Hafumi Nishi
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View article: Tyrosine bioconjugation using stably preparable urazole radicals
Tyrosine bioconjugation using stably preparable urazole radicals Open
Our ex situ tyrosine bioconjugation method utilizes the oxidation of N-methylurazole by Bobbitt's salt or electrochemical activation to generate stable radicals for selective tyrosine labeling, thereby addressing the longstanding challenge…
View article: Multi-Omics Profiling Reveals Phenotypic and Functional Heterogeneity of Neutrophils in COVID-19
Multi-Omics Profiling Reveals Phenotypic and Functional Heterogeneity of Neutrophils in COVID-19 Open
Accumulating evidence has revealed unexpected phenotypic heterogeneity and diverse functions of neutrophils in several diseases. Coronavirus disease (COVID-19) can alter the leukocyte phenotype based on disease severity, including neutroph…
View article: Laccase-catalyzed tyrosine click reaction with 1-methyl-4-arylurazole: rapid labeling on protein surfaces
Laccase-catalyzed tyrosine click reaction with 1-methyl-4-arylurazole: rapid labeling on protein surfaces Open
Our study shows efficient tyrosine labeling using 1-methyl-4-arylurazole (MAUra) with laccase under mild conditions. This method achieves a high efficiency ( k cat / K m = 7.88 × 10 4 M −1 s −1 ), selectively targeting exposed tyrosine sit…
View article: Single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients
Single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients Open
Introduction Infection with SARS-CoV-2 leads to coronavirus disease 2019 (COVID-19), which can result in acute respiratory distress syndrome and multiple organ failure. However, its comprehensive influence on pathological immune responses …
View article: Multi-omics profiling reveals phenotypic and functional heterogeneity of neutrophils in COVID-19
Multi-omics profiling reveals phenotypic and functional heterogeneity of neutrophils in COVID-19 Open
Background Accumulating evidence has revealed unexpected phenotypic heterogeneity and diverse functions of neutrophils in several diseases. Coronavirus disease (COVID-19) can alter the leukocyte phenotype based on disease severity, includi…
View article: Elevator motion of chloride ion transporter SLC26A9 induced by STAS domain
Elevator motion of chloride ion transporter SLC26A9 induced by STAS domain Open
The anion exchanger SLC26A9, consisting of the transmembrane (TM) domain and the cytoplasmic STAS domain, plays an essential role in regulating chloride transport across cell membranes. Recent studies have indicated that C-terminal helices…
View article: Physicochemical, functional, and evolutionary characteristics of protein loop regions in human and<i>Escherichia coli</i>proteomes
Physicochemical, functional, and evolutionary characteristics of protein loop regions in human and<i>Escherichia coli</i>proteomes Open
Protein loops often play crucial roles in the formation of binding and enzyme active sites. However, the general structural and biological characteristics of these loops remain unclear. In this study, we investigated protein loop regions o…
View article: Integrated analyses of single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients
Integrated analyses of single-cell RNA-seq public data reveal the gene regulatory network landscape of respiratory epithelial and peripheral immune cells in COVID-19 patients Open
Introduction Infection with SARS-CoV-2 leads to coronavirus disease 2019 (COVID-19), which can result in acute respiratory distress syndrome and multiple organ failure. However, its comprehensive influence on pathological immune responses …
View article: Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning
Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning Open
Despite the advances in surface-display systems for directed evolution, variants with high affinity are not always enriched due to undesirable biases that increase target-unrelated variants during biopanning. Here, our goal was to design a…
View article: Selective Elimination of NRF2-Activated Cells by Competition With Neighboring Cells in the Esophageal Epithelium
Selective Elimination of NRF2-Activated Cells by Competition With Neighboring Cells in the Esophageal Epithelium Open
View article: Transcriptome analysis of Homo sapiens and Mus musculus reveals mechanisms of CD8+ T cell exhaustion caused by different factors
Transcriptome analysis of Homo sapiens and Mus musculus reveals mechanisms of CD8+ T cell exhaustion caused by different factors Open
T cell exhaustion is a state of T cell dysfunction during chronic infection and cancer. Antibody-targeting immune checkpoint inhibitors to reverse T cell exhaustion is a promising approach for cancer immunotherapy. However, molecular mecha…
View article: Meta-analysis of exhausted CD8+ T cells from <i>Homo sapiens</i> and <i>Mus musculus</i> provides robust targets for immunotherapy
Meta-analysis of exhausted CD8+ T cells from <i>Homo sapiens</i> and <i>Mus musculus</i> provides robust targets for immunotherapy Open
T cell exhaustion is a state of T cell dysfunction during chronic infection and cancer. Antibody-targeting immune checkpoint inhibitors to reverse T cell exhaustion is a promising approach for cancer immunotherapy. However, the therapeutic…
View article: Prediction and Characterization of Disorder-Order Transition Regions in Proteins by Deep Learning
Prediction and Characterization of Disorder-Order Transition Regions in Proteins by Deep Learning Open
The biological functions of proteins are traditionally thought to depend on well-defined three-dimensional structures, but many experimental studies have shown that disordered regions lacking fixed three-dimensional structures also have cr…
View article: Application of Next-Generation Sequencing Analysis in the Directed Evolution for Creating Antibody Mimic
Application of Next-Generation Sequencing Analysis in the Directed Evolution for Creating Antibody Mimic Open
View article: Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex
Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex Open
View article: New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj) Open
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in c…
View article: Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach
Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach Open
View article: Additional file 1: of Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach
Additional file 1: of Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach Open
The dataset used in this study. (XLS 101 kb)
View article: H255Y and K508R missense mutations in tumour suppressor<i>folliculin (FLCN)</i>promote kidney cell proliferation
H255Y and K508R missense mutations in tumour suppressor<i>folliculin (FLCN)</i>promote kidney cell proliferation Open
Germline H255Y and K508R missense mutations in the folliculin (FLCN) gene have been identified in patients with bilateral multifocal (BMF) kidney tumours and clinical manifestations of Birt-Hogg-Dubé (BHD) syndrome, or with BMF kidney tumo…
View article: Structural and Functional Characteristics of Protein Phosphorylation Revealed by Bioinformatic Approaches
Structural and Functional Characteristics of Protein Phosphorylation Revealed by Bioinformatic Approaches Open
Protein phosphorylation plays a key role in numerous biological processes. Although several well-known phosphoproteins give us deep insights into the detailed properties of protein phosphorylation, comprehensive analyses are still required…
View article: Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins
Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins Open
Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome seq…
View article: Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency
Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency Open
Recent advances in DNA sequencing techniques have identified rare single-nucleotide variants with less than 1% minor allele frequency. Despite the growing interest and physiological importance of rare variants in genome sciences, less atte…