Cyclo­linopeptide B methanol tris­olvate

The title compound, C56H83N9O9S·3CH3OH, is a methanol tris­olvate of the cyclo­linopeptide cyclo(Met1—Leu2—Ile3—Pro4—Pro5—Phe6—Phe7—Val8—Ile9) (henceforth referred to as CLP-B), which was isolated from flaxseed oil. All the amino acid residues are in an l-configuration based on the CORN rule. The cyclic nona­peptide exhibits eight trans peptide bonds and one cis peptide bond observed between the two proline residues. The conformation is stabilized by an α-turn and two consecutive β-turns each containing a N—H⋯O hydrogen bond between the carbonyl group O atom of the first residue and the amide group H atom of the fourth (α-turn) or the third residue (β-turns), repectively. In the crystal, the components of the structure are linked by N—H⋯O and O—H⋯O hydrogen bonds into chains parallel to the a axis

Minimum message length inference of secondary structure from protein coordinate data

Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data

Malt in Combination with Lactobacillus rhamnosus Increases Concentrations of Butyric Acid in the Distal Colon and Serum in Rats Compared with Other Barley Products but Decreases Viable Counts of Cecal Bifidobacteria123

Several substances, including glutamine and propionic acid but in particular butyric acid, have been proposed to be important for colonic health. β-Glucans lead to the formation of comparatively high amounts of butyric acid, and germinated barley foodstuff obtained from brewer’s spent grain (BSG), containing high amounts of β-glucans and glutamine, has been reported to reduce the inflammatory response in the colon of patients with ulcerative colitis. The present study examines how 3 barley products, whole grain barley, malt, and BSG, affect SCFA in the hindgut and serum of rats and whether the addition of Lactobacillus rhamnosus 271 to each of these diets would have further effects. Amino acids in plasma and the cecal composition of the microbiota were also analyzed. The butyric acid concentration in the distal colon and serum was higher in the malt groups than in the other groups as was the serum concentration of propionic acid. The concentrations of propionic and butyric acids were higher in the cecum and serum of rats given L. rhamnosus than in those not given this strain. The proportion of plasma glutamine and the cecal number of bifidobacteria were lower in the malt groups than in the other groups. L. rhamnosus decreased the number of cecal bifidobacteria, whereas plasma glutamine was unaffected. We conclude that malt together with L. rhamnosus 271 had greater effects on propionic and butyric acid concentrations in rats than the other barley products. This is interesting when developing food with effects on colonic health

Effect of onion and beet on plasma and liver lipids, platelet aggregation, and erythrocyte Na efflux in simvastatin treated hypercholesterolmic rats

This study was purposed to investigate the effect of onion or beet on plasma and liver lipids, erythrocyte Na efflux channels and platelet aggregation in simvastatin (SIM) treated hypercholesterolemic rats. Forty Sprague Dawley rats were divided into four groups and fed 0.5% cholesterol based diets containing 2 mg/kg BW simvastatin or simvastatin with 5% onion or beet powder. Plasma total cholesterol was significantly increased in SIM group compared with the control (p<0.01), and the elevated plasma total cholesterol of SIM group was significantly decreased in SIM-onion and SIM-beet groups (p<0.05). HDL-cholesterol in SIM-beet group was significantly increased compared with other groups (p<0.05). Platelet aggregation in both the maximum and initial slope was significantly decreased in SIM group compared with SIM-onion group (p<0.05). Na-K ATPase was significantly decreased in SIM group compared with the control, SIM-onion and SIM-beet groups (p<0.05). Na passive leak was significantly increased in all groups treated with SIM compared with the control (p<0.05). The total Na efflux was decreased in SIM group and increased in SIM-onion group and the difference between these two groups was significant (p<0.05). There was no difference in intracellular Na among groups. In present study, simvastatin, a HMG CoA reductase inhibitor at dose of 2mg/kg BW/day rather increased plasma total cholesterol in rats, inferring that the action mechanism of simvastatin on cholesterol metabolism differ between rat and human. Onion and beet play favorable roles in cardiovascular system by restoring the reduced Na efflux through Na-K ATPase and Na-K cotransport in SIM treated rats

Structural and functional consequences of removing the N-terminal domain from the magnesium chelatase ChlH subunit of Thermosynechococcus elongatus

Magnesium chelatase (MgCH) initiates chlorophyll biosynthesis by catalysing the ATP-dependent insertion of Mg2+ into protoporphyrin. This large enzyme complex comprises ChlH, I and D subunits, with I and D involved in ATP hydrolysis, and H the protein that handles the substrate and product. The 148 kDa ChlH subunit has a globular N-terminal domain attached by a narrow linker to a hollow cage-like structure. Following deletion of this ~18 kDa domain from the Thermosynechoccus elongatus ChlH, we used single particle reconstruction to show that the apo- and porphyrin-bound forms of the mutant subunit consist of a hollow globular protein with three connected lobes; superposition of the mutant and native ChlH structures shows that, despite the clear absence of the N-terminal ‘head’ region, the rest of the protein appears to be correctly folded. Analyses of dissociation constants shows that the ΔN159ChlH mutant retains the ability to bind protoporphyrin and the Gun4 enhancer protein, although the addition of I and D subunits yields an extremely impaired active enzyme complex. Addition of the Gun4 enhancer protein, which stimulates MgCH activity significantly especially at low Mg2+ concentrations, partially reactivates the ΔN159ChlH–I–D mutant enzyme complex, suggesting that the binding site or sites for Gun4 on H do not wholly depend on the N-terminal domain

Enzymatic “Click” Ligation: Selective Cysteine Modification in Polypeptides Enabled by Promiscuous Glutathione S-Transferase

Singled out for special treatment: Naturally occurring glutathione S-transferase (GST) was used to catalyze an efficient “click” ligation between polypeptides with an N-terminal glutathione sequence and biomolecules or chemical probes containing perfluorinated aromatic groups (see scheme). The site-specific modification of one cysteine residue was possible in the presence of other unprotected cysteine residues and reactive functional groups.National Institutes of Health (U.S.) (GM101762)National Institutes of Health (U.S.) (Award GM46059)MIT Faculty Start-up FundDamon Runyon Cancer Research FoundationAmgen Inc. (Summer Graduate Research Fellowship

Cyclo­linopeptide K butanol disolvate monohydrate

The title compound, C56H83N9O11S·2C4H10O·H2O, is a butanol–water solvate of the cyclo­linopeptide cyclo(Metsulfone1-Leu2–Ile3–Pro4–Pro5–Phe6–Phe7–Val8–Ile9) (henceforth referred to as CLP-K) which was isolated from flax oil. All the amino acid residues are in an l configuration based on the CORN rule. The cyclic nona­peptide exhibits eight trans peptide bonds and one cis peptide bond observed between the two proline residues. The conformation is stabilized by an α- and a β-turn, each containing an N—H⋯O hydrogen bond between the carbonyl group O atom of the first residue and the amide group H atom of the fourth (α-turn) and the third residue (β-turn), repectively. In the crystal, the components of the structure are linked by inter­molecular N—H⋯O and O—H⋯O hydrogen bonds into a two-dimensional network parallel to (001). The –C(H2)OH group of one of the butanol solvent mol­ecules is disordered over two sets of sites with refined occupancies of 0.863 (4) and 0.137 (4)

Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity

The MCM complex from the archaeon Methanother-mobacter thermautotrophicus is a model for the eukaryotic MCM2-7 helicase. We present electron-microscopy single-particle reconstructions of a DNA treated M.thermautotrophicus MCM sample and a ADP·AlF(x) treated sample, respectively assembling as double hexamers and double heptamers. The electron-density maps display an unexpected asymmetry between the two rings, suggesting that large conformational changes can occur within the complex. The structure of the MCM N-terminal domain, as well as the AAA+ and the C-terminal HTH dom-ains of ZraR can be fitted into the reconstructions. Distinct configurations can be modelled for the AAA+ and the HTH domains, suggesting the nature of the conformational change within the complex. The pre-sensor 1 and the helix 2 insertions, important for the activity, can be located pointing towards the centre of the channel in the presence of DNA. We propose a mechanistic model for the helicase activity, based on a ligand-controlled rotation of the AAA+ subunits

Patient-derived mutations within the N-terminal domains of p85α impact PTEN or Rab5 binding and regulation

The p85α protein regulates flux through the PI3K/PTEN signaling pathway, and also controls receptor trafficking via regulation of Rab-family GTPases. In this report, we determined the impact of several cancer patient-derived p85α mutations located within the N-terminal domains of p85α previously shown to bind PTEN and Rab5, and regulate their respective functions. One p85α mutation, L30F, significantly reduced the steady state binding to PTEN, yet enhanced the stimulation of PTEN lipid phosphatase activity. Three other p85α mutations (E137K, K288Q, E297K) also altered the regulation of PTEN catalytic activity. In contrast, many p85α mutations reduced the binding to Rab5 (L30F, I69L, I82F, I177N, E217K), and several impacted the GAP activity of p85α towards Rab5 (E137K, I177N, E217K, E297K). We determined the crystal structure of several of these p85α BH domain mutants (E137K, E217K, R262T E297K) for bovine p85α BH and found that the mutations did not alter the overall domain structure. Thus, several p85α mutations found in human cancers may deregulate PTEN and/or Rab5 regulated pathways to contribute to oncogenesis. We also engineered several experimental mutations within the p85α BH domain and identified L191 and V263 as important for both binding and regulation of Rab5 activit