Biology subjects

Kudo, S.

Publications and source records attributed to Kudo, S..

7 recordsLinked to original sources

bioRxiv2026

De novo masking domains that gate TNF-family ligand assembly and activity

Tumor necrosis factor family ligands (TNFLs) are central regulators of immunity and promising agents for cancer therapy, but their clinical use is often limited by dose-limiting systemic toxicity. Conditional activation and genetic fusion with antibodies could improve safety and pharmacokinetics, yet these features are difficult to combine because TNFLs form obligate homotrimers that are structurally mismatched with antibody architectures. Here we use AI-enabled protein design to create de novo protein masks that conditionally control TNFL assembly. The masks are genetically fused to TNFLs through protease-sensitive linkers and prevent trimer formation by competitively binding the TNFL trimerization interface. We demonstrate with TNF, OX40L, and 4-1BBL that protease-mediated release of the mask promotes trimer assembly, receptor binding and biological activity. These monomeric, switchable TNFLs are readily incorporated into full-length IgG formats, enabling plug-and-play construction of conditionally activatable antibody fusions. These fusions can be designed either to release activated soluble TNFLs upon protease treatment or, by reordering the fusion architecture, to trigger antibody multimerization and signaling by membrane-type TNFLs. When this multimerization strategy is applied to antibody-drug conjugates, conditional trimerization enhances cell killing by [~]30-fold, thereby improving the therapeutic window and enabling multiple strategies for selective tumor microenvironment targeting.

bioengineering↗

bioRxiv2024

Mora-ERP-based RNN-Transformer for decoding single-trial EEGs during silent Japanese speeches

We developed a method for decoding single-trial electroencephalography (EEG) during silent Japanese speeches. In order to cope with problems that there would be always noises in single-trial EEGs, a recurrent neural network (RNN) was used which could reproduce signals under noises. Each of silent-mora-related potentials and the single-trial EEG minus the event-related potential (ERP) were assigned to the signal and the noise, respectively, with reference to the averaging principle. Next, in our Transformer, dot product between the RNN output and the single-trial EEG after positional encoding then Softmax with Loss yielded probabilities of moras, each of which consists of silent Japanese words, phrases or part of sentences. The present decoding was completed by tracing the maximal probability at each block representing time. Average mora error rates (MERs) on pretrained and validated performances for the patient was as low as 1.5 % and 0 %, respectively. The performance for the testing would be refined by many single-trial EEGs during silent Japanese speeches obtained by EEG Web interfaces. This method might be applied to other "mora" languages.

neuroscience↗

bioRxiv2024

Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis

Malaria parasites have evolved unusual metabolic adaptations that specialize them for growth within heme-rich human erythrocytes. During blood-stage infection, Plasmodium falciparum parasites internalize and digest abundant host hemoglobin within the digestive vacuole. This massive catabolic process generates copious free heme, most of which is biomineralized into inert hemozoin. Parasites also express a divergent heme oxygenase (HO)-like protein (PfHO) that lacks key active-site residues and has lost canonical HO activity. The cellular role of this unusual protein that underpins its retention by parasites has been unknown. To unravel PfHO function, we first determined a 2.8 [A]-resolution X-ray structure that revealed a highly -helical fold indicative of distant HO homology. Localization studies unveiled PfHO targeting to the apicoplast organelle, where it is imported and undergoes N-terminal processing but retains most of the electropositive transit peptide. We observed that conditional knockdown of PfHO was lethal to parasites, which died from defective apicoplast biogenesis and impaired isoprenoid-precursor synthesis. Complementation and molecular-interaction studies revealed an essential role for the electropositive N-terminus of PfHO, which selectively associates with the apicoplast genome and enzymes involved in nucleic acid metabolism and gene expression. PfHO knockdown resulted in a specific deficiency in levels of apicoplast-encoded RNA but not DNA. These studies reveal an essential function for PfHO in apicoplast maintenance and suggest that Plasmodium repurposed the conserved HO scaffold from its canonical heme-degrading function in the ancestral chloroplast to fulfill a critical adaptive role in organelle gene expression.

biochemistry↗

bioRxiv2022

Collective gradient sensing by swimming bacteria without clustering

We characterize the taxis enhancement of swimming bacteria by collective migration without apparent clustering. We confine dilute Salmonella suspension in a shallow channel and evaluate the thermotaxis response to local heating and diffusion. By combining cell tracking analysis and numerical simulation based on simple modeling, we show that the alignment interaction suppresses orientation fluctuation, strengthens migration bias, and also prevents the dispersion of accumulated population. The results show a prominent example of how a collective motion of active matter implements a biological function.

biophysics↗

bioRxiv2022

Aberrant association of chromatin with nuclear periphery induced by Rif1 leads to mitotic defect and cell death.

Chromatin is compartmentalized in nuclei and its architecture and nuclear location may have impacts on chromatin events. Rif1, identified as a potent suppressor of hsk1-null mutation (defective in initiation of DNA replication) in fission yeast, recognizes G-quadruplex structures and inhibits origin firing in their 50[~]100-kb vicinity, leading us to postulate that Rif1 may generate chromatin higher-order structures inhibitory for initiation. However, effects of Rif1 on chromatin localization in nuclei have not been known. We show here that overexpression of Rif1 causes growth inhibition and eventually cell death in fission yeast. Chromatin binding activities of Rif1, but not recruitment of phosphatase PP1, are required for growth inhibitory effect. Overexpression of a PP1 binding site mutant of Rif1 does not delay S-phase, but still causes cell death, indicating that cell death is caused not by S-phase problems but by issues in other phases of cell cycle, most likely M-phase. Indeed, Rif1 overexpression generates cells with unequally segregated chromosomes. Rif1 overexpression relocates chromatin near nuclear periphery in a manner dependent on its chromatin-binding ability, and this correlates with growth inhibition and cell death induction. Thus, regulated Rif1-mediated chromatin association with nuclear periphery is important for coordinated progression of S- and M-phases.

molecular biology↗

bioRxiv2020

On-rate modulation of cadherin interactions by chemical fragments

Many cadherin family proteins are associated with diseases such as cancer. Since cell adhesion requires homodimerization of cadherin molecules, a small-molecule regulator of dimerization would have therapeutic potential. Herein, we describe identification of a P-cadherin-specific chemical fragment that inhibits P-cadherin-mediated cell adhesion. Although the identified molecule is a fragment compound, it binds to a cavity of P-cadherin that has not previously been targeted, indirectly prevents formation of hydrogen bonds necessary for formation of an intermediate called the X dimer and thus modulates the on-rate of X dimerization. Our findings will impact on a strategy for kinetic regulation of protein-protein interactions and stepwise assembly of protein complexes using small molecules.

biochemistry↗

bioRxiv2017

Spatial and temporal translocation of PKCα in single endothelial cell in response to focal mechanical stimulus

We observed the kinetics of protein kinase C (PKC) and the intracellular Ca2+ wave in endothelial cells (ECs) in response to microscopic mechanical stress to investigate the effect of mechanical stress on PKC translocation. The results show that a focal mechanical stimulus induced biphasic and directional PKC translocation; PKC initially translocated toward distinct spots near or at the membrane and then accumulated at the stimulus point. The low initial translocation occurred simultaneously in parallel with the increase in Ca2+. Initial translocation was inhibited in spite of Ca2+ increase when the diacylglycerol (DAG) binding domain of PKC was inhibited, suggesting that translocation requires intracellular Ca2+ increase and DAG. On the other hand, high secondary translocation was delayed, occurring after the Ca2+ wave; however, this secondary translocation occurred even when Ca2+ release from the endoplasmic reticulum was inhibited, while it did not occur when the mechanosensitive (MS) channel was inhibited. These results indicated that at least Ca2+ influx through MS channels is required. Our results support the implication of PKC in the Ca2+ signaling pathway in response to mechanical stress in ECs.\n\nSummary statementIn response to a focal mechanical stimulus, PKC in an endothelial cell was initially translocated toward distinct spots near or at the membrane and then accumulated at the stimulus point.

cell biology↗