Koh Takeuchi
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View article: <scp>IMPDH</scp> and <scp>GTP</scp> Metabolism in Cancer: Mechanisms, Regulation, and Translational Scope
<span>IMPDH</span> and <span>GTP</span> Metabolism in Cancer: Mechanisms, Regulation, and Translational Scope Open
Guanosine triphosphate (GTP) is increasingly recognized as a critical actor in cancer cell proliferation, yet its regulatory mechanism remains incompletely defined. A key contributor to elevated GTP levels in tumors is inosine monophosphat…
View article: Counterfactual Evaluation for Blind Attack Detection in LLM-based Evaluation Systems
Counterfactual Evaluation for Blind Attack Detection in LLM-based Evaluation Systems Open
This paper investigates defenses for LLM-based evaluation systems against prompt injection. We formalize a class of threats called blind attacks, where a candidate answer is crafted independently of the true answer to deceive the evaluator…
View article: Dynamic Feature Selection from Variable Feature Sets Using Features of Features
Dynamic Feature Selection from Variable Feature Sets Using Features of Features Open
Machine learning models usually assume that a set of feature values used to obtain an output is fixed in advance. However, in many real-world problems, a cost is associated with measuring these features. To address the issue of reducing me…
View article: <scp>PI</scp>5<scp>P</scp>4<scp>K</scp> inhibitors: promising opportunities and challenges
<span>PI</span>5<span>P</span>4<span>K</span> inhibitors: promising opportunities and challenges Open
Phosphatidylinositol 5‐phosphate 4‐kinases (PI5P4K), also known as type II PIPKs or PIPKIIs, convert the lipid second messenger PI5P to PI(4,5)P 2 . The PI5P4K family consists of three isozymes in mammals—PI5P4Kα, β, and γ—which notably ut…
View article: Bottom-up design of peptide shapes in water using oligomers of <i>N</i> -methyl- <scp>l</scp> / <scp>d</scp> -alanine
Bottom-up design of peptide shapes in water using oligomers of <i>N</i> -methyl- <span>l</span> / <span>d</span> -alanine Open
Conformationally constrained N -methyl- l / d -alanine residues enable the bottom-up design of diverse peptide shapes.
View article: Structural basis of the residence time of adenosine A <sub>2A</sub> receptor ligands revealed by NMR
Structural basis of the residence time of adenosine A <sub>2A</sub> receptor ligands revealed by NMR Open
Our NMR analysis of adenosine A 2A receptor (A 2A AR) revealed that spatial arrangement surrounding the E165–H264 salt bridge correlates with the residence time—the average time a drug remains bound to its receptor.
View article: Late post-endovascular abdominal aortic repair rupture due solely to type II endoleak without other types of endoleak
Late post-endovascular abdominal aortic repair rupture due solely to type II endoleak without other types of endoleak Open
Rupture of abdominal aortic aneurysm (AAA) due to an isolated type II endoleak (TIIEL) is rarely reported, accounting for less than 1% of all TIIELs; typically, rupture associated with TIIEL is accompanied by type I or type III endoleaks. …
View article: Improvement of biodegradability prediction QSAR system through optimal combination of algorithms
Improvement of biodegradability prediction QSAR system through optimal combination of algorithms Open
This paper introduces a novel quantitative structure-activity relationship (QSAR) system for predicting the biodegradability of chemicals. The system focuses on evaluating the ratio of biochemical oxygen demand (BOD) to theoretical oxygen …
View article: Divergent Mechanisms Activating RAS and Small GTPases Through Post-translational Modification
Divergent Mechanisms Activating RAS and Small GTPases Through Post-translational Modification Open
RAS is a founding member of the RAS superfamily of GTPases. These small 21 kDa proteins function as molecular switches to initialize signaling cascades involved in various cellular processes, including gene expression, cell growth, and dif…
View article: Isolation and Structure Elucidation of JBIR-157, a Skeletally Novel Aromatic Polyketide Produced by the Heterologous Expression of a Cryptic Gene Cluster
Isolation and Structure Elucidation of JBIR-157, a Skeletally Novel Aromatic Polyketide Produced by the Heterologous Expression of a Cryptic Gene Cluster Open
Heterologous expression of natural compound biosynthetic gene clusters (BGCs) is a robust approach for not only revealing the biosynthetic mechanisms leading to the compounds, but also for discovering new products from uncharacterized BGCs…
View article: A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2
A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2 Open
How a peptoid binds to a protein was revealed by a co-crystal structure and systematic physicochemical studies.
View article: Decoding Atomic Addresses: Solution NMR Resonance Assignment of Proteins
Decoding Atomic Addresses: Solution NMR Resonance Assignment of Proteins Open
NMR is a powerful analytical technique that permits the exploration of biomolecules under physiological conditions with atomic resolution. It is especially applicable for examining protein structures and their interactions and dynamics in …
View article: Optimal selection of learning data for highly accurate QSAR prediction of chemical biodegradability: a machine learning-based approach
Optimal selection of learning data for highly accurate QSAR prediction of chemical biodegradability: a machine learning-based approach Open
Prior to the manufacture of new chemicals, regulations mandate a thorough review of the chemicals under risk management. This review involves evaluating their effects on the environment and human health. To assess these effects, a review r…
View article: ULK1-regulated AMP sensing by AMPK and its application for the treatment of chronic kidney disease
ULK1-regulated AMP sensing by AMPK and its application for the treatment of chronic kidney disease Open
AMP-activated protein kinase (AMPK) is a central kinase involved in energy homeostasis. Increased intracellular adenosine monophosphate (AMP) levels result in AMPK activation through the binding of AMP to the γ-subunit of AMPK. Recently, w…
View article: Bleeding alert map (BAM): The identification method of the bleeding source in real organs using datasets made on mimicking organs
Bleeding alert map (BAM): The identification method of the bleeding source in real organs using datasets made on mimicking organs Open
In thoraco-laparoscopic surgery, the identification of a bleeding source is recognized as one of the most important issues with hemostasis during operation. However, previously proposed techniques are only capable of detecting an approxima…
View article: The oxidative folding of nascent polypeptides provides electrons for reductive reactions in the ER
The oxidative folding of nascent polypeptides provides electrons for reductive reactions in the ER Open
The endoplasmic reticulum (ER) maintains an oxidative redox environment that is advantageous for the oxidative folding of nascent polypeptides entering the ER. Reductive reactions within the ER are also crucial for maintaining ER homeostas…
View article: Nonthermal acceleration of protein hydration by sub-terahertz irradiation
Nonthermal acceleration of protein hydration by sub-terahertz irradiation Open
The collective intermolecular dynamics of protein and water molecules, which overlap in the sub-terahertz (THz) frequency region, are relevant for expressing protein functions but remain largely unknown. This study used dielectric relaxati…
View article: Bottom-up design of peptide nanoshapes in water using oligomers of N-methyl-L/D-alanine
Bottom-up design of peptide nanoshapes in water using oligomers of N-methyl-L/D-alanine Open
De novo design of peptide nanoshapes is of great interest in biomolecular science since the local peptide nanoshapes formed by a short peptide chain in the proteins are often key to the biological activities. Here, we show that the de novo…
View article: Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides
Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides Open
Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we r…
View article: Functional molecular evolution of a <scp>GTP</scp> sensing kinase: <scp>PI5P4Kβ</scp>
Functional molecular evolution of a <span>GTP</span> sensing kinase: <span>PI5P4Kβ</span> Open
Over 4 billion years of evolution, multiple mutations, including nucleotide substitutions, gene and genome duplications and recombination, have established de novo genes that translate into proteins with novel properties essential for high…
View article: Possible Colchicine Poisoning: Case Study
Possible Colchicine Poisoning: Case Study Open
We have experienced a case of colchicine toxicity presenting with rapidly progressive gastrointestinal symptoms, hemodynamic instability, and multiple organ failure.
An 86-year-old Japanese man presented to our hospital with subarachnoida…
View article: Function-Related Conformational Dynamics of GPCRs Revealed by Solution NMR
Function-Related Conformational Dynamics of GPCRs Revealed by Solution NMR Open
NMR methods provide information about conformational dynamics of GPCRs over a wide range of frequencies in aqueous media at near-physiological temperature, with minimal modification of the wild-type GPCR covalent structures. Here we review…
View article: CCDC 2049403: Experimental Crystal Structure Determination
CCDC 2049403: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …