Biology subjects

Koizumi, Y.

Publications and source records attributed to Koizumi, Y..

4 recordsLinked to original sources

bioRxiv2025

Single-molecule behavior and cell-growth regulation in human RTKs

Receptor tyrosine kinases (RTKs) are a major family of cell surface receptor proteins responsible for various cellular functions in animal cells, including fate decisions, metabolism, polarization and migration. Lateral mobility, dimerization, clustering, and oligomerization are crucial behaviors in the activation process of RTKs on the cell surface. However, relationships between these molecular behaviors and molecular function remain to be elucidated, except for a few RTK members. Here, using an automated live-cell single-molecule imaging and analysis system, we studied the behavior of 52 of the 58 human RTK species on living cells over time during stimulation with ligands. We extracted 72 single-molecule parameters for each RTK species to examine their relationship to function, structure, and evolution. We noticed that RTKs ability to inhibit or support cell growth, as observed in a large-scale loss-of-function experiment in the public domain, significantly relates to their behavior. Growth-inhibitory signaling was coupled with the immediate formation of immobile clusters, followed by the enlargement of immobile and slow-mobile domains. In contrast, growth-supportive signaling coupled with higher lateral diffusivity and delayed clustering of immobile molecules. The relationship between structure and function suggests that functional differences are related to partitioning into membrane rafts and changes in mobility associated with phosphatidylinositol turnover. In multiple linear regression models, molecular behavior explained half or more of the molecular function related to cell growth. This level of explainability is comparable to that of evolutionary grouping.

biophysics↗

bioRxiv2021

Liquid-liquid phase separation of florigen activation complex induces flowering

Floral transition, regulated by the systemic action of the mobile florigen protein FLOWERING LOCUS T (FT), is essential for successful plant reproduction1. How FT controls downstream gene expression remains incompletely understood, although it relies on the florigen activation complex (FAC), a core component of FT function2-4. The FAC is a nucleus-localized transcriptional activator of genes encoding MADS-box transcription factors critical to reproductive development and consists of florigen FT; a scaffold 14-3-3 protein that is a key component for complex assembly; and FD, a basic leucine-zipper protein that recruits the FAC to DNA. Here we report that the FAC exhibits phase separation. In rice shoot apical meristem cells, rice florigen Heading date 3a (Hd3a) fused to the green fluorescent protein formed speckles in the nucleus. The FAC speckle is formed in a FAC-dependent manner in tobacco cells. Recombinant Hd3a, but not OsFD1, phase-separated in vitro, and this effect was enhanced in the presence of 14-3-3 protein. Furthermore, mutations affecting functionally important residues in the pocket region or C-terminal disordered region of Hd3a affected FAC phase separation, providing a biochemical framework for the proteins effect on flowering. The ability to form condensates via phase transition represents a previously unknown mechanism for gene activation by the FAC.

plant biology↗

bioRxiv2020

Multidrug treatment with nelfinavir and cepharanthine against COVID-19

Antiviral treatments targeting the emerging coronavirus disease 2019 (COVID-19) are urgently required. We screened a panel of already-approved drugs in a cell culture model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and identified two new antiviral agents: the HIV protease inhibitor Nelfinavir and the anti-inflammatory drug Cepharanthine. In silico modeling shows Nelfinavir binds the SARS-CoV-2 main protease consistent with its inhibition of viral replication, whilst Cepharanthine inhibits viral attachment and entry into cells. Consistent with their different modes of action, in vitro assays highlight a synergistic effect of this combined treatment to limit SARS-CoV-2 proliferation. Mathematical modeling in vitro antiviral activity coupled with the known pharmacokinetics for these drugs predicts that Nelfinavir will facilitate viral clearance. Combining Nelfinavir/Cepharanthine enhanced their predicted efficacy to control viral proliferation, to ameliorate both the progression of disease and risk of transmission. In summary, this study identifies a new multidrug combination treatment for COVID-19.

microbiology↗

bioRxiv2020

Required concentration index quantifies effective drug combinations against HCV infection

Successful clinical drug development requires rational design of combination treatments based on preclinical data. Anti-HCV drugs exhibit significant diversity in antiviral effect. Dose-response assessments can be used to determine parameters profiling the diverse antiviral effect during combination treatment. In the current study, a combined experimental and mathematical approaches were used to compare and score different combinations of anti-hepatitis C virus (HCV) treatments. A "required concentration index" was generated and used to rank the antiviral profile of possible double- and triple-drug combinations against HCV genotype 1 and 2. Rankings varied based on target HCV genotype. Interestingly, multidrug (double and triple) treatment not only augmented antiviral activity, but also reduced genotype-specific efficacy, suggesting another advantage of multidrug treatment. The current study provides a quantitative method for profiling drug combinations against viral genotypes, to better inform clinical drug development.

systems biology↗