Biology subjects

Shim, H.-J.

Publications and source records attributed to Shim, H.-J..

3 recordsLinked to original sources

bioRxiv2026

Rational Redesign of an Fc-Binding Peptide for Multivalent Antibody Assembly

Multivalent antibody assemblies offer opportunities to enhance avidity, organize immune complexes, and modulate higher-order protein interactions, but constructing such architectures from existing immunoglobulin G (IgG) molecules without redesigning the antibody scaffold remains challenging. Here, we report the rational redesign of a Protein A-derived Fc-binding peptide into ADP1, a stable dimeric Fc-binding peptide that directs Fc-mediated antibody assembly. ADP1 was designed from the parent Fc-binding peptide Z34C by preserving the Fc-recognition surface while redesigning the opposite helical surface to promote peptide-peptide association. Biophysical characterization showed that ADP1 retained nanomolar Fc-binding affinity while exhibiting markedly enhanced chemical and proteolytic stability compared with the parent peptide. Structural analyses of ADP1-Fc complexes revealed that ADP1 bridges neighboring Fc regions through a combined ADP1-Fc and ADP1-ADP1 interface, generating spiral higher-order Fc assemblies. This assembly principle was further extended to full-length IgG, where ADP1 promoted higher-order antibody association in a concentration-sensitive manner. In addition, covalent ADP1 functionalization enabled Fc-directed modification of full-length IgG while retaining Fab-mediated antigen recognition, demonstrating the utility of ADP1 as an antibody assembly and functionalization module. Finally, competitive addition of the parent Z34C peptide modulated ADP1-driven antibody assembly, suggesting a potential route for tuning Fc-mediated assembly propagation. Together, this work establishes a redesigned Fc-binding peptide platform for directing multivalent antibody assembly and functionalization without genetic reengineering of the IgG scaffold. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/737354v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@57cadeorg.highwire.dtl.DTLVardef@1c7d8e6org.highwire.dtl.DTLVardef@170fb85org.highwire.dtl.DTLVardef@90e6d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

AI-guided Protein Inhibitor Design for Modulating FAD-dependent Glucose Dehydrogenase Redox Output

Flavin adenine dinucleotide-dependent glucose dehydrogenase (FAD-GDH) is a redox enzyme widely used in glucose monitoring, bioelectronic devices, and enzymatic biofuel cells because of its oxygen-independent catalysis and compatibility with electron-transfer processes. However, protein-based regulators that directly bind GDH and modulate its redox output remain underdeveloped. Here, we present an AI-guided strategy for developing a de novo protein inhibitor targeting FAD-GDH. GDH-targeting candidates generated through structure-based computational design were evaluated by yeast surface display and fluorescence-activated cell sorting, leading to the identification of FAD-GDH inhibitor-1 (FGI-1) as a GDH-targeting inhibitory scaffold. Purified His-MBP-FGI-1 reduced GDH-mediated DCIP reduction, demonstrating attenuation of GDH-derived redox output. Random mutagenesis followed by secondary FACS screening yielded evolved variants with increased GDH-binding signals and enhanced redox-output suppression, showing that the de novo inhibitory scaffold could be functionally tuned through experimental evolution. In addition, an FGI-1-based construct fused to a larger protein module retained GDH-output suppressive activity, and electrode-based measurements showed reduced GDH-derived current output. Because electrode-associated measurements may be influenced by protein-mediated surface shielding and altered electron-transfer accessibility, this decrease was interpreted conservatively as attenuation of GDH-derived electrochemical output rather than direct evidence of active-site inhibition. Together, this work establishes an AI-guided design-validation workflow for developing protein inhibitors that modulate FAD-GDH redox output and provides a foundation for protein-level control of enzyme output in biosensing and bioelectronic applications.

biochemistry↗

bioRxiv2026

Deafness rapidly reorganizes functional brain networks in adult mice

Sensory loss triggers crossmodal reorganization across sensory modalities, and accumulating evidence indicates that this adaptive capacity persists into adulthood. However, the global organizing principles of such plasticity remain poorly understood, as conventional animal model approaches do not permit longitudinal, whole-brain measurements. Here, we use ultra-high-field (15.2T) BOLD fMRI to map deafening-induced functional reorganization across the entire brain in young adult mice. Within one week of deafening, the auditory cortex is recruited by somatosensory and visual inputs, while stimulus-evoked responses are potentiated in the spared sensory pathways. Reorganization extends beyond sensory cortices to higher-order association areas, including anterior cingulate, retrosplenial, and posterior parietal cortices. Resting-state fMRI further reveals strengthened coupling both within sensory systems and between sensory systems and a default mode-like network. These findings demonstrate that adult-onset deafness rapidly reorganizes functional brain networks and further implicate the default mode-like network as a potential mediator of crossmodal integration.

neuroscience↗