6MY5

Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]

6MY5 の概要

• エントリーDOI: 10.2210/pdb6my5/pdb
• 関連するPDBエントリー: 6MXR 6MXS 6MY4
• 分子名称: anti-VEGF-A Fab fragment bH1 heavy chain, anti-VEGF-A Fab fragment bH1 light chain, 1,2-ETHANEDIOL, ... (4 entities in total)
• 機能のキーワード: fab fragment, antibody assembly, dimeric fab, immune system
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 99178.67

構造登録者

Shi, R. (登録日: 2018-11-01, 公開日: 2019-07-31, 最終更新日: 2024-11-20)

主引用文献

Schrag, J.D.,Picard, M.E.,Gaudreault, F.,Gagnon, L.P.,Baardsnes, J.,Manenda, M.S.,Sheff, J.,Deprez, C.,Baptista, C.,Hogues, H.,Kelly, J.F.,Purisima, E.O.,Shi, R.,Sulea, T.
Binding symmetry and surface flexibility mediate antibody self-association.
Mabs, 11:1300-1318, 2019

PubMed Abstract: Solution stability is an important factor in the optimization of engineered biotherapeutic candidates such as monoclonal antibodies because of its possible effects on manufacturability, pharmacology, efficacy and safety. A detailed atomic understanding of the mechanisms governing self-association of natively folded protein monomers is required to devise predictive tools to guide screening and re-engineering along the drug development pipeline. We investigated pairs of affinity-matured full-size antibodies and observed drastically different propensities to aggregate from variants differing by a single amino-acid. Biophysical testing showed that antigen-binding fragments (Fabs) from the aggregating antibodies also reversibly associated with equilibrium dissociation constants in the low-micromolar range. Crystal structures (PDB accession codes 6MXR, 6MXS, 6MY4, 6MY5) and bottom-up hydrogen-exchange mass spectrometry revealed that Fab self-association occurs in a symmetric mode that involves the antigen complementarity-determining regions. Subtle local conformational changes incurred upon point mutation of monomeric variants foster formation of complementary polar interactions and hydrophobic contacts to generate a dimeric Fab interface. Testing of popular tools generally indicated low reliabilities for predicting the aggregation propensities observed. A structure-aggregation data set is provided here in order to stimulate further improvements of tools for prediction of native aggregation. Incorporation of intermolecular docking, conformational flexibility, and short-range packing interactions may all be necessary features of the ideal algorithm.

PubMed: 31318308
DOI: 10.1080/19420862.2019.1632114

実験手法

X-RAY DIFFRACTION (1.73 Å)