SU(2) Cosmological Solitons

We present a class of numerical solutions to the SU(2) nonlinear $\sigma$-model coupled to the Einstein equations with cosmological constant $\Lambda\geq 0$ in spherical symmetry. These solutions are characterized by the presence of a regular static region which includes a center of symmetry. They are parameterized by a dimensionless ``coupling constant'' $\beta$, the sign of the cosmological constant, and an integer ``excitation number'' $n$. The phenomenology we find is compared to the corresponding solutions found for the Einstein-Yang-Mills (EYM) equations with positive $\Lambda$ (EYM$\Lambda$). If we choose $\Lambda$ positive and fix $n$, we find a family of static spacetimes with a Killing horizon for $0 \leq \beta < \beta_{max}$. As a limiting solution for $\beta = \beta_{max}$ we find a {\em globally} static spacetime with $\Lambda=0$, the lowest excitation being the Einstein static universe. To interpret the physical significance of the Killing horizon in the cosmological context, we apply the concept of a trapping horizon as formulated by Hayward. For small values of $\beta$ an asymptotically de Sitter dynamic region contains the static region within a Killing horizon of cosmological type. For strong coupling the static region contains an ``eternal cosmological black hole''.Comment: 20 pages, 6 figures, Revte

Two-Dimensional Infrared Spectroscopy of Antiparallel β-Sheet Secondary Structure

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel β-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-L-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-L-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel β-sheet. In the proteins with antiparallel β-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic “Z”-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.

Molecular Mechanism of Thymidylate Synthase Inhibition by N 4 Hydroxy dCMP in View of Spectrophotometric and Crystallographic Studies

Novel evidence is presented allowing further clarification of the mechanism of the slow binding thymidylate synthase TS inhibition by N4 hydroxy dCMP N4 OH dCMP . Spectrophotometric monitoring documented time and temperature , and N4 OH dCMP dependent TS catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N4 OH dCMP and N5,10 methylenetetrahydrofolate, known to inactivate the enzyme by the covalent binding of the inhibitor, suggesting the demonstrated reaction to be uncoupled from the pyrimidine C 5 methylation. The latter was in accord with the hypothesis based on the previously presented structure of mouse TS cf. PDB ID 4EZ8 , and with conclusions based on the present structure of the parasitic nematode Trichinella spiralis, both co crystallized with N4 OH dCMP and N5,10 methylenetetrahdrofolate. The crystal structure of the mouse TS N4 OH dCMP complex soaked with N5,10 methylenetetrahydrofolate revealed the reaction to run via a unique imidazolidine ring opening, leaving the one carbon group bound to the N 10 atom, thus too distant from the pyrimidine C 5 atom to enable the electrophilic attack and methylene group transfe

Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases

CAG repeats occur predominantly in the coding regions of human genes, which suggests their functional importance. In some genes, these sequences can undergo pathogenic expansions leading to neurodegenerative polyglutamine (poly-Q) diseases. The mutant transcripts containing expanded CAG repeats possibly contribute to pathogenesis in addition to the well-known pathogenic effects of mutant proteins. We have analysed two crystal forms of RNA duplexes containing CAG repeats: (GGCAGCAGCC)2. One of the structures has been determined at atomic resolution (0.95 Å) and the other at 1.9 Å. The duplexes include non-canonical A–A pairs that fit remarkably well within a regular A-helix. All the adenosines are in the anti-conformation and the only interaction within each A–A pair is a single C2-H2···N1 hydrogen bond. Both adenosines in each A–A pair are shifted towards the major groove, although to different extents; the A which is the H-bond donor stands out more (the ‘thumbs-up’ conformation). The main effect on the helix conformation is a local unwinding. The CAG repeats and the previously examined CUG structures share a similar pattern of electrostatic charge distribution in the minor groove, which could explain their affinity for the pathogenesis-related MBNL1 protein

Spider chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle

Chitin, as a fundamental polysaccharide in invertebrate skeletons, continues to be actively investigated, especially with respect to new sources and the development of effective methods for its extraction. Recent attention has been focused on marine crustaceans and sponges; however, the potential of spiders (order Araneae) as an alternative source of tubular chitin has been overlooked. In this work, we focused our attention on chitin from up to 12 cm-large Theraphosidae spiders, popularly known as tarantulas or bird-eating spiders. These organisms “lose” large quantities of cuticles during their molting cycle. Here, we present for the first time a highly effective method for the isolation of chitin from Caribena versicolor spider molt cuticle, as well as its identification and characterization using modern analytical methods. We suggest that the tube-like molt cuticle of this spider can serve as a naturally prefabricated and renewable source of tubular chitin with high potential for application in technology and biomedicine. © 2019 by the authors

The crystal structure of an ‘All Locked’ nucleic acid duplex

‘Locked nucleic acids’ (LNAs) are known to introduce enhanced bio- and thermostability into natural nucleic acids rendering them powerful tools for diagnostic and therapeutic applications. We present the 1.9 Å X-ray structure of an ‘all LNA’ duplex containing exclusively modified β-d-2′-O-4′C-methylene ribofuranose nucleotides. The helix illustrates a new type of nucleic acid geometry that contributes to the understanding of the enhanced thermostability of LNA duplexes. A notable decrease of several local and overall helical parameters like twist, roll and propeller twist influence the structure of the LNA helix and result in a widening of the major groove, a decrease in helical winding and an enlarged helical pitch. A detailed structural comparison to the previously solved RNA crystal structure with the corresponding base pair sequence underlines the differences in conformation. The surrounding water network of the RNA and the LNA helix shows a similar hydration pattern

Outer-sphere electron-transfer between horse heart cytochrome c and anionic Cu(II/I) complexes: Evidence for precursor formation and coordination sphere reorganization for electron transfer

The outer-sphere electron-transfer reaction between anionic bis(5,6-bis(4-sulfonatophenyl)-3- (2-pyridyl)-1,2,4-triazine)Cu(II) and cytochrome cII was investigated as a function of pH, ionic strength, concentration, temperature and pressure. The plot of the observed pseudo-first-order rate constant as a function of the Cu(II) complex concentration showed saturation at higher Cu(II) concentrations, from which the precursor formation constant and the electron transfer rate constant could be separated (K = (7.7 ′ 0.5) × 103 M 1 and kET= 6.2 ′ 0.4 s -1 at I = 0.2 M, pH 7.4 and 288 K). The pseudo-first-order electron-transfer rate constant was measured as a function of temperature and pressure at (low and) high Cu(II) concentrations (ΔH= (85 ′ 4) 89 ′ 4 kJ mol -1; ΔS= (-61 ′ 13) -79 ′ 15 J K-1 mol-1; ΔG (288 K) = (67.6) 66.1 kJ mol-1; ΔV= (+8.8 ′ 0.6)+8.0 ′ 0.7 cm3 mol-1). Within the volume change for the overall reaction, the volume profile for the electron transfer step is almost symmetrical. The redox process and the change in coordination of the copper centre are proposed to be clearly separated. The back reaction between the Cu(I) complex and cytochrome cIII was investigated as a function of Cu(I) concentration at pH 7.4 at l bar. The observed pseudo-first-order rate constant reaches a saturation at high Cu(I) concentrations from which the precursor formation constant and the electron-transfer rate constant were estimated (K' = (2.0 ′ 0.2) × 103 M-1 and k'ET = 0.014 ′ 0.001 s-1 at I = 0.2 M, pH 7.4 and 288 K). Simulations of the measured cyclovoltammogramms applying an EC mechanism with two redox systems and two homogeneous chemical reactions were performed. The results are discussed with reference to earlier studies involving Co, Ru and Cr complexes as redox partners for cytochrome c