Akinobu Senoo

The intestinal brush border (BB), composed of densely packed microvilli on enterocytes, is essential for nutrient absorption and host defense. Its organization relies on the intermicrovillar adhesion complex (IMAC), mediated by protocadherins CDHR2 and CDHR5. Despite their clinical relevance in inflammatory bowel disease and several carcinomas, structural details of IMAC assemblies have remained elusive. Herein, we report the Cryo-EM structure of the adhesive complex at 3.4 Å resolution, revealing a heterotetrameric ensemble composed of a dimer of CDHR2 and a dimer of CDHR5. This assembly ensures uniform adhesive strength between neighboring microvilli, and facilitates hexagonal packing of microvilli. Biophysical analyses and molecular dynamics simulations revealed a kinked, Ca²⁺-free linker between domains EC3 and EC4 of CDHR5 conferring the necessary flexibility to withstand the shear stress caused during intestinal peristalsis. Collectively, these findings provide a structural framework for understanding BB organization and suggest strategies for therapeutics targeting IMAC in intestinal disorders.

Human noroviruses are a leading cause of acute gastroenteritis worldwide, yet the molecular principles governing antibody recognition of their highly repetitive capsid remain poorly understood. Here, we immunized mice with virus‐like particles (VLPs) from the pandemic GII.4 strain and the emergent GII.17 strain, generating monoclonal IgM and IgG antibodies via hybridoma technology. High‐speed atomic force microscopy visualized IgM antibodies scanning and engaging multiple protruding (P) domains on intact VLPs. Surface plasmon resonance (SPR) analyses of engineered antibodies with identical Fab sequences but different valencies revealed that, unlike monovalent IgG, multivalent IgM exhibits dramatic affinity gains—up to 100‐fold—as antigen density increases. This avidity‐driven enhancement arises from the dense, repetitive P‐domain architecture of the norovirus capsid, enabling IgM to achieve high functional affinity despite modest intrinsic Fab binding. Our findings define how antibody valency and epitope organization cooperate to boost viral recognition, offering a mechanistic framework for designing next‐generation vaccines and antiviral antibodies that harness multivalent engagement.

OX40 and OX40L belong to the tumor necrosis factor receptor superfamily (TNFRSF) and tumor necrosis factor superfamily (TNFSF), respectively. Protein–protein interactions between OX40 and OX40L facilitate T cell responses, triggering various immunological and pathophysiological events. Excessive activation frequently contributes to the onset of autoimmune and allergic diseases. Therefore, the OX40/OX40L system is considered a promising target for drug discovery. Given that the structure of the OX40–OX40L complex exhibits some unique features compared to other members of these protein super families, it is reasonable to assume that this tandem possesses distinct interaction mechanisms. However, detailed interaction analysis using quantitative parameters such as binding kinetics or thermodynamics, with remains to be performed for OX40/OX40L. In this study, we identified several hot spot residues from the OX40 cysteine‐rich domains (CRDs) 1 to 3 by alanine scanning. Kinetic and thermodynamic analysis combined with molecular dynamics simulations highlighted the characteristics of a hot spot from CRD3 due to its indirect influence on those from CRD1 and CRD2, providing insights into the interaction mechanism and a strategy for drug discovery targeting this interaction.

Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment‐based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single‐chain variable fragments and camelid heavy‐chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single‐chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs.

Human norovirus, a leading cause of viral gastroenteritis, results in significant global health and economic burden, requiring sensitive and accurate diagnosis and effective therapeutics and vaccines. In this study, we immunized mice with the virus like capsid particles of GII.4, a mainstream strain, and GII.17, a modern strain that began to circulate in 2014, and used hybridoma technology to generate hybridoma cells that produce norovirus-binding antibodies against GII.4 and GII.17, respectively. Selection of these hybridoma cells yielded monoclonal IgG and IgM antibodies against these strains. Characterization of these antibodies revealed that avidity effect by multivalent binding is necessary for IgM to bind to norovirus at high efficiency, while IgG achieve high affinity even by monovalent binding. Surface plasmon resonance and ELISA data suggest that the high density of antigen protrusion domain in the norovirus capsid, containing approximately protomers, facilitates IgM to bind to norovirus capsid with high efficiency.

Immunoglobulin G (IgG) is a molecule that plays an important role in biological defense; IgG molecules have been applied as drugs due to their high specificity for antigens and their ability to activate immunity via effector molecules on immune cells. On the other hand, the flexibility of the hinge region makes it difficult to apply conventional structural biology approaches due to its dynamic conformational changes, and the mechanism of action of the molecule as a whole has not been elucidated. Here, we introduced a deletion amino acid mutation in the hinge region to elucidate the role of the hinge region and its effect on the structure and function of the IgG molecule. Deletion of Pro230 resulted in the formation of a half-molecular in which the interaction between heavy chains was lost. We elucidated the mechanism of half-IgG formation by structural analysis using nuclear magnetic resonance (NMR) measurements and by disulfide quantification using peptide mapping using LC-MS/MS. For this purpose, a new NMR stable isotope labeling method was introduced. Finally, cell assay revealed that the IgG half-molecules have specific FcγRI-mediated activity. This report provides new insights into the higher-order structure formation of IgG molecules and is expected to contribute to the elucidation of the molecular basis of the Fcγ receptor-mediated activation mechanism of the immune system.

Small molecules that regulate protein–protein interactions can be valuable drugs; however, the development of such small molecules is challenging as the molecule must interfere with an interaction that often involves a large surface area. Herein, we propose that modulating the conformational ensemble of the proteins participating in a given interaction, rather than blocking the interaction by directly binding to the interface, is a relevant strategy for interfering with a protein–protein interaction. In this study, we applied this concept to P‐cadherin, a cell surface protein forming homodimers that are essential for cell–cell adhesion in various biological contexts. We first determined the crystal structure of P‐cadherin with a small molecule inhibitor whose inhibitory mechanism was unknown. Molecular dynamics simulations suggest that the inhibition of cell adhesion by this small molecule results from modulation of the conformational ensemble of P‐cadherin. Our study demonstrates the potential of small molecules altering the conformation ensemble of a protein as inhibitors of biological relevant protein–protein interactions.