Search results for: Yuji Goto

Items from 1 to 20 out of 142 results

article

Effects of low and high levels of maternal nutrition consumed for the entirety of gestation on the development of muscle, adipose tissue, bone, and the organs of Wagyu cattle fetuses

Yi Zhang, Kounosuke Otomaru, Kazunaga Oshima, Yuji Goto, more

Animal Science Journal > 92 > 1 > n/a - n/a

This study aimed to investigate the effects of high and low levels of energy intake during the entire gestation period on the skeletal muscle development, organ development, and adipose tissue accumulation in fetuses of Wagyu (Japanese Black) cows, a breed with highly marbled beef. Cows were allocated to a high‐nutrition (n = 6) group (fed 120% of the nutritional requirement) or low‐nutrition (n = 6)...

article

Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein

Masatomo So, Yuto Kimura, Keiichi Yamaguchi, Toshihiko Sugiki, more

Protein Science > 30 > 8 > 1701 - 1713

Amyloid fibril formation is associated with various amyloidoses, including neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Amyloid fibrils form above the solubility of amyloidogenic proteins or peptides upon breaking supersaturation, followed by a nucleation and elongation mechanism, which is similar to the crystallization of solutes. Many additives, including salts, detergents,...

article

Front Cover: The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug‐Like Miniprotein (Chem. Eur. J. 9/2020)

Nóra Taricska, Dániel Horváth, Dóra K. Menyhárd, Hanna Ákontz‐Kiss, more

Chemistry – A European Journal > 26 > 9 > 1888 - 1888

Studying the early phases of amyloid formation is of crucial importance both for understanding the initialization of various pathophysiological processes and for aiding the design of non‐toxic peptide medications that will not become initiators of such processes themselves. This work reports a new monitoring technique using ECD measurements of amyloid progression that can be applied even if the amyloid...

article

The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug‐Like Miniprotein

Nóra Taricska, Dániel Horváth, Dóra K. Menyhárd, Hanna Ákontz‐Kiss, more

Chemistry – A European Journal > 26 > 9 > 1893 - 1893

Invited for the cover of this issue is the group of András Perczel at Eötvös Loránd University, Budapest, Hungary and colleagues from Osaka University, Japan. The image depicts the amyloid buildup of an Exenatide derivate miniprotein (E5) monitored on a simplified hyperspace. Read the full text of the article at 10.1002/chem.201903826.

article

The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug‐Like Miniprotein

Nóra Taricska, Dániel Horváth, Dóra K. Menyhárd, Hanna Ákontz‐Kiss, more

Chemistry – A European Journal > 26 > 9 > 1968 - 1978

The amyloid formation of the folded segment of a variant of Exenatide (a marketed drug for type‐2 diabetes mellitus) was studied by electronic circular dichroism (ECD) and NMR spectroscopy. We found that the optimum temperature for E5 protein amyloidosis coincides with body temperature and requires well below physiological salt concentration. Decomposition of the ECD spectra and its barycentric representation...

article

Salt-induced formations of partially folded intermediates and amyloid fibrils suggests a common underlying mechanism

Yuji Goto, Masayuki Adachi, Hiroya Muta, Masatomo So

Biophysical Reviews > 2018 > 10 > 2 > 493-502

Amyloid fibrils are misfolded forms of proteins and are involved in various diseases. They have been studied extensively with the aim to obtain a comprehensive understanding of protein folding and misfolding and to use this knowledge to develop therapeutic strategies against the associated diseases. Salt conditions are important factors determining the formation and stability of amyloid fibrils. In...

article

Asymmetric larval head and mandibles of Hydrophilus acuminatus (Insecta: Coleoptera, Hydrophilidae): Fine structure and embryonic development

Shun'ichi Sato, Toshio Inoda, Shuhei Niitsu, Souichirou Kubota, more

Arthropod Structure & Development > 2017 > 46 > 6 > 824-842

The larvae of a water scavenger beetle, Hydrophilus acuminatus, have strongly asymmetric mandibles; the right one is long and slender, whereas the left one is short and stout. The fine structure and embryonic development of the head capsule and mandibles of this species were examined using light and scanning electron microscopy, and asymmetries in shape were detected in these structures applying an...

article

Drastic acceleration of fibrillation of insulin by transient cavitation bubble

Kichitaro Nakajima, Daisuke Nishioka, Masahiko Hirao, Masatomo So, more

Ultrasonics Sonochemistry > 2017 > 36 > C > 206-211

Amyloid-fibril formation of proteins can be accelerated by ultrasonic irradiation to the peptide solutions. Although this phenomenon contributes to understanding pathogenic behavior of amyloidosis, its physical mechanism has not been clarified, because several factors (cavitation, temperature increase, stirring effect, and so on) related to ultrasonic irradiation can participate in the fibrillation...

article

Heparin‐induced amyloid fibrillation of β₂‐microglobulin explained by solubility and a supersaturation‐dependent conformational phase diagram

Masatomo So, Yasuko Hata, Hironobu Naiki, Yuji Goto

Protein Science > 26 > 5 > 1024 - 1036

Amyloid fibrils are fibrillar deposits of denatured proteins associated with amyloidosis and are formed by a nucleation and growth mechanism. We revisited an alternative and classical view of amyloid fibrillation: amyloid fibrils are crystal‐like precipitates of denatured proteins formed above solubility upon breaking supersaturation. Various additives accelerate and then inhibit amyloid fibrillation...

article

Measurement of amyloid formation by turbidity assay—seeing through the cloud

Ran Zhao, Masatomo So, Hendrik Maat, Nicholas J. Ray, more

Biophysical Reviews > 2016 > 8 > 4 > 445-471

Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations...

article

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, more

Journal of Computational Chemistry > 37 > 31 > 2687 - 2700

The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational...

article

Recognizing and analyzing variability in amyloid formation kinetics: Simulation and statistical methods

Damien Hall, Ran Zhao, Masatomo So, Masayuki Adachi, more

Analytical Biochemistry > 2016 > 510 > C > 56-71

We examine the phenomenon of variability in the kinetics of amyloid formation and detail methods for its simulation, identification and analysis. Simulated data, reflecting intrinsic variability, were produced using rate constants, randomly sampled from a pre-defined distribution, as parameters in an irreversible nucleation-growth kinetic model. Simulated kinetic traces were reduced in complexity...

article

Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions

Damien Hall, Ran Zhao, Ian Dehlsen, Nathaniel Bloomfield, more

Analytical Biochemistry > 2016 > 498 > C > 78-94

Due to their colloidal nature, all protein aggregates scatter light in the visible wavelength region when formed in aqueous solution. This phenomenon makes solution turbidity, a quantity proportional to the relative loss in forward intensity of scattered light, a convenient method for monitoring protein aggregation in biochemical assays. Although turbidity is often taken to be a linear descriptor...

article

A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions

Cardine N. Nokwe, Manuel Hora, Martin Zacharias, Hisashi Yagi, more

Journal of Molecular Biology > 2016 > 428 > 6 > 1315-1332

The aggregation of mostly antibody light chain variable (V_L) domains into amyloid fibrils in various tissues is the main cause of death in systemic amyloid light chain amyloidosis. Point mutations within the domain are important to shift the V_L into the fibrillar pathway, but why and how only some site-specific mutations achieve this still remains elusive. We show here that both destabilizing and...

article

Amorphous Aggregation of Cytochrome C with Inherently low Amyloidogenicity is Characterized by the Metastability of Supersaturation and the Phase Diagram

Yuxi Lin, József kardos, Koichiro Ishimori, Yuji Goto, more

Biophysical Journal > 2016 > 110 > 3 Supplement 1 > 399a

article

X-ray Observation of Novel Nucleation Factor in Protein Supersaturated Solution

Yufuku Matsushita, Hiroshi Sekiguchi, Noboru Ohta, Keigo Ikezaki, more

Biophysical Journal > 2016 > 110 > 3 Supplement 1 > 223a

book

Water and Biomolecules

Kunihiro Kuwajima, Yuji Goto, Fumio Hirata, Mikio Kataoka, more

Biological and Medical Physics, Biomedical Engineering

Life is produced by the interplay of water and biomolecules. This book deals with the physicochemical aspects of such life phenomena produced by water and biomolecules, and addresses topics including "Protein Dynamics and Functions", "Protein and DNA Folding", and "Protein Amyloidosis". All sections have been written by internationally recognized front-line researchers...

article

Revisiting supersaturation as a factor determining amyloid fibrillation

Masatomo So, Damien Hall, Yuji Goto

Current Opinion in Structural Biology > 2016 > 36 > C > 32-39

Amyloid fibrils involved in various diseases are formed by a nucleation-growth mechanism, similar to the crystallization of solutes from solution. Solubility and supersaturation are two of the most important factors determining crystallization of solutes. Moreover, crystallization competes with glass formation in which solutes collapse into amorphous aggregates. Recent studies on the formation of...

article

Thermal and chemical unfolding pathways of PaSdsA1 sulfatase, a homo‐dimer with topologically interlinked chains

César Aguirre, Yuji Goto, Miguel Costas, Miguel De la Rosa

FEBS Letters > 590 > 2 > 202 - 214

Understanding the mechanisms as to how interlinked proteins entangle and fold is a challenge. PaSdsA1 sulfatase is a homo‐dimer containing two zinc atoms per monomer. The monomer chains are interlinked in a dimerization domain. To study the unfolding pathways denaturation experiments were performed. In the native protein three forms coexist in chemical equilibrium, each with a different number of...

article

Prevention of allergic rhinitis by ginger and the molecular basis of immunosuppression by 6-gingerol through T cell inactivation

Yoshiyuki Kawamoto, Yuki Ueno, Emiko Nakahashi, Momoko Obayashi, more

The Journal of Nutritional Biochemistry > 2016 > 27 > Complete > 112-122

The incidence of allergies has recently been increasing worldwide. Immunoglobulin E (IgE)-mediated hypersensitivity is central to the pathogenesis of asthma, hay fever and other allergic diseases. Ginger (Zingiber officinale Roscoe) and its extracts have been valued for their medical properties including antinausea, antiinflammation, antipyresis and analgesia properties. In this study, we investigated...

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Keywords

AMYLOID FIBRIL (26)
PROTEIN FOLDING (19)
Β2-MICROGLOBULIN (17)
NMR (10)
Β-LACTOGLOBULIN (10)
AGGREGATION (8)
DIALYSIS-RELATED AMYLOIDOSIS (8)
CIRCULAR DICHROISM (6)
PROTEIN MISFOLDING (6)
SUPERSATURATION (6)
Α-HELIX (6)
AMYLOID (5)
HYDROGEN/DEUTERIUM EXCHANGE (5)
PROTEIN AGGREGATION (5)
SOLUBILITY (5)
AMYLOID FIBRILS (4)
CALORIMETRY (4)
SMALL-ANGLE X-RAY SCATTERING (4)
TRIFLUOROETHANOL (4)
ULTRASONICATION (4)
AMORPHOUS AGGREGATION (3)
ATOMIC FORCE MICROSCOPY (3)
HEAT CAPACITY (3)
HYDROPHOBIC INTERACTION (3)
IMMUNOGLOBULIN FOLD (3)
LIPOSOME (3)
SALT EFFECTS (3)
TANFORD TRANSITION (3)
Β 2 -MICROGLOBULIN (2)
ALCOHOL (2)
ALZHEIMER'S DISEASE (2)
AMYLOID BETA-PEPTIDES (2)
AMYLOID Β PEPTIDE (2)
ANTIBODY AMYLOID (2)
APOMYOGLOBIN (2)
DOMAIN STABILITY (2)
FLUORESCENCE MICROSCOPY (2)
GUANIDINE HYDROCHLORIDE (2)
HETERONUCLEAR NMR (2)
IMMUNOGLOBULIN DOMAIN (2)
INTERMEDIATE OF FIBRIL ELONGATION (2)
MELITTIN (2)
MOLTEN GLOBULE (2)
NUCLEAR MAGNETIC RESONANCE (2)
PARKINSON'S DISEASE (2)
PRESSURE (2)
PROTEIN FOLDING AND AGGREGATION DISEASE (2)
PROTEIN FOLDING AND MISFOLDING (2)
PROTEIN MODELING (2)
PROTEIN–LIGAND INTERACTION (2)
SECONDARY STRUCTURE (2)
STOPPED-FLOW FLUORESCENCE (2)
TRYPTOPHAN FLUORESCENCE (2)
Β-LACTOGLOBULIN; TRIFLUOROETHANOL; Α-HELIX; PROTEIN FOLDING; SECONDARY STRUCTURE PREDICTION (2)
Β 2 -GLYCOPROTEIN I (1)
XIST (1)
1‐ANILINONAPHTHALENE‐8‐SULFONATE (1)
2,2,2-TRIFLUOROETHANOL (1)
2D-NMR (1)
6-GINGEROL (1)
ACCESSION MIYAKOJIMA MG-20 (1)
ACOUSTIC FIELD ANALYSIS (1)
AGGREGATION ACCELERATION (1)
AGGREGATION ASSAY (1)
AGGREGATION CHIMERA (1)
AGROBACTERIUM TUMEFACIENS (1)
AIR–WATER INTERFACE (1)
AL-AMYLOIDOSIS (1)
ALCOHOL CLUSTERING (1)
ALCOHOL EFFECTS (1)
ALLERGY (1)
ALPHA-SYNUCLEIN (1)
ALZHEIMER’S DISEASE (1)
AMIDE PROTON EXCHANGE (1)
AMYLOID AGGREGATION KINETICS (1)
AMYLOID BETA (1)
AMYLOID BETA FIBRILS (1)
AMYLOID BIOPHYSICS (1)
AMYLOID FIBRIL FORMATION (1)
AMYLOID FIBRILLATION (1)
AMYLOID FORMATION (1)
AMYLOID NUCLEATION (1)
AMYLOID Β (1)
AMYLOID Β-PEPTIDE (1)
AMYLOIDFIBRILLEN (1)
AMYLOIDGENIC INTERMEDIATE (1)
AMYLOIDOSIS (1)
ANTI-AMYLOID DRUG SCREENING (1)
ANTI-AMYLOID LIGAND SCREEN (1)
ANTIBODY LIGHT CHAIN (1)
APOLIPOPROTEIN H (1)
APOMYOGLOBIN; DIFFERENTIAL SCANNING CALORIMETRY; HYDROPHOBIC INTERACTIONS; MOLTEN GLOBULE; PROTEIN FOLDING (1)
APOMYOGLOBIN; MOLTEN GLOBULE; SOLUTION X-RAY SCATTERING; PROTEIN FOLDING; MOLECULAR COMPACTNESS (1)
ARSENIC (1)
ASYMMETRY (1)
AΒ (1)
BACKBONE DYNAMICS (1)
BARNASE (1)
BINDING THERMODYNAMIC (1)
BIREFRINGENCE (1)
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Elsevier (96)
ACS (25)
Wiley (13)
Springer (7)
ieee (1)

Journal

Journal of Molecular Biology (40)
Biochemistry (17)
BBA - Proteins and Proteomics (15)
FEBS Letters (10)
Journal of the American Chemical Society (5)
Biophysical Journal (4)
Biochemical and Biophysical Research Communications (3)
Biophysical Reviews (3)
Chemistry – A European Journal (3)
Folding and Design (3)
Analytical Biochemistry (2)
Animal Science Journal (2)
Journal of Bioscience and Bioengineering (2)
Protein Science (2)
Accounts of Chemical Research (1)
Alzheimer's & Dementia (1)
Analytical Chemistry (1)
Angewandte Chemie (1)
Angewandte Chemie International Edition (1)
Arthropod Structure & Development (1)
BBA - Biomembranes (1)
BBA - General Subjects (1)
Biochemical Engineering Journal (1)
Bioorganic & Medicinal Chemistry (1)
Biosensors and Bioelectronics (1)
Chemistry of Materials (1)
Chirality (1)
Chromosoma (1)
Chromosome Research (1)
Current Opinion in Structural Biology (1)
Genomics (1)
Journal of Computational Chemistry (1)
Journal of Controlled Release (1)
Journal of Fermentation and Bioengineering (1)
Journal of Structural Biology (1)
Molecular Immunology (1)
Physics of Particles and Nuclei (1)
Proteins: Structure, Function, and Bioinformatics (1)
Science and Technology of Advanced Materials (1)
The Journal of Nutritional Biochemistry (1)
Thermochimica Acta (1)
Toxicology in Vitro (1)
Ultrasonics Sonochemistry (1)
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INFONA - science communication portal

Search results for: Yuji Goto

Effects of low and high levels of maternal nutrition consumed for the entirety of gestation on the development of muscle, adipose tissue, bone, and the organs of Wagyu cattle fetuses

Polyphenol‐solubility alters amyloid fibril formation of α‐synuclein

Front Cover: The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug‐Like Miniprotein (Chem. Eur. J. 9/2020)

The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug‐Like Miniprotein

The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug‐Like Miniprotein

Salt-induced formations of partially folded intermediates and amyloid fibrils suggests a common underlying mechanism

Asymmetric larval head and mandibles of Hydrophilus acuminatus (Insecta: Coleoptera, Hydrophilidae): Fine structure and embryonic development

Drastic acceleration of fibrillation of insulin by transient cavitation bubble

Heparin‐induced amyloid fibrillation of β₂‐microglobulin explained by solubility and a supersaturation‐dependent conformational phase diagram

Measurement of amyloid formation by turbidity assay—seeing through the cloud

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

Recognizing and analyzing variability in amyloid formation kinetics: Simulation and statistical methods

Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions

A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions

Amorphous Aggregation of Cytochrome C with Inherently low Amyloidogenicity is Characterized by the Metastability of Supersaturation and the Phase Diagram

X-ray Observation of Novel Nucleation Factor in Protein Supersaturated Solution

Water and Biomolecules

Revisiting supersaturation as a factor determining amyloid fibrillation

Thermal and chemical unfolding pathways of PaSdsA1 sulfatase, a homo‐dimer with topologically interlinked chains

Prevention of allergic rhinitis by ginger and the molecular basis of immunosuppression by 6-gingerol through T cell inactivation

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