Reduction and methyl transfer kinetics of the alpha subunit from acetyl coenzyme a synthase

Stopped-flow was used to evaluate the methylation and reduction kinetics of the isolated alpha subunit of acetyl-Coenzyme A synthase from Moorella thermoacetica. This catalytically active subunit contains a novel Ni-X-Fe4S4 cluster and a putative unidentified n = 2 redox site called D. The D-site must be reduced for a methyl group to transfer from a corrinoid-iron-sulfur protein, a key step in the catalytic synthesis of acetyl-CoA. The Fe4S4 component of this cluster is also redox active, raising the possibility that it is the D-site or a portion thereof. Results presented demonstrate that the D-site reduces far faster than the Fe4S4 component, effectively eliminating this possibility. Rather, this component may alter catalytically important properties of the Ni center. The D-site is reduced through a pathway that probably does not involve the Fe4S4 component of this active-site cluster.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Synthesis of an Acyloxymethyl Prodrug of the Inositol Phosphate α-Trinositol

ABSTRACT

Acyloxymethylation of an acylated silver salt of α-trinositol gives, after deprotection, membrane permeable 1D-myo-inositol 1,2,6-tris(ethoxycarbonyloxymethyl sodium phosphate). The acyl groups, 3-(4,5-methylenedioxy-2-nitrophenyl)propanoyl, are cleaved by hydrogenolysis.     

Effect of sodium sulfide on Ni-containing carbon monoxide dehydrogenases

The structure of the active-site C-cluster in CO dehydrogenase from Carboxydothermus hydrogenoformans includes a mu(2)-sulfide ion bridged to the Ni and unique Fe, whereas the same cluster in enzymes from Rhodospirillum rubrum (CODH(Rr)) and Moorella thermoacetica (CODH(Mt)) lack this ion. This difference was investigated by exploring the effects of sodium sulfide on activity and spectral properties. Sulfide partially inhibited the CO oxidation activity of CODH(Rr) and generated a lag prior to steady-state. CODH(Mt) was inhibited similarly but without a lag. Adding sulfide to CODH(Mt) in the C(red1) state caused the g(av) = 1.82 EPR signal to decline and new features to appear, including one with g = 1.95, 1.85 and (1.70 or 1.62). Removing sulfide caused the g(av) = 1.82 signal to reappear and activity to recover. Sulfide did not affect the g(av) = 1.86 signal from the C(red2) state. A model was developed in which sulfide binds reversibly to C(red1), inhibiting catalysis. Reducing this adduct causes sulfide to dissociate, C(red2) to develop, and activity to recover. Using this model, apparent K(I) values are 40 +/- 10 nM for CODH(Rr) and 60 +/- 30 microM for CODH(Mt). Effects of sulfide are analogous to those of other anions, including the substrate hydroxyl group, suggesting that these ions also bridge the Ni and unique Fe. This proposed arrangement raises the possibility that CO binding labilizes the bridging hydroxyl and increases its nucleophilic tendency toward attacking Ni-bound carbonyl.     

Ein Zusatzgerät zum vermeiden des Übersaugens bei dem Mikro-Kjeldahlapparat von Parnas-Wagner

Zusammenfassung Es wird ein Zusatzgerät zu dem bekannten Mikro-Kjeldahlapparat vonJ. K. Parnas undR. Wagner beschrieben. Mit Hilfe dieses Gerätes, das einen Druckausgleich während der Wasserdampfdestillation ermöglicht, läßt sich das schädliche Zurücksteigen der Probeflüssigkeitwährend des Destillierens vermeiden.

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Summary (H) An addition to the well-known micro Kjeldahl apparatus ofJ. K. Parnas andR. Wagner is described. By the use of this device, which effects an equalisation of pressure during the steam distillation, the objectionable sucking back of the test liquid during the distillation is entirely prevented.

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Résumé (W) L'auteur décrit une pièce complémentaire à l'appareil micro-Kjeldahl bien connu deJ. K. Parnas etR. Wagner. A l'aide de ce dispositif, qui rend possible, pendant la distillation à la vapeur d'eau, l'égalisation de pression, on évite le retour préjudiciable de la prise d'essai pendant la distillation.

     

The electron affinity of tungsten

The electron affinity of tungsten has been measured using laser photodetachment threshold spectroscopy in a collinear geometry. The electron affinity was determined to 6583.6(6) cm^-1 by observing the onset of the process when W^- ions in the 5d⁵6s²5d^56s^2 ⁶S_5/2 ground state are photodetached producing neutral W atoms in the 5d⁴6s²5d^46s^2 ⁵D₀ ground state. The measured value is in agreement with previous measurements and improves the accuracy by almost two orders of magnitude. Further, a photodetachment signal below the ground state photodetachment threshold was found, which indicates the existence of a bound excited state in W^-.     

Mossbauer evidence for an exchange-coupled {[Fe4S4]1+ Nip1+} A-cluster in isolated alpha subunits of acetyl-coenzyme A synthase/carbon monoxide dehydrogenase

The active site A-cluster in the alpha subunit of the title enzyme consists of an Fe4S4 cluster coordinated to a [Nip Nid] subcomponent. The cluster must be activated for catalysis using low-potential reductants such as Ti(III) citrate. Relative to the inactive {[Fe4S4]2+ Nip2+ Nid2+} state, the activated state appears to be 2-electrons more reduced, but the location of these electrons within the A-cluster is uncertain, with {[Fe4S4]2+ Nip0 Nid2+} and {[Fe4S4]1+ Nip1+ Nid2+} configurations proposed. Recombinant apo-alpha subunits oligomerize after activation with NiCl2. The dimer fraction, upon reduction with excess Ti(III)citrate, exhibited M?ssbauer spectra consisting of two quadrupole doublets representing 51% and 21% of the Fe, with parameters indicating [Fe4S4]1+ states. Spectra recorded in strong magnetic fields were typical of diamagnetic systems, indicating an exchange-coupled S = 0 {[Fe4S4]1+ Nip1+} state. Additional treatment with CO altered the doublet M?ssbauer parameters, suggesting an interaction with CO, but maintaining the cluster in the {[Fe4S4]1+ Nip1+} state. Reduction with substoichiometric equivalents of Ti(III) citrate afforded an EPR signal typical of Ni1+ ions, with g parallel = 2.10 and g perpendicular = 2.02. Addition of more Ti caused the signal intensity to decline, suggesting that it arises from the semireduced {[Fe4S4]2+ Nip1+} state.     

Epitaxial NiO (1 0 0) and NiO (1 1 1) films grown by atomic layer deposition

Epitaxial NiO (1 1 1) and NiO (1 0 0) films have been grown by atomic layer deposition on both MgO (1 0 0) and α-Al₂O₃ (0 0 l) substrates at temperatures as low as 200 °C by using bis(2,2,6,6-tetramethyl-3,5-heptanedionato)Ni(II) and water as precursors. The films grown on the MgO (1 0 0) substrate show the expected cube on cube growth while the NiO (1 1 1) films grow with a twin rotated 180° on the α-Al₂O₃ (0 0 l) substrate surface. The films had columnar microstructures on both substrate types. The single grains were running throughout the whole film thickness and were significantly smaller in the direction parallel to the surface. Thin NiO (1 1 1) films can be grown with high crystal quality with a FWHM of 0.02–0.05° in the rocking curve measurements.     

The compton spectrometer

This is the story about how knowledge of the Compton profile led to the technical development of a useful apparatus. It is also the story of interdisciplinary collaboration between condensed matter theorists and medical physicists.