Insights into substrate recognition and specificity for IgG by Endoglycosidase S2

Area of Science:

• Biochemistry and Molecular Biology
• Immunology
• Structural Biology

Background:

• Antibodies, particularly IgG, are key components of the immune system, binding antigens with high specificity.
• The N-glycan on IgG significantly influences antibody effector functions.
• Bacterial enzymes like Streptococcus pyogenes endoglycosidase EndoS2 can deglycosylate IgG to evade immune responses.

Purpose of the Study:

• To elucidate the structural mechanisms underlying EndoS2's catalytic activity on IgG.
• To understand the roles of the carbohydrate-binding module (CBM) and glycoside hydrolase (GH) domains in EndoS2 function.
• To investigate the flexibility and domain interactions of EndoS2 during IgG deglycosylation.

Main Methods:

• Enhanced-sampling molecular-dynamics (MD) simulations to model EndoS2-Fc complexes.
• Site-identification by ligand competitive saturation (SILCS) docking.
• Reconstruction and multi-microsecond MD simulations for detailed analysis.

Main Results:

• EndoS2 initially engages IgG via its CBM, followed by GH domain interaction, forming catalytically competent states.
• The CBM and GH domains can interact with the same or different Fc domains, leading to closed or open EndoS2 conformations.
• Glycan transfer from EndoS2's CBM to its GH domain was predicted, aiding complex formation, with a specific loop facilitating glycan extraction.
• Simulations align with experimental Hydrogen/Deuterium Exchange data and EndoS2's specificity for IgG glycans.

Conclusions:

• The study provides structural insights into EndoS2's mechanism of IgG deglycosylation.
• Flexible interactions between EndoS2's CBM and GH domains are critical for its catalytic activity.
• The predicted models support the functional roles of specific EndoS2 domains and their interactions with IgG.