Biology subjects

Yokoyama, N.

Publications and source records attributed to Yokoyama, N..

4 recordsLinked to original sources

bioRxiv2026

Site-resolved spatial and structural interactome of a human cell

The spatial and structural arrangement of proteins determine virtually every process in human cells. We combined gentle subcellular fractionation by differential ultracentrifugation with cross-linking mass spectrometry to systematically map this cellular proteome architecture with residue-level evidence, identifying 164,146 residue-to-residue links in HEK293 cells. These links capture spatial protein arrangement at a resolution sufficient to pinpoint protein localizations at sub-organelle level, determine protein orientations within cellular membranes, and identify inter-organelle contact sites. The residue-level information provides evidence for 18,074 direct protein-protein interactions (PPIs), which we integrate into AlphaFold-based pipelines to nominate PPI-mediating short linear motifs and generate assembly models of large protein complexes. Guided by these spatial and structural readouts, we discover new PPIs within the endomembrane system that regulate the compartmental localization of trafficking machinery. Leveraging a network topology-driven strategy, we augment our HEK293 dataset with PPI data from different cell lines and methods, expanding the spatial and structural interactome of human cells.

systems biology↗

bioRxiv2026

Antiglycation effects of imidazole dipeptides and 2-oxo-imidazole dipeptides on glyceraldehyde-induced intracellular protein glycation and neuronal cell death

Glyceraldehyde (GA) contributes to the development of various diseases, such as diabetes and Alzheimers disease via protein glycation and the formation of advanced glycation end products (AGEs); however, effective strategies for neutralizing GA are limited. Carnosine (Car), an imidazole dipeptide (IDP) that is abundant in meat, suppresses protein glycation by scavenging reactive aldehydes. There are only a few reports on the antiglycation activity of Car against GA. For other IDPs, such as anserine, balenine (Bal), and homocarnosine, there are almost no reports on their antiglycation activity. In this study, we demonstrated the antiglycation activity of four types of IDPs and 2-oxocarnosine (2-oxo-Car), an oxidized form of Car, against GA-induced intracellular protein glycation and neuronal cytotoxicity. Car and Bal exhibited significantly higher reactivity with GA compared with other IDPs and 2-oxo-Car. An in silico analysis suggested that the difference in reactivity is dependent upon intramolecular hydrogen bond formation and the conformation of each IDP. Although there were differences in reactivity with GA, LC-MS analysis revealed that all of the IDPs and 2-oxo-Car reacted with two molecules of GA to form adducts containing pyridinium rings. Car and Bal exhibited high reactivity with GA and markedly suppressed GA-induced cytotoxicity in SH-SY5Y cells. Western blot and qPCR analyses revealed that IDPs suppressed GA-induced protein glycation and the upregulation of endoplasmic reticulum and oxidative stress response genes. Our results indicate that IDPs represent a novel preventive approach to AGE-related diseases and provide a foundation for the development of strategies to treat GA-related neurotoxicity. Graphical abstractCarnosine and balenine, which are imidazole dipeptides (IDPs), scavenged two molecules of glyceraldehyde to form adducts containing pyridinium rings and suppressed intracellular protein glycation and neuronal cell death. The formation of intramolecular hydrogen bond of IDPs played a crucial role in the strength of antiglycation activity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/734660v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@11d82dorg.highwire.dtl.DTLVardef@187aff0org.highwire.dtl.DTLVardef@12fe482org.highwire.dtl.DTLVardef@14327ee_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

How the TREX-2 complex associates with the nuclear pore

Nuclear pore complexes (NPCs) control nucleocytoplasmic transport in eukaryotes, yet their architecture remains incompletely understood. Here we report a substantially extended structure of the human NPC, obtained by combining cryo-electron tomography, crosslinking mass spectrometry, and AI-assisted integrative modeling. We resolve the molecular arrangement of TPR, NUP153, NUP50 and ZC3HC1, and reveal that five additional proteins -- TMEM209, SMPD4, GANP, Centrin-2 and ENY2 -- are incorporated into the NPC. Unexpectedly, GANP, Centrin-2 and ENY2, core members of the TREX-2 mRNA export complex, are built into the nuclear ring. This finding establishes TREX-2 not as a transiently associated factor, but as an integral NPC module, positioning it opposite of the cytoplasmic NUP214 mRNA export platform. Together, our results redefine the molecular composition of the inner ring, nuclear ring and nuclear basket. They suggest a direct structural basis that couples TREX-2-mediated mRNP remodeling to NPC-facilitated transport.

cell biology↗

bioRxiv2018

The effects of trans-chalcone and chalcone hydrate on the growth of Babesia and Theileria

BackgroundChemotherapy is a principle tool for the control and prevention of piroplasmosis. The search for a new chemotherapy against Babesia and Theileria parasites has become increasingly urgent due to the toxic side effects of and developed resistance to the current drugs. Chalcones have attracted much attention due to their diverse biological activities. With the aim to discover new drugs and drug targets, in vitro and in vivo antibabesial activity of trans-chalcone (TC) and chalcone hydrate (CH) alone and combined with diminazene aceturate (DA), clofazimine (CF) and atovaquone (AQ) were investigated.\n\nMethodology/Principal findingsThe fluorescence-based assay was used for evaluating the inhibitory effect of TC and CH on five of Babesia and Theileria species, including B. bovis, B. bigemina, B. divergens, B. caballi, and T. equi, the combination with DA, CF, and AQ on in vitro cultures, and on the multiplication of a B. microti-infected mouse model. The cytotoxicity of compounds was tested on Madin- Darby bovine kidney (MDBK), mouse embryonic fibroblast (NIH/3T3), and human foreskin fibroblast (HFF) cell lines. The half maximal inhibitory concentration (IC50) values of TC and CH against B. bovis, B. bigemina, B. divergens, B. caballi, and T. equi were 69.6 {+/-} 2.3, 33.3 {+/-} 1.2, 64.8 {+/-} 2.5, 18.9 {+/-} 1.7, and 14.3 {+/-} 1.6 {micro}M and 138.4 {+/-} 4.4, 60.9 {+/-} 1.1, 82.3 {+/-} 2.3, 27.9 {+/-} 1.2, and 19.2 {+/-} 1.5 {micro}M, respectively. In toxicity assays, TC and CH affected the viability of MDBK, NIH/3T3, and HFF cell lines the with half maximum effective concentration (EC50) values of 293.9 {+/-} 2.9, 434.4 {+/-} 2.7, and 498 {+/-} 3.1 {micro}M and 252.7 {+/-} 1.7, 406.3 {+/-} 9.7, and 466 {+/-} 5.7 {micro}M, respectively. In the mouse experiment, TC reduced the peak parasitemia of B. microti by 71.8% when administered intraperitoneally at 25 mg/kg. Combination therapies of TC-diminazene aceturate and TC-clofazimine were more potent against B. microti infection in mice than their monotherapies.\n\nConclusions/SignificanceIn conclusion, both TC and CH inhibited the growth of Babesia and Theileria in vitro, and TC inhibited the growth of B. microti in vivo. Therefore, TC and CH could be candidates for the treatment of piroplasmosis after further studies.\n\nAuthor summaryProtozoa of the genus Babesia are the second most common blood-borne parasites of mammals after the trypanosomes. Babesia and Theileria are the etiological agents of piroplasmosis, a tick-transmitted disease causing substantial losses of livestock and companion animals worldwide and has recently gained attention as one of the emerging zoonosis in humans. Diminazene aceturate and imidocarb dipropionate are still the first choices for the treatment of animals. However, these drugs cause many adverse effects. Furthermore, they are not approved for human medicine. Therefore, the development of alternative treatment remedies against babesiosis is urgently required. In the present study we evaluated the effects chalcone hydrate (CH) and trans-chalcone (TC), against the growth of four species of Babesia and T. equi. Furthermore, we studied the chemotherapeutic potential of TC on B. microti in mice. The effects of the combined treatment of TC with DA, CF and AQ revealed that TC was found to diminish the adverse effects of these drugs

microbiology↗