Direct structure determination using residual dipolar couplings: reaction-site conformation of methionine sulfoxide reductase in solution

Residual dipolar couplings (RDC) from partially aligned molecules provide long-range structural data and are thus particularly well adapted to rapid structure validation or protein fold recognition. Extensive measurements in two alignment media can also provide precise de novo structure from RDC alone. We have applied a novel combination of these approaches to the study of methionine sulfoxide reductase (MsrA) from Erwinia chrysanthemi, a 27 kDa enzyme essential for repairing oxidative stress damage. The tertiary fold was initially validated by comparing backbone RDC to expected values from the crystal structure of the homologous MsrA from Escherichia coli. Good agreement was found throughout the chain, verifying the overall topology of the molecule, with the exception of the catalytically important peptide P196-L202, where strong and systematic RDC violation was observed. No evidence for local differential mobility in this region was detected, implying that the structure of the strand differs in the two molecules. We have therefore applied the de novo approach meccano to determine the conformation of this peptide using only RDC. A single conformation is found that is in agreement with all measured data. The aligned peptide can be docked onto the expected covalence of the rest of the template molecule while respecting its strictly defined relative orientation. In contrast to the structure of MsrA from E. coli, the reactive side chain of Cys200 is oriented toward the interior of the molecule and therefore closer to the catalytic Cys53, obviating the need for previously proposed conformational reorganization prior to formation of this disulfide intermediate. This analysis requires only backbone assignment and uses unambiguously assigned and readily measurable structural data, thereby greatly economizing investigation time compared to established nuclear Overhauser effect- (nOe-) based structure calculation methods.     

Synthesis of an unsymmetrically doubly bridged calix[4]arene in the 1,3-alternate conformation

We report the synthesis of the first calix[4]arene constrained to a 1,3-alternate conformation by one crown ether and one di-aza-benzo crown ether bridgings. Preliminary binding properties are also given.     

Synthesis of 3-Deaza-2′-deoxyadenosine and 3-Deaza-2′,3′-dideoxyadenosine: Glycosylation of the 4-Chloroimidazo[4,5-c]pyridinyl Anion

The convergent syntheses of 3-deazapurine 2′-deoxy-β-D -ribonucleosides and 2′,3′-dideoxy-D -ribonucleosides, including 3-deaza-2′-deoxyadenosine ( 1a ) and 3-deaza-2′,3′-dideoxyadenosine ( 1b ) is described. The 4-chloro-lH-imidazo[4,5-c]pyridinyl anion derived from 5 was reacted with either 2′-deoxyhalogenose 6 or 2′,3′-dideoxyhalogenose 10 yielding two regioisomeric (N¹ and N³) glycosylation products. They were deprotected and converted into 4-substituted imidazo[4,5-c]pyridine 2′-deoxy-β-D -ribonucleosides and 2′,3′-dideoxy-D -ribonucleosides. Compounds 1a and 1b proved to be more stable against proton-catalyzed N-glycosylic bond hydrolysis than the parent purine nucleosides and were not deaminated by adenosine deaminase.     

Two Years of Pesticides Monitoring in a Belgian Watershed

A monitoring study was carried out in 1998-1999 on a medium-sized (c. 4580 km²) watershed of the Dyle (or Dijle) river in central Belgium, composed of both rural and urbanized areas. This watershed may be considered as representative of a large part of the country. Samples were taken each month from seven sites along the course of the river, plus one from its major affluent the Demer. The eight molecules monitored were the main herbicides used on the major crops in the area, plus some used in nonagricultural sectors. The concentrations found were mostly in the 0-3 μg/L range, with some peaks between 3 and 14 μg/L. The averages over all spring and summer samples analyzed ranged from 0.14 (bentazone) to 1.54 μg/L (diuron). Time and space specific patterns could be observed.     

ℋ︁‐LU factorization in preconditioners for augmented Lagrangian and grad‐div stabilized saddle point systems

The (mixed finite element) discretization of the linearized Navier–Stokes equations leads to a linear system of equations of saddle point type. The iterative solution of this linear system requires the construction of suitable preconditioners, especially in the case of high Reynolds numbers. In the past, a stabilizing approach has been suggested which does not change the exact solution but influences the accuracy of the discrete solution as well as the effectiveness of iterative solvers. This stabilization technique can be performed on the continuous side before the discretization, where it is known as ‘grad‐div’ (GD) stabilization, as well as on the discrete side where it is known as an ‘augmented Lagrangian’ (AL) technique (and does not change the discrete solution). In this paper, we study the applicability of ??‐LU factorizations to solve the arising subproblems in the different variants of stabilized saddle point systems. We consider both the saddle point systems that arise from the stabilization in the continuous as well as on the discrete setting. Recently, a modified AL preconditioner has been proposed for the system resulting from the discrete stabilization. We provide a straightforward generalization of this approach to the GD stabilization. We conclude the paper with numerical tests for a variety of problems to illustrate the behavior of the considered preconditioners as well as the suitability of ??‐LU factorization in the preconditioners. Copyright © 2010 John Wiley & Sons, Ltd.     

Monofluoroalkene-Isostere as a 19F NMR Label for the Peptide Backbone: Synthesis and Evaluation in Membrane-Bound PGLa and (KIGAKI)3

Solid-state ¹⁹F NMR is a powerful method to study the interactions of biologically active peptides with membranes. So far, in labelled peptides, the ¹⁹F-reporter group has always been installed on the side chain of an amino acid. Given the fact that monofluoroalkenes are non-hydrolyzable peptide bond mimics, we have synthesized a monofluoroalkene-based dipeptide isostere, Val-Ψ[(Z)-CF=CH]-Gly, and inserted it in the sequence of two well-studied antimicrobial peptides: PGLa and (KIGAKI)₃ are representatives of an α-helix and a β-sheet. The conformations and biological activities of these labeled peptides were studied to assess the suitability of monofluoroalkenes for ¹⁹F NMR structure analysis.     

Copper-based metal–organic framework decorated by CuO hair-like nanostructures: Electrocatalyst for oxygen evolution reaction

We report a Cu-based metal–organic framework (MOF) decorated by CuO nanostructures as an efficient catalyst for the oxygen evolution reaction (OER). MIL-53(Cu) was synthesized by a hydrothermal approach using 1,4-bezenedicarboxylic acid as organic precursor and further annealed at 300°C to form CuO nanostructures on its surface. The produced electrocatalyst, CuO@MIL-53(Cu), was characterized using various techniques. Under alkaline conditions, the developed electrocatalyst exhibited an overpotential of 801 and 336 mV versus RHE at 10 and 1 mA cm⁻², respectively. The reproducibility of the catalytic performance was validated using several electrodes. It was confirmed that the CuO hair-like nanostructures grown on MIL-53(Cu) using thermal treatment exhibit high OER activity, good kinetics and durability. CuO@MIL-53(Cu) is an economic noble-metal-free OER electrocatalyst. It has potential for application as anode material for sustainable energy technologies like batteries, fuel cells and water electrolysis.