Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

Destan, E.; Turkut, E.; Aldeniz, A.; Kang, J.; Tosha, T.; Yabashi, M.; Yilmaz, B.; Timucin, A. C.; Matsuura, H.; Kawano, Y.; Cinkaya, I.; DeMirci, H.

doi:10.1101/2024.08.18.608484

bioRxiv · 10.1101/2024.08.18.608484

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

Destan, E.·Turkut, E.·Aldeniz, A.·Kang, J.·Tosha, T.·Yabashi, M.·Yilmaz, B.·Timucin, A. C.·Matsuura, H.·Kawano, Y.·Cinkaya, I.·DeMirci, H.

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Abstract

The constant fragment (Fc) of the Immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half-life. A prime example is VEGF-Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)-1 and VEGFR-2. The Fc regions role in N-glycosylation is particularly important, as it significantly influences protein stability. In this study, we present the first near-physiological temperature structures of the N-glycan-bound Fc fragment of IgG1 subtype from a biosimilar VEGF-Trap, determined using the SPring-8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including our own data, reveals alternate conformations within the glycan-binding pocket. Furthermore, molecular dynamics (MD) simulations highlight an unexpected degree of structural plasticity. These findings offer new insights into the molecular basis of Fc-mediated functions and provide valuable information for the design of next-generation therapeutics.

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Destan, E., Turkut, E., Aldeniz, A., Kang, J., Tosha, T., Yabashi, M., Yilmaz, B., Timucin, A. C., Matsuura, H., Kawano, Y., Cinkaya, I., DeMirci, H.. 2024-08-18. Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap. https://doi.org/10.1101/2024.08.18.608484

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