6MXS

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

Summary for 6MXS

• Entry DOI: 10.2210/pdb6mxs/pdb
• Related: 6MXR 6MY4 6MY5
• Descriptor: anti-VEGF-A Fab fragment bH1 heavy chain, anti-VEGF-A Fab fragment bH1 light chain, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: fab fragment, antibody assembly, aggregation, immune system
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 99008.20

Authors

Shi, R.,Picard, M.-E.,Manenda, M.S. (deposition date: 2018-10-31, release date: 2019-07-31, Last modification date: 2024-10-23)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.95 Å)