Racemization of the substrate and product by serine palmitoyltransferase from Sphingobacterium multivorum yields two enantiomers of the product from d-serine.

Serine palmitoyltransferase (SPT) catalyzes the pyridoxal-5'-phosphate (PLP)-dependent decarboxylative condensation of l-serine and palmitoyl-CoA to form 3-ketodihydrosphingosine (KDS). Although SPT was shown to synthesize corresponding products from amino acids other than l-serine, it is still arguable whether SPT catalyzes the reaction with d-serine, which is a question of biological importance. Using high substrate and enzyme concentrations, KDS was detected after the incubation of SPT from Sphingobacterium multivorum with d-serine and palmitoyl-CoA. Furthermore, the KDS comprised equal amounts of 2S and 2R isomers. 1H-NMR study showed a slow hydrogen-deuterium exchange at Cα of serine mediated by SPT. We further confirmed that SPT catalyzed the racemization of serine. The rate of the KDS formation from d-serine was comparable to those for the α-hydrogen exchange and the racemization reaction. The structure of the d-serine-soaked crystal (1.65 Å resolution) showed a distinct electron density of the PLP-l-serine aldimine, interpreted as the racemized product trapped in the active site. The structure of the α-methyl-d-serine-soaked crystal (1.70 Å resolution) showed the PLP-α-methyl-d-serine aldimine, mimicking the d-serine-SPT complex prior to racemization. Based on these enzymological and structural analyses, the synthesis of KDS from d-serine was explained as the result of the slow racemization to l-serine, followed by the reaction with palmitoyl-CoA, and SPT would not catalyze the direct condensation between d-serine and palmitoyl-CoA. It was also shown that the S. multivorum SPT catalyzed the racemization of the product KDS, which would explain the presence of (2R)-KDS in the reaction products.

Five New Analogs of Streptogramin Antibiotic Viridogrisein Isolated from Streptomyces niveoruber.

Five new viridogriseins B-F were isolated from Streptomyces niveoruber, along with viridogrisein and griseoviridin which belong to streptogramin family antibiotics. A combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and the advanced Marfey's method elucidated the structures of viridogriseins B-F, each featuring distinct constituent amino acids. Consistent with other streptogramin family antibiotics, these viridogrisein analogs exhibited potent antibacterial activity against Staphylococcus aureus. Furthermore, equimolar mixtures of each viridogrisein analog and griseoviridin inhibited the growth of S. aureus more potently than each analog treatment alone. Finally, an in vitro functional analysis of SgvY, encoded in the viridogrisein biosynthetic gene cluster, revealed that SgvY detoxifies viridogrisein against S. aureus by linearization. Considering that viridogrisein is not autotoxic to S. niveoruber, SgvY likely contributes to the self-resistance system against viridogrisein in S. niveoruber.

Lanthanide and Actinide Ion Complexes Containing Organic Ligands Investigated by Surface-Enhanced Infrared Absorption Spectroscopy.

A new technique, surface-enhanced infrared absorption (SEIRA) spectroscopy, was used for the structural investigation of lanthanide (Ln) and actinide (An) complexes containing organic ligands. We synthesized thiol derivatives of organic ligands with coordination sites similar to those of 2-[N-methyl-N-hexanethiol-amino]-2-oxoethoxy-[N',N'-diethyl]-acetamide [diglycolamide (DGA)], Cyanex-272, and N,N,N',N'-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN), which have been used for separating Ln and An through solvent extraction. These ligands were attached on a gold surface deposited on an Si prism through S-Au covalent bonds; the gold surface enhanced the IR absorption intensity of the ligands. Aqueous solutions of Ln (Eu3+, Gd3+, and Tb3+) and An (Am3+) ions were loaded onto the gold surface to form ion complexes. The IR spectra of the ion complexes were obtained using Fourier transform infrared spectroscopy in the attenuated total reflection mode. In this study, we developed a new sample preparation method for SEIRA spectroscopy that enabled us to obtain the IR spectra of the complexes with a small amount of ion solution (5 µL). This is a significant advantage for the IR measurement of radiotoxic Am3+ complexes. In the IR spectra of DGA, the band attributed to C═O stretching vibrations at ∼1630 cm-1 shifted to a lower wavenumber by ∼20 cm-1 upon complexation with Ln and An ions. Moreover, the amount of the red shift was inversely proportional to the extraction equilibrium constant reported in previous studies on solvent extraction. The coordination ability of DGA toward Ln and An ions could be assessed using the band position of the C═O band. The Cyanex-272- and TPEN-like ligands synthesized in this report also showed noticeable SEIRA signals for Ln and An complexes. This study indicates that SEIRA spectroscopy can be used for the structural investigation of ion complexes and provides a microscopic understanding of selective extraction of Ln and An.

Evaluation of Plant Ceramide Species-Induced Exosome Release from Neuronal Cells and Exosome Loading Using Deuterium Chemistry.

The extracellular accumulation of aggregated amyloid-ß (Aß) in the brain leads to the early pathology of Alzheimer's disease (AD). The administration of exogenous plant-type ceramides into AD model mice can promote the release of neuronal exosomes, a subtype of extracellular vesicles, that can mediate Aß clearance. In vitro studies showed that the length of fatty acids in mammalian-type ceramides is crucial for promoting neuronal exosome release. Therefore, investigating the structures of plant ceramides is important for evaluating the potential in releasing exosomes to remove Aß. In this study, we assessed plant ceramide species with D-erythro-(4E,8Z)-sphingadienine and D-erythro-(8Z)-phytosphingenine as sphingoid bases that differ from mammalian-type species. Some plant ceramides were more effective than mammalian ceramides at stimulating exosome release. In addition, using deuterium chemistry-based lipidomics, most exogenous plant ceramides were confirmed to be derived from exosomes. These results suggest that the ceramide-dependent upregulation of exosome release may promote the release of exogenous ceramides from cells, and plant ceramides with long-chain fatty acids can effectively release neuronal exosomes and prevent AD pathology.

X-ray photoelectron spectroscopy and transmission electron microscopy analysis of silver-coated gold nanorods designed for bionanotechnology applications.

Multicomponent nano-agents were designed and built via a core-shell approach to enhance their surface enhanced Raman scattering (SERS) signals. These nano-agents had 36 nm × 12 nm gold nanorod cores coated by 4 nm thick silver shell films and a subsequent thin bifunctional thiolated polyethylene glycol (HS-PEG-COOH) layer. Ambient time-lapsed SERS signal measurements of these functionalized nanorods taken over a two-week period indicated no signal degradation, suggesting that large portions of the silver shells remained in pure metallic form. The morphology of the nanorods was characterized by transmission electron microscopy (TEM) and ultra-high resolution scanning TEM. X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES) were utilized to assess the oxidation states of the silver shells covered by HS-PEG-COOH. The binding energies of Ag 3d XPS spectra yielded very small chemical shifts with oxidation; however, the AES peak shapes gave meaningful information about the extent of oxidation undergone by the nano-agent. While the silver shells without HS-PEG-COOH coatings oxidized significantly, the silver shells with HS-PEG-COOH remained predominantly metallic. In fact, six month-old samples still retained mostly metallic silver shells. These findings further demonstrate the stability and longevity of the nanostructures, indicating their significant potential as plasmonically active agents for highly sensitive detection in various biological systems, including cancer cells, tissues, or even organisms.

UV and IR Spectroscopy of Cryogenically Cooled, Lanthanide-Containing Ions in the Gas Phase.

We measure UV and IR spectra in the gas phase for EuOH+, EuCl+, and TbO+ ions, which are produced by an electrospray ionization source and cooled to ∼10 K in a cold, 22-pole ion trap. The UV photodissociation (UVPD) spectra of these ions show a number of sharp, well-resolved bands in the 30000-38000 cm-1 region, although a definite assignment of the spectra is difficult because of a high degree of congestion. We also measure an IR spectrum of the EuOH+ ion in the 3500-3800 cm-1 region by IR-UV double-resonance spectroscopy, which reveals an OH stretching band at 3732 cm-1. We perform density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations of these ions in order to examine the nature of the transitions. The DFT results indicate that the states of highest-spin multiplicity (octet for EuOH+ and EuCl+ and septet for TbO+) are substantially more stable than other states of lower-spin multiplicity. The TD-DFT calculations suggest that UV absorption of the EuOH+ and EuCl+ ions arises from Eu(4f) → Eu(5d,6p) transitions, whereas electronic transitions of the TbO+ ion are mainly due to the electron promotion of O(2p) → Tb(4f,6s). The UVPD results of the lanthanide-containing ions in this study suggest the possibility of using lanthanide ions as "conformation reporters" for gas-phase spectroscopy for large molecules.