Succinate: quinone oxidoreductases: new insights from X-ray crystal structures

AbstractMembrane-bound succinate dehydrogenases (succinate:quinone reductases, SQR) and fumarate reductases (quinol:fumarate reductases, QFR) couple the oxidation of succinate to fumarate to the reduction of quinone to quinol and also catalyse the reverse reaction. SQR (respiratory complex II) is involved in aerobic metabolism as part of the citric acid cycle and of the aerobic respiratory chain. QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor, and is part of an electron transport chain catalysing the oxidation of various donor substrates by fumarate. QFR and SQR complexes are collectively referred to as succinate:quinone oxidoreductases (EC 1.3.5.1), have very similar compositions and are predicted to share similar structures. The complexes consist of two hydrophilic and one or two hydrophobic, membrane-integrated subunits. The larger hydrophilic subunit A carries covalently bound flavin adenine dinucleotide and subunit B contains three iron-sulphur centres. QFR of Wolinella succinogenes and SQR of Bacillus subtilis contain only one hydrophobic subunit (C) with two haem b groups. In contrast, SQR and QFR of Escherichia coli contain two hydrophobic subunits (C and D) which bind either one (SQR) or no haem b group (QFR). The structure of W. succinogenes QFR has been determined at 2.2 Å resolution by X-ray crystallography (C.R.D. Lancaster, A. Kröger, M. Auer, H. Michel, Nature 402 (1999) 377–385). Based on this structure of the three protein subunits and the arrangement of the six prosthetic groups, a pathway of electron transfer from the quinol-oxidising dihaem cytochrome b to the site of fumarate reduction and a mechanism of fumarate reduction was proposed. The W. succinogenes QFR structure is different from that of the haem-less QFR of E. coli, described at 3.3 Å resolution (T.M. Iverson, C. Luna-Chavez, G. Cecchini, D.C. Rees, Science 284 (1999) 1961–1966), mainly with respect to the structure of the membrane-embedded subunits and the relative orientations of soluble and membrane-embedded subunits. Also, similarities and differences between QFR transmembrane helix IV and transmembrane helix F of bacteriorhodopsin and their implications are discussed

The adsorption structure of furan on Pd(1 1 1)

The structure of molecular furan, C4H4O, on Pd(1 1 1) has been investigated by O K-edge near-edge X-ray absorption fine structure (NEXAFS) and C 1s scanned-energy mode photoelectron diffraction (PhD). NEXAFS shows the molecule to be adsorbed with the molecular plane close to parallel to the surface, a conclusion confirmed by the PhD analysis. Chemical-state specific C 1s PhD data were obtained for the two inequivalent C atoms in the furan, the α-C atoms adjacent to the O atom, and the β-C atoms bonded only to C atoms, but only the PhD modulations for the α-C emitters were of sufficiently large amplitude for detailed evaluation using multiple scattering calculations. This analysis shows the α-C atoms to be located approximately 0.6 Å off-atop surface Pd atoms with an associated C–Pd bondlength of 2.13 ± 0.03 Å. Two alternative local geometries consistent with the data place the O atom in off-atop or near-hollow locations, and for each of these local structures there are two equally-possible registries relative to the fcc and hcp hollow sites. The results are in good agreement with earlier density functional theory calculations which indicate that the fcc and hcp registries are equally probable, but the PhD results fail to distinguish the two distinct local bonding geometries

Defect distribution in a-plane GaN on Al2O3

The authors studied the structural and point defect distributions of hydride vapor phase epitaxial GaN film grown in the [11−20] a direction on (1−102) r-plane sapphire with metal-organic vapor phase deposited a-GaN template using transmission electron microscopy, secondary ion mass spectrometry, and positron annihilation spectroscopy. Grown-in extended and point defects show constant behavior as a function of thickness, contrary to the strong nonuniform defect distribution observed in GaN grown along the [0001] direction. The observed differences are explained by orientation-dependent and kinetics related defect incorporation.Peer reviewe

A structural study of a C3H3 species coadsorbed with CO on Pd(1 1 1)

The combination of chemical-state-specific C 1s scanned-energy mode photoelectron diffraction (PhD) and O K-edge near-edge X-ray absorption fine structure (NEXAFS) has been used to determine the local adsorption geometry of the coadsorbed C3H3 and CO species formed on Pd(1 1 1) by dissociation of molecular furan. CO is found to adopt the same geometry as in the Pd(1 1 1)c(4 × 2)-CO phase, occupying the two inequivalent three-fold coordinated hollow sites with the C–O axis perpendicular to the surface. C3H3 is found to lie with its molecular plane almost parallel to the surface, most probably with the two ‘outer’ C atoms in equivalent off-atop sites, although the PhD analysis formally fails to distinguish between two distinct local adsorption sites

Chemical Self-Enrichment of HII Regions by the Wolf-Rayet Phase of an 85 Msun star

It is clear from stellar evolution and from observations of WR stars that massive stars are releasing metal-enriched gas through their stellar winds in the Wolf-Rayet phase. Although HII region spectra serve as diagnostics to determine the present-day chemical composition of the interstellar medium, it is far from being understood to what extent the HII gas is already contaminated by chemically processed stellar wind. Therefore, we analyzed our models of radiative and wind bubbles of an isolated 85 Msun star with solar metallicity (Kr\"oger et al. 2006) with respect to the chemical enrichment of the circumstellar HII region. Plausibly, the hot stellar wind bubble (SWB) is enriched with 14N during the WN phase and even much higher with 12C and 16O during the WC phase of the star. During the short period that the 85 Msun star spends in the WC stage enriched SWB material mixes with warm HII gas of solar abundances and thus enhances the metallicity in the HII region. However, at the end of the stellar lifetime the mass ratios of the traced elements N and O in the warm ionized gas are insignificantly higher than solar, whereas an enrichment of 22 % above solar is found for C. Important issues from the presented study comprise a steeper radial gradient of C than O and a decreasing effect of self-enrichment for metal-poor galaxies.Comment: 5 pages, 3 figures, accepted for publication in A&A Letter

Boltzmann equation and hydrodynamic fluctuations

We apply the method of invariant manifolds to derive equations of generalized hydrodynamics from the linearized Boltzmann equation and determine exact transport coefficients, obeying Green-Kubo formulas. Numerical calculations are performed in the special case of Maxwell molecules. We investigate, through the comparison with experimental data and former approaches, the spectrum of density fluctuations and address the regime of finite Knudsen numbers and finite frequencies hydrodynamics.Comment: This is a more detailed version of a related paper: I.V. Karlin, M. Colangeli, M. Kroger, PRL 100 (2008) 214503, arXiv:0801.2932. It contains comparison between predictions and experiment, in particular. 11 pages, 6 figures, 2 table