Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations

Abstract

The Fc portion of immunoglobulin G (IgG) is a horseshoe-shaped homodimer, which interacts with various effector proteins, including Fcγ receptors (FcγRs). These interactions are critically dependent on the pair of N-glycans packed between the two CH2 domains. Fucosylation of these N-glycans negatively affects human IgG1-FcγRIIIa interaction. The IgG1-Fc crystal structures mostly exhibit asymmetric quaternary conformations with divergent orientations of CH2 with respect to CH3. We aimed to provide dynamic views of IgG1-Fc by performing long-timescale molecular dynamics (MD) simulations, which were experimentally validated by small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our simulation results indicated that the dynamic conformational ensembles of Fc encompass most of the previously reported crystal structures determined in both free and complex forms, although the major Fc conformers in solution exhibited almost symmetric, stouter quaternary structures, unlike the crystal structures. Furthermore, the MD simulations suggested that the N-glycans restrict the motional freedom of CH2 and endow quaternary-structure plasticity through multiple intramolecular interaction networks. Moreover, the fucosylation of these N-glycans restricts the conformational freedom of the proximal tyrosine residue of functional importance, thereby precluding its interaction with FcγRIIIa. The dynamic views of Fc will provide opportunities to control the IgG interactions for developing therapeutic antibodies.

Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition

“…The 3D structures obtained from the simulation can then be used to determine the extent to which glycosylation has altered the protein's antigenicity 19 or other properties. When the structure of specific glycans at particular glycosites is known, these glycans can be employed in the simulation 19,20,31,32 , however this data is often unavailable and plausible glycosylation states may have to be assumed, particularly in the case of proteins with multiple permutations of glycoforms 16 .…”

On-Membrane Dynamic Interplay between Anti-GM1 IgG Antibodies and Complement Component C1q

“…This ordering process is entropically unfavorable; therefore, it is promoted selectively under on-membrane conditions, where diffusion of IgG molecules is considerably restricted. Upon loss of the constraint of disulfide bonds at the hinge, IgG antibodies gain greater degrees of motional freedom of the C H 2 domains, with an increase in the population of extremely asymmetric quaternary conformations [25]. Therefore, the reduction and alkylation of the hinge disulfides of IgG causes an increase in the conformational entropic penalty for hexamerization, resulting in the impaired formation of IgG rings reactive with C1q.…”

Antibody Structure and Function: The Basis for Engineering Therapeutics

“…The specific glycan attachments (fucosylation, sialylation, galactosylation, high-mannose, and bisecting glycans) have great importance to the antibody properties [213,214] (See Figure 5). Simulations of the dynamic interface between the glycans and the Fc domains have been described [215]. However, it is also important to remember that under physiological temperature and pH conditions, antibody deamidation, c terminal cleavage, and glycation kinetics do occur and can affect the serum lifetime of antibodies [209,216,217].…”