Veratridine binding to a transmembrane helix of sodium channel Na1.4 determined by solid-state NMR.

The multi-step ligand action to a target protein is an important aspect when understanding mechanisms of ligand binding and discovering new drugs. However, structurally capturing such complex mechanisms is challenging. This is particularly true for interactions between large membrane proteins and small molecules.

Simple and accurate single base resolution analysis of 5-hydroxymethylcytosine by catalytic oxidative bisulfite sequencing using micelle incarcerated oxidants.

Oxidation of 5-methylcytosine (5mC) is catalyzed by ten-eleven translocation (TET) enzymes to produce 5-hydroxymethylcytosine (5hmC) and following oxidative products. The oxidized nucleotides were shown to be the intermediates for DNA demethylation, as the nucleotides are removed by base excision repair system initiated by thymine DNA glycosylase. A simple and accurate method to determine initial oxidation product 5hmC at single base resolution in genomic DNA is necessary to understand demethylation mechanism.

Selective oxidation of 5-hydroxymethylcytosine with micelle incarcerated oxidants to determine it at single base resolution.

5-Methylcytosine (5mC) is oxidized by ten-eleven translocation (TET) enzymes. This process followed by thymine DNA glycosylase is proposed to be the mechanism for methylcytosine demethylation. 5-Hydroxymethylcytosine (5hmC) is one of the most important key oxidative metabolites in the demethylation process, and therefore, simple and accurate method to determine 5hmC at single base resolution is desired.

Identification of okadaic acid binding protein 2 in reconstituted sponge cell clusters from Halichondria okadai and its contribution to the detoxification of okadaic acid.

Okadaic acid (OA) and OA binding protein 2 (OABP2) were previously isolated from the marine sponge Halichondria okadai. Because the amino acid sequence of OABP2 is completely different from that of protein phosphatase 2A, a well-known target of OA, we have been investigating the production and function of OABP2. In the present study, we hypothesized that OABP2 plays a role in the detoxification of OA in H.

Crystal Structure of Okadaic Acid Binding Protein 2.1: A Sponge Protein Implicated in Cytotoxin Accumulation.

Okadaic acid (OA) is a marine polyether cytotoxin that was first isolated from the marine sponge Halichondria okadai. OA is a potent inhibitor of protein serine/threonine phosphatases (PP) 1 and 2A, and the structural basis of phosphatase inhibition has been well investigated. However, the role and mechanism of OA retention in the marine sponge have remained elusive.

Brevisulcatic acids, marine ladder-frame polyethers from the red tide dinoflagellate Karenia brevisulcata in New Zealand.

The isolation and structural determination of new marine ladder-frame polyethers, brevisulcatic acids-1 (1) and -4 (2) are reported. Brevisulcatic acids were isolated from the dinoflagellate Karenia brevisulcata, which was identified as the causative species of a major red tide event in New Zealand in 1998. The ether ring composition and a β-hydroxy, γ-methylene valeric acid side chain of 1 and 2 are common, but 2 has a γ-lactone as the 5-membered A-ring while 1 is the seco acid analogue.

Interaction analysis of a ladder-shaped polycyclic ether and model transmembrane peptides in lipid bilayers by using Förster resonance energy transfer and polarized attenuated total reflection infrared spectroscopy.

Ladder-shaped polycyclic ethers (LSPs) are predicted to interact with membrane proteins; however, the underlying mechanism has not been satisfactorily elucidated. It has been hypothesized that LSPs possess non-specific affinity to α-helical segments of transmembrane proteins. To verify this hypothesis, we constructed a model LSP interaction system in a lipid bilayer.

Structure-activity relationships of the truncated norzoanthamines exhibiting collagen protection toward anti-osteoporotic activity.

The marine alkaloid norzoanthamine is a candidate drug for osteoporosis treatment. Due to its structural complexity, simplified analogues possessing similar biological activities are needed for further research. Recently, we found that the bisaminal unit, representing two-thirds of the original structure, is a bioactive equivalent.

Truncated norzoanthamine exhibiting similar collagen protection activity, toward a promising anti-osteoporotic drug.

The marine alkaloid, norzoanthamine, is considered to be a promising drug for osteoporosis treatment. Due to its rarity and complicated structure, a practical supply method must be developed. Here, we designed a truncated norzoanthamine, which has two-thirds of the original structure, and found that it exhibited similar collagen protection activity.

Ophiobolin O and 6-epi-ophiobolin O, two new cytotoxic sesterterpenes from the marine derived fungus Aspergillus sp.

Two new sesterterpenes, ophiobolin O (1) and 6-epi-ophiobolin O (2), together with the known ophiobolins G (3), H (4), and K (5), and 6-epi-ophiobolin K (6) were isolated from the marine derived fungus Aspergillus sp. The structures of these compounds were elucidated based on chemical and physicochemical evidence, including MS, UV, IR and NMR spectra. T h e stereochemistry of 1 was further confirmed by catalytic reaction of 5 with p-TsOH as acatalyst.

Origins of oxygen atoms in a marine ladder-frame polyether: evidence of monooxygenation by 18O-labeling and using tandem mass spectrometry.

Yessotoxin is a ladder-frame polyether produced by the dinoflagellate Protoceratium reticulatum. Previous labeling experiments using (13)C-acetate established the unique assembly of the carbon chain from intact and cleaved acetate units. The origins of ether and hydroxy oxygens in the molecule, which would yield further information regarding the assembly of the ladder-frame structure, have yet to be established.

Solution NMR analysis of the binding mechanism of DIVS6 model peptides of voltage-gated sodium channels and the lipid soluble alkaloid veratridine.

Voltage-gated sodium channels (VGSCs) are responsible for generating action potentials in nervous systems. Veratridine (VTD), a lipid soluble alkaloid isolated from sabadilla lily seed, is believed to bind to segment 6 of VGSCs and act as a partial agonist. However, high resolution structural interaction mechanism between VGSCs and VTD is difficult to elucidate because of the large size and membrane localization of VGSCs.

Brevisulcenal-F: a polycyclic ether toxin associated with massive fish-kills in New Zealand.

A novel marine toxin, brevisulcenal-F (KBT-F, from karenia brevisulcata toxin) was isolated from the dinoflagellate Karenia brevisulcata. A red tide of K. brevisulcata in Wellington Harbour, New Zealand, in 1998 was extremely toxic to fish and marine invertebrates and also caused respiratory distress in harbor bystanders.

Prorocentrol, a polyoxy linear carbon chain compound isolated from the toxic dinoflagellate Prorocentrum hoffmannianum.

A polyoxy linear carbon chain compound, prorocentrol (1), was isolated from cultured cells of the dinoflagellate Prorocentrum hoffmannianum, which produces a polyether carboxylic acid, okadaic acid. The structure of 1 was elucidated by detailed analyses of 2D NMR spectra. Compound 1 possesses 30 hydroxy groups, 1 ketone, and 8 double bonds on the C65-linear carbon chain.

Total synthesis of (-)-brevisin: a concise synthesis of a new marine polycyclic ether.

The first and highly efficient total synthesis of (-)-brevisin has been achieved. The title compound was synthesized in only 29 steps (longest linear sequence) from commercially available starting materials. The synthesis provided over 70 mg of a marine polycyclic ether compound.

Binding of diarrheic shellfish poisoning toxins to okadaic acid binding proteins purified from the sponge Halichondria okadai.

Okadaic acid (OA) and dinophysistoxin-1 (DTX1) cause diarrheic shellfish poisoning. This article examines the biochemical interactions of the two toxins with novel okadaic acid binding proteins (OABPs) 2.1 and 2.

Distribution and possible function of the marine alkaloid, norzoanthamine, in the zoanthid Zoanthus sp. using MALDI imaging mass spectrometry.

The role of the marine alkaloid, norzoanthamine, in the colonial zoanthid Zoanthus sp. was previously unknown. High concentrations of norzoanthamine are present in the epidermal tissue of Zoanthus sp.

Skeletal protein protection: the mode of action of an anti-osteoporotic marine alkaloid, norzoanthamine.

Bone is composed of mineralized collagen fibrils. A marine alkaloid, norzoanthamine, accelerates the formation of a collagen-hydroxyapatite composite and enhances collagen release from an immobilized matrix vesicle model. Norzoanthamine recognizes a peptide chain nonspecifically and stabilizes its secondary structure, and collagen has polyvalent binding sites for norzoanthamine.

Computationally and experimentally derived general rules for fragmentation of various glycosyl bonds in sodium adduct oligosaccharides.

Mechanisms of fragmentation of glycosyl bond linkages in various saccharides were investigated by using computational calculations to find general rules of fragmentation of sodiated oligosaccharides in mass spectrometry. The calculations revealed that alpha-Glc, alpha-Gal, beta-Man, alpha-Fuc, beta-GlcNAc, and beta-GalNAc linkages were cleaved more easily than beta-Glc, beta-Gal, and alpha-Man linkages because the transition states of the former were stabilized by the anomeric effect. The 1-6 linkage was more stable than the others, since saccharides with flexible 1-6 linkages were more stabilized in energy than the other linkages by the sodium cation.

Total synthesis and structural confirmation of brevisamide, a new marine cyclic ether alkaloid from the dinoflagellate Karenia brevis.

The first total synthesis of brevisamide (1) has been accomplished in 21 linear steps starting from cis-but-2-ene-1,4-diol. A synthetic highlight is the Suzuki-Miyaura coupling between an ether ring fragment and a dienol side chain. This result confirmed the structure of 1 isolated from the dinoflagellate Karenia brevis.

N-terminal labeling of proteins by the Pictet-Spengler reaction.

The Pictet-Spengler reaction was applied to the N-terminal labeling of horse heart myoglobin. This was performed in the following two steps: (1) conversion of the N-terminal glycine residue to an alpha-keto aldehyde by a transamination reaction and (2) condensation of the resulting activated myoglobin with tryptamine analogues by the Pictet-Spengler reaction. Ultraviolet (UV)/visible (vis) absorption and circular dichroism (CD) spectral data revealed that the tertiary structure of myoglobin was not altered by the Pictet-Spengler reaction.

Conformations of 3-carboxylic esters essential for neurotoxicity in veratrum alkaloids are loosely restricted and fluctuate.

The lipid-soluble veratrum alkaloids, veratridine and cevadine, are plant neurotoxins that are agonists of voltage-gated sodium channel. Their conformations in a hydrophobic environment were analyzed by NMR spectroscopy in solution phase chloroform at low temperatures. The conformations around the 3-carboxylic esters which is essential for their neurotoxicity, was completely different from the previously reported X-ray crystallographic structure.

Isolation and characterization of okadaic acid binding proteins from the marine sponge Halichondria okadai.

Okadaic acid, first isolated from the marine sponge Halichondria okadai, is a potent inhibitor of protein phosphatases 1 and 2A (PP1 and PP2A, respectively). Photoaffinity labeling experiments previously performed with biotinylated photoreactive okadaic acid revealed the presence of okadaic acid binding protein (OABP) in the crude extract of H. okadai.

Solid-phase fluorescence and ionization efficiency in negative-ion matrix-assisted laser desorption/ionization of neutral oligosaccharides: interaction between beta-carboline matrix and ammonium salt.

Ammonium chloride (NH4Cl) with a beta-carboline harmine (7-methoxy-1-methyl-9H-pyrido[3,4-b]indole) Matrix promotes the generation of chloride-anionized molecules of neutral oligosaccharides in negative-ion ultraviolet matrix-assisted laser/desorption ionization mass spectrometry (MALDI MS). The relative abundances of anionized molecules and matrix ([Analyte + Cl]-/[matrix + Cl]-) correlate with the amount of NH4Cl added, and saturate at a level of NH4Cl approximately four times that of the matrix. Their solid-phase fluorescence spectra indicate that harmine and NH4Cl form a complex of the hydrochloride salt in the mixed crystal.