00:00+0000 2.28 Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant - Q9W
4WWI 2014-11-11T00:00:00+0000 2.31 Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution
3EO1 2008-09-26T00:00:00+0000 3.1 Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
5LG1 2016-07-05T00:00:00+0000 2.7 Room temperature structure of human IgG4-Fc from crystals analysed in situ
4D2N 2014-05-12T00:00:00+0000 2.7 Crystal structure of deglycosylated serum-derived human IgG4 Fc
1ADQ 1997-02-18T00:00:00+0000 3.15 CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC
4C54 2013-09-10T00:00:00+0000 1.9 Crystal structure of recombinant human IgG4 Fc
5W5N 2017-06-15T00:00:00+0000 1.85 Crystal structure of human IgG4-Sigma2 Fc fragment

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
200.0 L,M design of antibodies P01834 IGKC_HUMAN
190.2 H,I design of antibodies P01860 IGHG3_HUMAN
198.0 H,I design of antibodies P01857 IGHG1_HUMAN
184.2 H,I design of antibodies P01861 IGHG4_HUMAN