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In Silico Structural Dynamics and Downstream Bioprocess of Recombinant Human SUMO-IL-33

Kim-Hung Nguyen (University of Medicine and Pharmacy at Ho Chi Minh City), Tan Thanh Mai (University of Medicine and Pharmacy at Ho Chi Minh City), Thua-Phong Lam (Uppsala University, University of Medicine and Pharmacy at Ho Chi Minh City), Long-Hung Dinh Pham (University of Medicine and Pharmacy at Ho Chi Minh City, Imperial College London), Hoang-Han Do (University of Medicine and Pharmacy at Ho Chi Minh City), Minh-Thanh Quach (University of Medicine and Pharmacy at Ho Chi Minh City), Khac‐Minh Thai (Vietnam National University Ho Chi Minh City, Trường Đại học Khoa học Sức khỏe), Minh-Quan Le (University of Medicine and Pharmacy at Ho Chi Minh City), Quoc‐Thai Nguyen (University of Medicine and Pharmacy at Ho Chi Minh City)

Biomolecules
DOI: 10.3390/biom16101451 (Biochemistry, Genetics and Molecular Biology)
License: CC BY

Abstract: , whether this intact chimera can directly serve as a screening surrogate remains unresolved. Here, we combined in silico simulations with empirical bioprocess optimization to establish a high-yield pipeline for native human IL-33 production. AI-based structure predictions (AlphaFold and RoseTTAFold) revealed distinct inter-domain dynamics mediated by a flexible linker. Molecular dynamics simulations of the compact RoseTTAFold model suggested potential steric occlusion near receptor-binding interfaces, whereas AlphaFold models exhibited extended conformations, highlighting model-dependent variations that warrant further structural verification. To restore accessibility, tag cleavage was optimized using 1.0% (mol/mol) SUMO protease at 4 °C for 1 h, achieving near-complete digestion. Sandwich ELISA demonstrated an 87.6% molar epitope recognition recovery for cleaved IL-33 versus only 12.0% for the intact fusion, providing empirical evidence of substantial functional epitope masking by the SUMO tag. Two-step IMAC purification yielded ~19% mass recovery (~32.6% molar recovery). These findings demonstrate that tag removal is operationally essential for IL-33 functional availability in screening applications.

Published on 04 Oct. 2026