IRMPD Spectroscopy of a Protonated,Phosphorylated Dipeptide

The protonated, phosphorylated dipeptide [GpY+H]⁺ is characterized by mid‐infrared multiple‐photon dissociation (IRMPD) spectroscopy and quantum‐chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free‐electron laser. The IRMPD spectra are recorded in the 900–1730 cm^?1 range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP‐D and coupled cluster, is carried out to obtain reliable relative energies of the low‐energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P?O group in all low‐energy structures. This leads to a P?O stretching frequency for [GpY+H]⁺ that is closer to that of [pS+H]⁺ than to that of [pY+H]⁺ and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.     

Photoinduced Fluorescence Activation and Nitric Oxide Release with Biocompatible Polymer Nanoparticles

A viable strategy to encapsulate a fluorophore/photochrome dyad and a nitric oxide photodonor within supramolecular assemblies of a cyclodextrin‐based polymer in water was developed. The two photoresponsive guests do not interact with each other within their supramolecular container and can be operated in parallel under optical control. Specifically, the dyad permits the reversible switching of fluorescence on a microsecond timescale for hundreds of cycles, and the photodonor enables the irreversible release of nitric oxide. Furthermore, these supramolecular assemblies cross the membrane of human melanoma cancer cells and transport their cargo in the cytosol. The fluorescence of one component allows the visualization of the labeled cells, and its switchable character could, in principle, be used to acquire super‐resolution images, while the release of nitric oxide from the other induces significant cell mortality. Thus, our design logic for the construction of biocompatible nanoparticles with dual functionality might evolve into the realization of valuable photoresponsive probes for imaging and therapeutic applications.     

Probing affinity and ubiquitin linkage selectivity of ubiquitin-binding domains using mass spectrometry

Non-covalent interactions between ubiquitin (Ub)-modified substrates and Ub-binding domains (UBDs) are fundamental to signal transduction by Ub receptor proteins. Poly-Ub chains, linked through isopeptide bonds between internal Lys residues and the C-terminus of Ub, can be assembled with varied topologies to mediate different cellular processes. We have developed and applied a rapid and sensitive electrospray ionization-mass spectrometry (ESI-MS) method to determine isopeptide linkage-selectivity and affinity of poly-Ub·UBD interactions. We demonstrate the technique using mono-Ub and poly-Ub complexes with a number of α-helical and zinc-finger (ZnF) UBDs from proteins with roles in neurodegenerative diseases and cancer. Affinities in the 2-200 μM range were determined to be in excellent agreement with data derived from other biophysical techniques, where available. Application of the methodology provided further insights into the poly-Ub linkage specificity of the hHR23A-UBA2 domain, confirming its role in Lys48-linked poly-Ub signaling. The ZnF UBP domain of isopeptidase-T showed no linkage specificity for poly-Ub chains, and the Rabex-5 MIU also exhibited little or no specificity. The discovery that a number of domains are able to bind cyclic Lys48 di-Ub with affinities similar to those for the acyclic form indicates that cyclic poly-Ub may be capable of playing a role in Ub-signaling. Detection of a ternary complex involving Ub interacting simultaneously with two different UBDs demonstrated the co-existence of multi-site interactions, opening the way for the study of crosstalk between individual Ub-signaling pathways.     

Comparison theorems in Lorentzian geometry and applications to spacelike hypersurfaces

In this paper we prove Hessian and Laplacian comparison theorems for the Lorentzian distance function in a spacetime with sectional (or Ricci) curvature bounded by a certain function by means of a comparison criterion for Riccati equations. Using these results, under suitable conditions, we are able to obtain some estimates on the higher order mean curvatures of spacelike hypersurfaces satisfying a Omori-Yau maximum principle for certain elliptic operators.     

Microbial Oxidation of (-)-α-pinene to Verbenol Production by Newly Isolated Strains

Verbenol is a bicyclicbicycle secondary allylic alcohol, with pronounced camphor and mint flavor notes, mainly used as food flavoring. This compound is also used to control harmful insects, and hence has potential for using in agriculture, and is an intermediate in the synthesis of valuable perfume and medicinal substances. This work is focused on the microbial oxidation of (-)-α-pinene to verbenol production. To carry out the present study, 405 microorganisms were tested for their ability to bioconvert the substrate. From the isolated microorganisms, 193 were selected in the pre-screening using mineral medium for limonene degradation. At the screening step, 31 strains were able to convert (-)-α-pinene in verbenol. The highest concentration in verbenol from (-)-α-pinene was about 125.6 mg/L for yeast isolated from orange juice industrial residue.     

Effects of counterion valency on the damping of phonons propagating along the axial direction of liquid-crystalline DNA

The phonon propagation and damping along the axial direction of films of aligned 40 wt % calf-thymus DNA rods are studied by inelastic x-ray scattering (IXS). The IXS spectra are analyzed with the generalized three effective eigenmode theory, from which we extract the dynamic structure factor S(Q,E) as a function of transferred energy E=variant Planck's over 2piomega, and the magnitude of the transferred wave vector Q. S(Q,E) of a DNA sample typically consists of three peaks, one central Rayleigh scattering peak, and two symmetric Stokes and anti-Stokes Brillouin side peaks. By analyzing the Brillouin peaks, the phonon excitation energy and damping can be extracted at different Q values from about 4 to 30 nm(-1). A high-frequency sound speed is obtained from the initial slope of the linear portion of the dispersion relation below Q=4 nm(-1). The high-frequency sound speed obtained in this Q range is 3100 ms, which is about twice faster than the ultrasound speed of 1800 ms, measured by Brillouin light scattering at Q approximately 0.01 nm(-1) at the similar hydration level. Our observations provide further evidence of the strong coupling between the internal dynamics of a DNA molecule and the dynamics of the solvent. The effect on damping and propagation of phonons along the axial direction of DNA rods due to divalent and trivalent counterions has been studied. It is found that the added multivalent counterions introduce stronger phonon damping. The phonons at the range between approximately 12.5 and approximately 22.5 nm(-1) are overdamped by the added counterions according to our model analyses. The intermediate scattering function is extracted and it shows a clear two-step relaxation with the fast relaxation time ranging from 0.1 to 4 ps.     

One-step synthesis of low polydispersity, biotinylated poly(N-isopropylacrylamide) by ATRP

Low polydispersity poly(N-isopropylacrylamide) with a biotin end-group was obtained in one step from a biotinylated initiator for atom transfer radical polymerization and interacted with streptavidin to generate the thermosensitive polymer-protein conjugate.     

Effect of simulated solar light on the autocatalytic degradation of nitrobenzene using Fe3+ and hydrogen peroxide

The effect of simulated solar light on nitrobenzene degradation in Fe³⁺/H₂O₂ solutions was investigated under different experimental conditions. Consumption profiles of NBE and H₂O₂ display an autocatalytic kinetic behavior for both dark and photo-assisted degradation experiments. The rates of the initial slow phase that precedes the catalytic phase are significantly enhanced by irradiation, although the effect of simulated solar light on the rates of the fast phase is negligible. The absolute rates of the slow phase increase with the concentrations of Fe³⁺ and H₂O₂, whereas the initial rate of the degree of conversion increase decreases with organic matter loading. The reaction progress was characterized by HPLC, GC–MS, IC, TOC (total organic carbon) and toxicity analyses. The main products detected were 4-nitrophenol, 3-nitrophenol, 2-nitrophenol, 1,3-dinitrobenzene, phenol, oxalic acid, formic acid, NO₂^? and NO₃^?. Product distribution profiles are discussed in connection with TOC and toxicity measurements. The results show that dark treatment is neither capable of lowering the organic content nor capable of reducing the effluent toxicity to acceptable levels. On the other hand, photo-assisted processes induced by simulated solar light can significantly enhance both mineralization and detoxification efficiencies.