Biosynthesis of Streptolidine Involved Two Unexpected Intermediates Produced by a Dihydroxylase and a Cyclase through Unusual Mechanisms

Streptothricin‐F (STT‐F), one of the early‐discovered antibiotics, consists of three components, a β‐lysine homopolymer, an aminosugar D ‐gulosamine, and an unusual bicyclic streptolidine. The biosynthesis of streptolidine is a long‐lasting but unresolved puzzle. Herein, a combination of genetic/biochemical/structural approaches was used to unravel this problem. The STT gene cluster was first sequenced from a Streptomyces variant BCRC 12163, wherein two gene products OrfP and OrfR were characterized in vitro to be a dihydroxylase and a cyclase, respectively. Thirteen high‐resolution crystal structures for both enzymes in different reaction intermediate states were snapshotted to help elucidate their catalytic mechanisms. OrfP catalyzes an Fe^II‐dependent double hydroxylation reaction converting L ‐Arg into (3R,4R)‐(OH)₂‐L ‐Arg via (3S)‐OH‐L ‐Arg, while OrfR catalyzes an unusual PLP‐dependent elimination/addition reaction cyclizing (3R,4R)‐(OH)₂‐L ‐Arg to the six‐membered (4R)‐OH‐capreomycidine. The biosynthetic mystery finally comes to light as the latter product was incorporation into STT‐F by a feeding experiment.     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

Redox Chemistry of a Hydroxyphenyl‐Substituted Borane

Chemical reduction of a hydroxyphenyl‐substituted borane triggers a sequential electron‐ and intramolecular hydrogen‐atom‐transfer process to afford a hydridoborate phenoxide dianion. On the other hand, hydrogen‐atom abstraction of the borane leads to the isolation of a neutral borylated phenoxyl radical, which can be transformed to the corresponding benzoquinone borataalkene derivative by reduction with cobaltocene.     

D3R grand challenge 4: blind prediction of protein–ligand poses,affinity rankings,and relative binding free energies

Journal of Computer-Aided Molecular Design - The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and...     

Effects of Al concentration and resulting long-period superstructures on the plastic properties at room temperature of Al-rich TiAl single crystals

The role of Al₅Ti₃ and h-Al₂Ti long-period superstructures on the plastic properties of TiAl at room temperature is investigated on five single crystals with aluminium content comprised between 54.7 at.%, and 62.5 at.%. After annealing at 1200°C for 1?h, the Al₅Ti₃ superstructure develops in the L1₀ (γ) matrix upon increasing Al concentration except for Ti–62.5 at.%Al where h-Al₂Ti substitutes for Al₅Ti₃. The CRSS for <110]{111} first increases abruptly with the development of the Al₅Ti₃-type ordering. Then, the CRSS reaches a plateau at which dislocations assemble in groups of four to prevent extra anti-phase boundary (APB) from being engendered during glide throughout the Al₅Ti₃ phase. In Ti–62.5 at.%Al, the CRSS for ordinary slip further increases upon the precipitation of h-Al₂Ti in the L1₀ phase, whereas it decreases when the crystal is fully transformed into single-phased Al₅Ti₃. <101] superlattice dislocations are primarily activated under both the [210] and [1?1?8.6] load orientations irrespective of the Al concentration, but the dislocation microstructure strongly depends on orientation as well as on the degree of Al₅Ti₃ ordering. In the [210] orientation, the frequency of the decomposition of <101] dislocations into 1/2<110] and 1/2<112] dislocations decreases abruptly with the development of Al₅Ti₃. This is interpreted in terms of the increased difficulty to move ordinary dislocations. Under the [1?1?8.6] orientation, the density of faulted dipoles diminishes remarkably with the development of Al₅Ti₃. This is consistent with the transformation of the low energy extrinsic stacking fault of the L1₀ phase into a higher energy complex extrinsic stacking fault.     

Effects of group-delay difference on ultrashort pulse propagation in an active nonlinear LPFG

The effects of group-delay difference in an active nonlinear long-period fiber grating (LPFG) made in an erbium-doped amplifying fiber (EDF) are investigated by proposing a general model that include the effects of detuning, group-delay difference, gain saturation, gain bandwidth and Kerr nonlinearity. In particular, we observe a new feature caused by the interaction between the group-delay difference and the gain bandwidth: the pulse breakup effect due to the group-delay difference can be suppressed by the finite bandwidth of the linear gain.     

White light electroluminescence from graphene‐enhanced single polymer comprising two color emitters of equal molar ratios

White polymeric light‐emitting diode (WPLED) based on a single polymer, poly(3‐hexylthiophene‐alt‐9,9‐dioctylfluorene) (PTAF), has been successfully demonstrated. This conjugated alternating copolymer, PTAF, comprises 50 mol % of 3‐hexylthiophene which is an orange‐red color chromophore and 50 mol % 9,9‐dioctylfluorene which is a bluish‐green color chromophore. It was synthesized by Suzuki cross‐coupling reaction and has a molecular weight of 15,021 and polydispersity of 1.36. Nanocomposite consisting PTAF and graphene nanosheets enhances the optoelectronic properties and the device fabricated with a configuration of ITO/PEDOT:PSS/(PTAF + 1% graphene)/Ca/Al shows two‐color white electroluminescence with CIE 1931 coordinates of (0.28, 0.34). The white luminescence from a single polymer affords the WPLED device a simple structure and low fabrication cost. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

A well‐balanced upstream flux‐splitting finite‐volume scheme for shallow‐water flow simulations with irregular bed topography

This study extends the upstream flux‐splitting finite‐volume (UFF) scheme to shallow water equations with source terms. Coupling the hydrostatic reconstruction method (HRM) with the UFF scheme achieves a resultant numerical scheme that adequately balances flux gradients and source terms. The proposed scheme is validated in three benchmark problems and applied to flood flows in the natural/irregular river with bridge pier obstructions. The results of the simulations are in satisfactory agreement with the available analytical solutions, experimental data and field measurements. Comparisons of the present results with those obtained by the surface gradient method (SGM) demonstrate the superior stability and higher accuracy of the HRM. The stability test results also show that the HRM requires less CPU time (up to 60%) than the SGM. The proposed well‐balanced UFF scheme is accurate, stable and efficient to solve flow problems involving irregular bed topography. Copyright © 2009 John Wiley & Sons, Ltd.     

On the development of a triple‐preserving Maxwell's equations solver in non‐staggered grids

We present in this paper a finite difference solver for Maxwell's equations in non‐staggered grids. The scheme formulated in time domain theoretically preserves the properties of zero‐divergence, symplecticity, and dispersion relation. The mathematically inherent Hamiltonian can be also retained all the time. Moreover, both spatial and temporal terms are approximated to yield the equal fourth‐order spatial and temporal accuracies. Through the computational exercises, modified equation analysis and Fourier analysis, it can be clearly demonstrated that the proposed triple‐preserving solver is computationally accurate and efficient for use to predict the Maxwell's solutions. Copyright © 2009 John Wiley & Sons, Ltd.