Mechanisms Associated with Superoxide Radical Scavenging Reactions Involving Phenolic Compounds Deduced Based on the Correlation between Oxidation Peak Potentials and Second-Order Rate Constants Determined Using Flow-Injection Spin-Trapping EPR Methods.

Flow-injection spin-trapping electron paramagnetic resonance (FI-EPR) methods that involve the use of 5,5-dimethyl-pyrroline--oxide (DMPO) as a spin-trapping reagent have been developed for the kinetic study of the O radical scavenging reactions occurring in the presence of various plant-derived and synthetic phenolic antioxidants (Aox), such as flavonoid, pyrogallol, catechol, hydroquinone, resorcinol, and phenol derivatives in aqueous media (pH 7.4 at 25 °C). The systematically estimated second-order rate constants () of these phenolic compounds span a wide range (from 4.

Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.

Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnX) and mevalonate 5-phosphate dehydratase (AcnX), respectively. We herein elucidated the crystal structures of AcnX from Agrobacterium tumefaciens (AtAcnX) and AcnX from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates.

Nucleobase-involved native chemical ligation: a novel reaction between an oxanine nucleobase and N-terminal cysteine for oligonucleotide-peptide conjugation.

In bioconjugation chemistry, achieving a target-specific reaction for a non-modified amino acid is challenging. Here, we report a novel nucleobase-involved native chemical ligation (NbCL) that allows a site-specific oligonucleotide-peptide conjugation via a new S-N acyl transfer reaction between an oxanine nucleobase and N-terminal cysteine.

Novel non-phosphorylative pathway of pentose metabolism from bacteria.

Pentoses, including D-xylose, L-arabinose, and D-arabinose, are generally phosphorylated to D-xylulose 5-phosphate in bacteria and fungi. However, in non-phosphorylative pathways analogous to the Entner-Dodoroff pathway in bacteria and archaea, such pentoses can be converted to pyruvate and glycolaldehyde (Route I) or α-ketoglutarate (Route II) via a 2-keto-3-deoxypentonate (KDP) intermediate. Putative gene clusters related to these metabolic pathways were identified on the genome of Herbaspirillum huttiense IAM 15032 using a bioinformatic analysis.

Analysis of tolvaptan non-responders and outcomes of tolvaptan treatment of ascites.

Background And Aim: The goals of the study were to identify an effective treatment for ascites and to examine the influence of tolvaptan on outcomes by investigating non-responders to tolvaptan and comparing outcomes of hepatic cirrhosis in patients treated with and without tolvaptan.

Methods: In Study 1, of 145 patients with hepatic cirrhosis who were treated with tolvaptan between September 2013 and March 2018, 45 who did not achieve weight loss of ≥1.5 kg within one week were investigated.

Functional characterization of aconitase X as a cis-3-hydroxy-L-proline dehydratase.

In the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase X is not functionally annotated. The corresponding gene (LhpI) was often located within the bacterial gene cluster involved in L-hydroxyproline metabolism. Screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-L-proline to Δ-pyrroline-2-carboxylate.

Characterization of iron-sulfur clusters in flavin-containing opine dehydrogenase.

Flavin-containing opine dehydrogenase from Bradyrhizobium japonicum forms a heterooligomeric αβγ enzyme complex. An electron paramagnetic resonance spectroscopy analysis using wild-type and site-directed mutants revealed that [4Fe-4S] and [2Fe-2S] clusters bind to two different types of [Fe-S] binding sites in the γ- and α-subunits, respectively. The latter was found to be important for structural folding and enzyme catalysis.

Ability of water-soluble biosubstances to eliminate hydroxyl and superoxide radicals examined by spin-trapping ESR measurements: two-dimensional presentation of antioxidative ability.

The hydroxyl- and superoxide-radical-eliminating ability of water-soluble biosubstances was examined by ESR combined with the spin-trapping method, indicating a median inhibitory dose, ID(h)(50) (mM) and id(h)(50) (mg/mL) for the hydroxyl radical, and ID(s)(50) (mM) and id(s)(50) (mg/mL) for the superoxide radical. Both the 1/[ID(h)(50) (mM)] and 1/[ID(s)(50) (mM)] values of selected biosubstances were linearly related to the second-order rate constant, k(2) (M(-1) s(-1)), defined for the reaction between biosubstances and the radicals in a logarithmic presentation. The result indicates that ID(h)(50) (mM) and ID(s)(50) (mM) are suitable parameters for both types of radical-eliminating ability.

Creation of a binuclear purple copper site within a de novo coiled-coil protein.

Although various kinds of metal binding proteins have been constructed by de novo design, the creation of a binuclear metal binding site remains especially challenging. The purple copper site in subunit II of COX, referred to as the Cu(A) site, has two copper ions bridged by two Cys residues. We constructed the Cu(A) site consisting of two Cys and two His residues in a de novo designed four-helical coiled-coil protein.

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch.

Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of (1)H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO(6)CACTG)/d(CAGTGX(17)GTCAC), X = C or T]. (1)H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation.

T-quaternary structure of oxy human adult hemoglobin in the presence of two allosteric effectors, L35 and IHP.

The cooperative O(2)-binding of hemoglobin (Hb) have been assumed to correlate to change in the quaternary structures of Hb: T(deoxy)- and R(oxy)-quaternary structures, having low and high O(2)-affinities, respectively. Heterotropic allosteric effectors have been shown to interact not only with deoxy- but also oxy-Hbs causing significant reduction in their O(2)-affinities and the modulation of cooperativity. In the presence of two potent effectors, L35 and inositol hexaphosphate (IHP) at pH 6.

Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold.

Type 1 blue copper proteins uniquely coordinate Cu(2+) in a trigonal planar geometry, formed by three strong equatorial ligands, His, His, and Cys, in the protein. We designed a stable Cu(2+) coordination scaffold composed of a four-stranded α-helical coiled-coil structure. Two His residues and one Cys residue were situated to form the trigonal planar geometry and to coordinate the Cu(2+) in the hydrophobic core of the scaffold.

Identification of an antiamyloidogenic substance from mulberry leaves.

Fibrillar aggregates of amyloid beta-peptides are major constituents of the plaques found in the brains of patients with Alzheimer's disease, and have been implicated in the neurotoxicity of Alzheimer's. We previously reported that the methanol extract of mulberry leaves inhibits the formation of amyloid beta-peptide (1-42)-fibrils in vitro, and protects hippocampal neurons from amyloid beta-peptide (1-42)-induced cell death. In this study, we identified antiamyloidogenic substances, pheophorbide a, kaempferol -3-O-glucoside, and kaempferol -3-O-(6-malonyl) glucoside, from the methanol extract of mulberry leaves.

A cysteine residue near the propionate side chain of heme is the radical site in ascorbate peroxidase.

The radical scavenger 2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO(*)) and the spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) were used in conjunction with mass spectrometry to identify the protein-based radical sites of the H(2)O(2)-tolerant ascorbate peroxidase (APX) of the red alga Galdieria partita and the H(2)O(2)-sensitive stromal APX of tobacco. A cysteine residue in the vicinity of the propionate side chain of heme in both enzymes was labeled with TEMPO(*) and DMPO in an H(2)O(2)-dependent manner, indicating that these cysteine residues form thiyl radicals through interaction of APX with H(2)O(2). TEMPO(*) bound to the cysteine thiyl radicals, and sulfinylated and sulfonylated them.

Importance of inhibitor of DNA binding/differentiation 2 in hepatic stellate cell differentiation and proliferation.

Background/aim: In liver fibrosis, activated hepatic stellate cells (HSC) are transformed into myofibroblasts. Helix-loop-helix (HLH) transcriptional factors such as MyoD regulate the differentiation of myocytes, and the inhibitor of DNA binding/differentiation (Id) family comprises dominant negative HLH transcriptional regulators that inhibit differentiation and promote cell proliferation. In the present study, we investigated how the Id family proteins regulate HSC.

1H NMR study on equilibrium between parallel G-quartet structures.

Structural transition of parallel G-quartet formed by d(TG4T) are induced by monovalent cations. In the presence of K+ ion, G-quartet takes a single conformation, while in the presence of Na+ ion, the equilibrium between more than three conformations were observed.

Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism. Novel evolutionary insight into sugar metabolism.

Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T.

Human homologue of maid is a useful marker protein in hepatocarcinogenesis.

Background & Aims: Human homologue of maid (HHM) is a helix-loop-helix (HLH) transcriptional regulatory protein that is involved in the hepatic stem cell development and differentiation. We analyzed the potential involvement of HHM in hepatocarcinogenesis.

Methods: We analyzed HHM expression in the choline-deficient L-amino acid defined (CDAA) diet model of rat hepatocarcinogenesis and in human adenomatous hyperplasia (AH) and hepatocellular carcinoma (HCC) biopsy samples.

Percutaneous radiofrequency ablation with cooled electrodes combined with hepatic arterial balloon occlusion in hepatocellular carcinoma.

Background: We have reported that percutaneous radiofrequency ablation (RFA) with balloon occlusion of the hepatic artery (balloon-occluded RFA), using an expandable electrode, increases the coagulation area. In this study, we investigated the efficacy of balloon-occluded RFA and balloon-microcatheter-occluded RFA, using a cool RF single electrode.

Methods: We studies 41 patients with 47 hepatocellular carcinoma (HCC) lesions.

Solution structure of marinostatin, a natural ester-linked protein protease inhibitor.

Marinostatin is a unique protein protease inhibitor containing two ester linkages. We have purified a 12-residue marinostatin [MST(1-12), (1)FATMRYPSDSDE(12)] and determined the residues involved in the formation of the ester linkages and the solution structure by (1)H NMR spectroscopy and restrained molecular dynamics calculation. The two ester linkages of MST(1-12) are formed between hydroxyl and carboxyl groups, Thr(3)-Asp(9) and Ser(8)-Asp(11), indicating that MST(1-12) has two cyclic regions which are fused at the residues of Ser(8) and Asp(9).

Prognostic factors in patients with advanced hepatocellular carcinoma receiving hepatic arterial infusion chemotherapy.

Background: The prognosis of patients with advanced hepatocellular carcinoma (HCC) is poor. We aimed to clarify the prognostic factors in patients with advanced HCC receiving hepatic arterial infusion chemotherapy (HAIC).

Methods: Forty-four HCC patients were treated with HAIC, using low-dose cisplatin (CDDP) and 5-fluorouracil (5-FU) with/without leucovorin (or isovorin).

Two-metal ion, Ni(II) and Cu(II), binding alpha-helical coiled coil peptide.

Metalloproteins are an attractive target for de novo design. Usually, natural proteins incorporate two or more (hetero- or homo-) metal ions into their frameworks to perform their functions, but the design of multiple metal-binding sites is usually difficult to achieve. Here, we undertook the de novo engineering of heterometal-binding sites, Ni(II) and Cu(II), into a designed coiled coil structure based on an isoleucine zipper (IZ) peptide.

Selective formation of AAB- and ABC-type heterotrimeric alpha-helical coiled coils.

The alpha-helical coiled coils have a representative amino acid sequence of (abcdefg)(n) heptad repeats. We previously reported that two peptides named IZ-2A and IZ-2W formed an (IZ-2A)(2)/IZ-2W heterotrimer with an Ala-Ala-Trp interaction in the hydrophobic core. In this paper, we describe the selective formation of AAB- and ABC-type heterotrimers.