Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Crystals of Saccharomyces cerevisiae inorganic pyrophosphatase suitable for X-ray diffraction study were grown by cocrystallization of the enzyme with cobalt chloride and imidodiphosphate. Saccharomyces cerevisiae is a metal-dependent enzyme which catalyzes hydrolysis of inorganic pyrophosphate to orthophosphate. The three-dimensional structure of this enzyme was solved by the molecular-replacement method and refined at 1.8 Å resolution to an R factor of 19.5%. Cobalt and phosphate ions were revealed in the active centers of both identical subunits (A and B) of the pyrophosphatase molecule. In subunit B, a water molecule was found between two cobalt ions. It is believed that this water molecule acts as an attacking nucleophile in the enzymatic cleavage of the pyrophosphate bond. It was demonstrated that cobalt ions and a phosphate group occupy only part of the potential binding sites (two chemically identical and crystallographically independent subunits have different binding sites). The arrangement of ligands and the structure of the nucleophile-binding site are discussed in relation to the mechanism of action of the enzyme and the nature of the metal activator.     

Transition flow of rarefied gases: Current models and methods of simulation

Transition (molecular-viscous) isothermal channel flow of rarefied gases is considered. Present-day engineering physical models of transition gas flow and methods of simulation are analyzed and verified in terms of the kinetic theory on the micro-and macrolevels.     

A note on the necessary conditions for the algebraic Riccati equation

We derive some useful and easily computable necessary conditionsfor the existence of a positive semi-definite solution to thealgebraic Ricatti equation (ARE). A motivating example is givento highlight the usefulness of the conditions for controllerand observer designs for nonlinear systems. Further, an upperbound on the trace of the solution to the ARE is also derived.     

Karhunen–Loeve representations of turbulent channel flows using the method of snapshots

For three‐dimensional flows with one inhomogeneous spatial coordinate and two periodic directions, the Karhunen–Loeve procedure is typically formulated as a spatial eigenvalue problem. This is normally referred to as the direct method (DM). Here we derive an equivalent formulation in which the eigenvalue problem is formulated in the temporal coordinate. It is shown that this so‐called method of snapshots (MOS) has some numerical advantages when compared to the DM. In particular, the MOS can be formulated purely as a matrix composed of scalars, thus avoiding the need to construct a matrix of matrices as in the DM. In addition, the MOS avoids the need for so‐called weight functions, which emerge in the DM as a result of the non‐uniform grid typically employed in the inhomogeneous direction. The avoidance of such weight functions, which may exhibit singular behaviour, guarantees satisfaction of the boundary conditions. The MOS is applied to data sets recently obtained from the direct simulation of turbulence in a channel in which viscoelasticity is imparted to the fluid using a Giesekus model. The analysis reveals a steep drop in the dimensionality of the turbulence as viscoelasticity is increased. This is consistent with the results that have been obtained with other viscoelastic models, thus revealing an essential generic feature of polymer‐induced drag reduced turbulent flows. Published in 2006 by John Wiley & Sons, Ltd.     

Shell effects in the symmetric-modal fission of pre-actinide nuclei

Mass distributions of fragments in the low-energy fission of nuclei from ¹⁸⁷Ir to ²¹³At have been analysed. This analysis has shown that shell effects in symmetric-mode fragment mass yields from the fission of pre-actinide nuclei could be described if one assumes the existence of two strongly deformed neutron shells in the arising fragments with neutron numbers N₁ ≈ 52 and N₂ ≈ 68. A new method has been proposed for quantitatively describing the mass distributions of the symmetric fission mode for pre-actinides with A ≈ 180–220.     

Pseudo-Strong Regularity Around a Set

A generalization of strong regularity around a vertex subset C of a graph Γ, which makes sense even if Γis non-regular, is studied. Such a structure appears, together with a kind of distance-regularity around C , when an spectral bound concerning the so-called predistance polynomial of C is attained. As a main consequence of these results, it is shown that a regular (connected) graph Γwith d + 1 distinct eigenvalues is distance-regular, and its distance- d graph Γ d is strongly regular with parameters a = c , if and only if the number of vertices at distance d from each vertex satisfies an expression which depends only on the order of Γand the different eigenvalues of Γ.     

Electron-transfer kinetics and activation barriers for the reductions of nitrosonium and nitronium ions in aprotic solvents

Using the cyclic voltammetry (CV), the electron-transfer kinetics for the reductions of NO⁺ and NO₂⁺ cations have been studied at the Pt electrode in nitromethane, sulfolane, and propylene carbonate. The heterogeneous rate constants have been determined by two independent procedures from the transfer coefficient α, the diffusion coefficient D, from a detailed examination of the CV-peak separations, and from an inspection of the values of the cathodic peak potentials at different scan rates. The results have been compared to those reported in the literature, and discussed. In the classical model, outer-sphere electron-transfer reactions are considered subject to an activation energy arising from solvent reorganization and bond reorganization processes. The solvent and molecular reorganizational barriers for these electroreductions have been assessed in aprotic media. The Marcus-Hush theory has been applied to the self-exchange reactions of the NO₂⁺/NO₂ and NO⁺/NO couples in an attempt to predict the rate of electron transfer. The findings indicate some improvement between theory and experiment. However, it should be noted that the experimental values of k_s found for the NO₂⁺ reduction in the solvents used are still too high in comparison with those determined theoretically. In view of the fairly strong coordination of the solvent molecule(s) as ligand(s) to NO₂⁺ and NO⁺ cations, we believe that such discrepancies should stem, to some extent, from the involvement of an inner-sphere pathway by generation of an activated complex on the surface of the Pt electrode. © 1993 John Wiley & Sons, Inc.