8TJT | pdb_00008tjt

The Fab fragment of an anti-glucagon receptor (GCGR) antibody

PDB DOI: https://doi.org/10.2210/pdb8TJT/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2023-07-24 Released: 2024-02-14
Deposition Author(s): Dai, J., Carter, P.J., Sudhamsu, J., Kung, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.252 (Depositor), 0.251 (DCC)
R-Value Work:
0.204 (Depositor), 0.203 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG 1 antibody.

Dai, J., Izadi, S., Zarzar, J., Wu, P., Oh, A., Carter, P.J.

(2024) MAbs 16: 2304282-2304282

PubMed: 38269489 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1080/19420862.2024.2304282
Primary Citation Related Structures:
8TJT

PubMed Abstract:
Subcutaneous injection is the preferred route of administration for many antibody therapeutics for reasons that include its speed and convenience. However, the small volume limit (typically $\leq$ 2 mL) for subcutaneous delivery often necessitates antibody formulations at high concentrations (commonly ≥100 mg/mL), which may lead to physicochemical problems. For example, antibodies with large hydrophobic or charged patches can be prone to self-interaction giving rise to high viscosity. Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG ₁ antibody prone to self-interaction. An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~ 200 anti-GCGR IgG ₁ variants. A negative correlation was found between the viscosity determined at high concentration (180 mg/mL) and the DLS interaction parameter measured at low concentration (2-10 mg/mL). Additionally, anti-GCGR variants were readily identified with reduced viscosity and antigen-binding affinity within a few fold of the parent antibody, with no identified impact on overall developability. The methods described here may be useful in the optimization of other antibodies to facilitate their therapeutic administration at high concentration.