Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding

Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the TYRP1 gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability. Further, the mutant variant structures were built and simulated for 100 ns to generate free energy landscapes and perform docking experiments. Free energy landscapes formed by Y362, N378, and T391 indicate that the binding clefts of C30R and H215Y mutants are larger than the wild-type Tyrp1. In docking simulations, the hydrogen bond and salt bridge interactions that stabilize DHICA in the active site remain similar among Tyrp1, D308N, and R326H. However, the strengths of these interactions and stability of the docked ligand may decrease proportionally to mutation severity due to the larger and less well-defined natures of the binding clefts in mutants. Mutational perturbations in mutants that are not unfolded may result in allosteric alterations to the active site, reducing the stability of protein-ligand interactions.     

Sex pheromones of male yellowfin Baikal sculpin (Cottocomephorus grewingki): Isolation and chemical studies

Three components of the male yellowfin Baikal sculpin pheromonal signal have been isolated from urine by diethyl ether extraction, thinayer chromatography (TLC), and high-performance liquid chromatography (HPLC). Using mass spectrometry, we have identified two of them as testosterone (T) and 11-hydroxytestosterone (11HT). These steroids are synthesized in testes during full spermatogenesis, and they are excreted in male urine with milt. The third component is not a steroid. It is more likely to be a polyene alcohol (farnesol). 2Z,6E-Farnesol possesses behavioral activity.     

Light-induced electron spin polarization in the ground state of water-soluble copper porphyrins

Light-induced spin-polarized transient EPR spectra are reported for several water-soluble copper porphyrins. The spectra are assigned to the doublet ground state, with emissive spin polarization resulting from photoexcitation and subsequent electronic relaxation. In contrast to other systems for which polarization of a doublet ground state has been observed, the exchange interactions in the copper porphyrins are strong and the geometry is fixed. It is proposed that intersystem crossing from the photoexcited trip-doublet to the trip-quartet state can lead to net polarization of the spin system and that this polarization is maintained during electronic decay, possibly via charge-transfer and exciplex states. The intensity of the observed spin polarization is essentially independent of the molecular orientation in the external field, but is strongly dependent on the nature of the charged peripheral groups. Possible reasons for this behavior are discussed.     

Phase‐dependent binary interaction parameters in industrial low‐density polyethylene separators

In the production process of low‐density polyethylene (LDPE), an important step is the flash separation of monomers and other small molecules from the polymer produced. The process is carried out adiabatically in two stages. To improve the performance of thermodynamic models, it is very important to analyze the use of model binary interaction parameters (BIP) dependent on the phase characteristics for each phase (phase‐dependent BIP). In this work the PC‐SAFT (perturbed‐chain statistical associating fluid theory) equation of state (EOS) is applied to the flash simulation of LDPE industrial separators using eight different resins. The main numerical aspects are examined with emphasis on the optimization strategy for the EOS BIP that explicitly characterizes each phase involved separately. The results demonstrate good predictive behavior. As a result of improved and more consistent modeling, a new strategy for optimized operation can be envisaged for the sequence of separators. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 2106–2117, 2013     

Free‐radical grafting of trans‐ethylene‐1,2‐dicarboxylic acid onto molten ethylene‐vinyl acetate copolymer

Distinctive features of free‐radical grafting of trans‐ethylene‐1,2‐dicarboxylic acid (TEDA) onto macromolecules of molten ethylene‐vinyl acetate copolymer (EVA) in the course of reactive extrusion have been investigated along with structure, mechanical characteristics, and high‐elastic properties of molten functionalized products (EVA‐g‐TEDA). It is shown that EVA‐g‐TEDA yield depends on both the peroxide initiator concentration and content of vinyl acetate units in the copolymer molecular structure. At functionalization, acid grafting is accompanied by secondary reactions of macromolecular degradation and crosslinking. With a low‐peroxide initiator concentration (0.1 wt %), degradation prevails; with a higher (0.3 wt %) concentration, crosslinking of macromolecules prevails. It is reported that monomers being grafted attach mostly over secondary carbon atoms in the polymer chain. EVA‐g‐TEDA appears to have a less perfect crystal structure with a lower‐melting temperature and crystallinity as against the starting polymer. The functionalized products display enhanced rigidity and lower deformability in comparison with the initial copolymer. Variations in the swelling ratio and melt strength of EVA‐g‐TEDA depend on the course of competing secondary processes of macromolecular degradation and crosslinking. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

Pyridinedicarboxylic Acid Diamides as Selective Ligands for Extraction and Separation of Trivalent Lanthanides and Actinides: DFT Study

This article presents a general approach to solving the urgent practical problem of separation of 4f-(lanthanides, Ln³⁺) and 5f-elements (actinides, An³⁺) very similar in properties based on the DFT quantum-chemical supercomputer simulation of Ln³⁺ and An³⁺ complexes with polydentate nitrogen-containing heterocyclic ligands. The method allows to calculate the geometry parameters of ligands and complexes and the metal to ligand binding energies with accuracy, permitting a direct comparison of calculation results with the experimental data, and estimate selectivity factors for separation of Eu³⁺/Am³⁺ model pair cations (SF_Am/Eu) in extraction experiments on a semi-quantitative level.

The applicability of the method and the approach demonstrated by DFT-modeling (nonempirical PBE functional, extended relativistic full-electron basis set) of a large series of diamides of pyridine-2,6-dicarboxylic (dipicolinic) acid (L) with different substituents at the amide nitrogen atoms and in the pyridine cycle, as well as their complexes [LM]³⁺, (H₂O)_nM(NO₃)₃ (n = 3, 4), and LM(NO₃)₃ (M = Eu, Am).

Based on the theoretical analysis a new model is proposed that describes the mechanism of Ln³⁺ and An³⁺ extraction in two-phase system highly acidic water solution-organic solvent, according to which the formation of An³⁺ and Ln³⁺ complexes occurs at the water/organic interface as a substitution reaction of hydroxonium ion in a cavity of a protonated ligand for the metal cation.

Calculation results confirm the experimentally established higher extraction ability of dipicolinic acid diamides containing one aryl and one alkyl substituent at the amide nitrogen atoms compared to the N,N,N′,N′-tetraalkyl diamides (“effect of anomalous aryl strengthening”). Based on the simulation results the structure of the modified ligand L suggested that it should ensure maximum An³⁺/Ln³separation selectivity in the series of dipicolinic acid diamides.     

Plasmonic bandgap in random media

We present a dispersion theory of the surface plasmon polaritons (SPP) in random metal-dielectric nanocomposite (MDN) consisting of bulk metal embedded with dielectric inclusions. We demonstrate that embedding of dielectric nanoparticles in metal results in the formation of the plasmonic bandgap due to strong coupling of the SPP at the metal-vacuum interface and surface plasmons localized at the surface of nanoinclusions. Our results show that MDN can replace metals in various plasmonic devices, which properties can be tuned in a wide spectral range. Being compatible with waveguides and other photonic structures, MDN offers high flexibility in the plasmonic system design.     

Hydrogenolysis of alkanes and olefin polymerization on the silica-supported zirconium hydrides: A comparative DFT study

The model reactions of ethylene polymerization and hydrogenolysis of linear alkanes (propane, n-butane, and n-pentane) on the silica-supported zirconium hydrides (Si–O)₃Zr^IVH, (Si–O)₂Zr^IVH₂, and (Si–O)₂Zr^IIIH were studied using the DFT approach. Catalytic processes under study were shown to occur involving different surface hydrides. The ethylene polymerization was found to proceed at comparable rates on the zirconium monohydrides, (Si–O)₃ZrH, and dihydrides, (Si–O)₂ZrH₂. Cleavage of linear alkanes on the monohydrides (Si–O)₃ZrH is thermodynamically unfavorable; however, the dihydrides (Si–O)₂ZrH₂ can act as catalysts of the process under mild conditions. Hydrides of the trivalent zirconium, (Si–O)₂Zr^IIIH, can also contribute to the hydrogenolysis reaction. A feature of all the systems studied is low regioselectivity of the corresponding processes.     

Self-assembled silver nanoislands formed on glass surface via out-diffusion for multiple usages in SERS applications

We demonstrate that silver nanoisland film self-assembled on the surface of silver-containing glass in the course of thermal processing in hydrogen is capable to detect 10⁻⁷ M concentration of rhodamine 6G in water using surface enhanced Raman spectroscopy (SERS) technique. The film can be multiply restored on the same glass substrate via annealing of the glass in hydrogen. We showed that the film can be self-assembled after as much as ten circles of the substrate cleaning followed by annealing. The proposed technique of the silver nanoisland film formation enables multiple usage of the same glass substrate in SERS experiments.