Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.     

Oxygen excess nonstoichiometry and thermodynamic quantities of La2NiO4?+?δ

The oxygen excess nonstoichiometry of La₂NiO_4 + δ is measured as a function of temperature and oxygen partial pressure (pO₂) by coulometric titration method. A positive deviation from the ideal dilution solution behavior is exhibited, and the partial molar thermodynamic quantities of La₂NiO_4 + δ are calculated from the Gibbs–Helmholtz equation for regular solution by introducing the activity coefficient of the charge carriers. The activity coefficient of holes is successfully calculated by using the Joyce–Dixon approximation of the Fermi–Dirac integral. The effective mass of holes ( m_\texth^* m_{\text{h}}^{{*}} ) is 1.27–1.29 times the rest mass (m _h), which indicate the action of band-like conduction and allow the effect of the small degree of polaron hopping to be ignored. The activity coefficient of holes calculated against the oxygen nonstoichiometry clearly illustrates the early positive deviation of the activity coefficient of holes from unit, leading to g_{\texth ^·} \gamma_{{{\text{h}}^{ \bullet }}}  ≈ 14 at δ ≈ 0.08, which is quite close to the literature value of g_{\texth ^·} \gamma_{{{\text{h}}^{ \bullet }}}  ≈ 10 at δ ≈ 0.08. All the evaluated thermodynamic quantities are in good agreement with the experimental literature values.     

Nucleation and growth mechanism of Pd/Pt bimetallic clusters in sodium bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles as studied by in situ X-ray absorption spectroscopy

We report in situ X-ray absorption spectroscopy (XAS) investigations on the formation of palladium-platinum (Pd/Pt) bimetallic clusters at the early stage within the water-in-oil microemulsion system of water/AOT/n-heptane. The reduction of palladium and platinum ions and the formation of corresponding clusters are monitored as a function of dosage of reducing agent, hydrazine (N(2)H(5)OH). Upon successive addition of the reducing agent, hydrazine (N(2)H(5)OH), five distinguishable steps are observed in the formation process of Pd/Pt clusters at the early stage. Both in situ X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analysis for both the Pd K-edge and Pt L(III)-edge revealed the formation of Pd/Pt bimetallic clusters. A corresponding structural model is proposed for each step to provide a detailed insight into the nucleation and growth mechanism of Pd/Pt bimetallic clusters. We also discussed the atomic distribution of Pd and Pt atoms in Pd/Pt bimetallic clusters based on the calculated XAS structural parameters.     

Construction of triangular metallomacrocycles: [M3(1,2-bis(2,2':6',2''-terpyridin-4-yl-ethynyl)benzene)3][M = Ru(II), Fe(II), 2Ru(II)Fe(II)

Complexation of a predesigned (1,2-bis(2,2':6',2'-terpyridin-4-yl-ethynyl)benzene) ligand possessing a 60 degrees angle between two terpyridines with transition metals [Fe(II) and Ru(II)] afforded the self-assembled, triangular metallomacrocycles.     

Measuring Submicron-Sized Fractionated Particulate Matter on Aluminum Impactor Disks

Sub-micron sized airborne particulate matter (PM) is not collected well on regular quartz or glass fiber filter papers. We used a micro-orifice uniform deposit impactor (MOUDI) to fractionate PM into six size fractions and deposit it on specially designed high purity thin aluminum disks. The MOUDI separated PM into fractions 56-100 nm, 100-180 nm, 180-320 nm, 320-560 nm, 560-1000 nm, and 1000-1800 nm. Since the MOUDI has a low flow rate (30 L/min), it takes several days to collect sufficient carbon on 47 mm foil disks. The small carbon mass (20-200 microgram C) and large aluminum substrate (~25 mg Al) present several challenges to production of graphite targets for accelerator mass spectrometry (AMS) analysis. The Al foil consumes large amounts of oxygen as it is heated and tends to melt into quartz combustion tubes, causing gas leaks. We describe sample processing techniques to reliably produce graphitic targets for (14)C-AMS analysis of PM deposited on Al impact foils.     

Inhibition of phospholipase D2 induces autophagy in colorectal cancer cells

Autophagy is a conserved lysosomal self-digestion process used for the breakdown of long-lived proteins and damaged organelles, and it is associated with a number of pathological processes, including cancer. Phospholipase D (PLD) isozymes are dysregulated in various cancers. Recently, we reported that PLD1 is a new regulator of autophagy and is a potential target for cancer therapy. Here, we investigated whether PLD2 is involved in the regulation of autophagy. A PLD2-specific inhibitor and siRNA directed against PLD2 were used to treat HT29 and HCT116 colorectal cancer cells, and both inhibition and genetic knockdown of PLD2 in these cells significantly induced autophagy, as demonstrated by the visualization of light chain 3 (LC3) puncta and autophagic vacuoles as well as by determining the LC3-II protein level. Furthermore, PLD2 inhibition promoted autophagic flux via the canonical Atg5-, Atg7- and AMPK-Ulk1-mediated pathways. Taken together, these results suggest that PLD2 might have a role in autophagy and that its inhibition might provide a new therapeutic basis for targeting autophagy.     

Determination of Trace Iron(II) in the Presence of Iron(III)

The determination of trace iron(II) is usually interfered by the presence of iron(III) when ortho-phenanthroline colorimetric method is used. In this report a chromogenic reagent which contains ortho-phenanthroline-EDTA mixture has been developed to decrease the interference of ferric ion after adjusting the acidity of sample at 0.1 N by adding the sulfuric acid. The procedure is also simplified by introducing sulfamate buffer solution (pH= 1.5) without adjusting the acidity of sample with sulfuric acid. If iron(III) is not present in the sample, this method is also applicable. The comparative results are exhibited for the present method and the conventional o-phenanthroline method.     

Development of a peptide inhibitor-based cantilever sensor assay for cyclic adenosine monophosphate-dependent protein kinase

A highly sensitive nanomechanical cantilever sensor assay based on an electrical measurement has been developed for detecting activated cyclic adenosine monophosphate (cyclic AMP)-dependent protein kinase (PKA). Employing a peptide derived from the heat-stable protein kinase inhibitor (PKI), a magnetic bead system was first selected as a vehicle to immobilize the PKI-(5-24) peptide for capturing PKA catalytic subunit and the activity assay was applied for indirectly assessing the binding. Synergistic interactions of adenosine triphosphate (ATP) and the peptide inhibitor with the kinase were then investigated by a solution phase capillary electrophoretic assay, and by surface plasmon resonance technology which involved immobilization of the peptide inhibitor. After systemically evaluated by a homogeneous direct binding assay, the ATP-dependent recognition of the catalytic subunit of PKA by PKI-(5-24) was successfully transferred on to the nanomechanical cantilevers at protein concentrations of 6.6 pM-66 nM, exhibiting much higher sensitivity and wider dynamic range than the conventional activity assay. Thus, direct assessment of activated kinases using the cantilever sensor system functionalized with specific peptide inhibitors holds great promise in analytical applications and clinical medicine.     

Briarenolide E: the first 2-ketobriarane diterpenoid from an octocoral Briareum sp. (Briareidae)

A novel 2-ketobriarane diterpenoid, briarenolide E (1), was isolated from an octocoral Briareum sp. The structure of briarane 1 was elucidated by interpretations of spectral data. Compound 1 displayed modestly inhibitory effects on the generation of superoxide anions and the release of elastase by human neutrophils.