Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Paracoccus”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,189 records · Page 66Linked to original sources
PubMed2005

The ligand geometry of copper determines the stability of amicyanin.

Solution differential scanning calorimetry (DSC) of oxidized amicyanin, a Type I copper protein, at pH 7.5 reveals two thermal transitions. The major transition at 67.7 degrees C corresponds to the disruption of the Cys(92) thiolate to Cu(II) charge transfer as evidenced by a corresponding temperature-dependent loss of amicyanin visible absorbance. A minor transition at 75.5 degrees C describes the further irreversible protein unfolding. Reduced amicyanin exhibits a pH-dependent change of the copper ligand geometry. At pH 8.5 where the Type I tetrahedral geometry is maintained, DSC reveals two thermal transitions with T(m) values similar to that of oxidized amicyanin. At pH 6.2 where the Cu(I) coordination is trigonal planar, reduced amicyanin exhibits a single thermal transition with a lower T(m) of 64.0 degrees C. Apoamicyanin, from which copper has been removed, also exhibits a single thermal transition but with a much lower T(m) of 51.8 degrees C. Thus, the thermal stability of amicyanin is dictated both by the presence or absence of copper and its ligand geometry, but not its redox state. The physiological relevance of these data is discussed.

Bacterial Proteins↗
PubMed2005

Analysis of the kinetics of the membrane potential generated by cytochrome c oxidase upon single electron injection.

In a recent work from this group (Popovic, D. M.; Stuchebrukhov A. A. FEBS Lett. 2004, 566, 126), a model of proton pumping by cytochrome c oxidase (CcO) was proposed. The key element of the model is His291 (bovine notation), a histidine ligand to enzyme's CuB redox center, which plays the role of the pump element. The model assumes that upon electron transfer between heme a and the binuclear catalytic center of the enzyme, two sequential proton transfers occur: First, a proton from Glu242 is transferred to an unprotonated His291, then a second proton, after reprotonation of Glu242 from the negative side of the membrane, is transferred to a hydroxyl group in the binuclear center, a water molecule is formed, and the first proton, due to proton-proton repulsion, is expelled from His291 to the positive side of the membrane, resulting in a pumping event. In the process the free energy of water formation (i.e., reduction of oxygen) is transformed into a proton gradient across the membrane. The model possesses specific kinetic features. It assumes, for example, that upon electron transfer the first proton is transferred to the proton-loading site of the pump, His291, and not to the catalytic center of the enzyme. Here, we analyze the kinetic properties of the proposed model, and calculate the time dependence of the membrane potential generated by CcO upon a single electron injection into the enzyme. These data are directly compared with recent experimental measurements of the membrane potential generated by CcO. Specifically, F to O, and O to E transitions will be discussed. Several enzymes from different organisms (bovine, two bacterial enzymes, and several mutants) are compared and discussed in detail. The kinetic description, however, is phenomenological, and does not include explicitly the nature of the groups involved in proton translocation, except in terms of their position depth within the membrane; thus, the kinetic equations developed here are in fact describe a generic model, similar, e.g., to that proposed earlier by Peter Rich (P.R. Rich, Towards an understanding of the chemistry of oxygen reduction and proton translocation in the iron-copper respiratory oxidases. Aust. J. Plant Physiol. 22 (1995) 479-486), and which is based on the idea of displacement of the pumped protons by the chemical ones.

Animals↗
PubMed2004

Biotinylated polypyrrole films: an easy electrochemical approach for the reagentless immobilization of bacteria on electrode surfaces.

Biotinylated bacteria were immobilized onto biotin/avidin modified electrode surfaces. Firstly, an electrospotting deposition method, followed by fluorescence microscopy, showed that bacteria were specifically grafted onto a gold surface. Fluorescence intensity versus the quantity of bacteria deposited on the surface was correlated, allowing determination of the microbial saturation point. Secondly, biotinylated bacteria were immobilized onto a glassy carbon macro-electrode in order to assess immobilized bacterial denitrification activity. During a 7-day trial, the modified electrode completely denitrified 5 mM nitrate, with a rate of 1.66 mM/day over the first 3 days. When the same electrode was placed in fresh nitrate solution, the denitrification rate dropped to 0.80 mM/day. Crucially, the immobilized bacteria did not become detached from the electrode during the study.

Bacterial Adhesion↗
PubMed2006

Performance of a reactor containing denitrifying immobilized biomass in removing ethanol and aromatic hydrocarbons (BTEX) in a short operating period.

A horizontal-flow anaerobic immobilized biomass reactor (HAIB) containing denitrifying biomass was evaluated with respect to its ability to remove, separately and in a short operating period (30 days), organic matter, nitrate, and the hydrocarbons benzene (41.4 mg L-1), toluene (27.8 mg L-1), ethylbenzene (31.1 mg L-1), o-xylene (28.5 mg L-1), m-xylene (28.4 mg L-1) and p-xylene (32.1 mg L-1). The purified culture, which was grown in the presence of the specific hydrocarbon, was used as the source of cells to be immobilized in the polyurethane foam. After 30 days of operation, the foam was removed and a new immobilized biomass was grown in the presence of another hydrocarbon. The average hydrocarbon removal efficiency attained was 97%. The organic matter, especially ethanol, was removed with an average efficiency of 83% at a mean influent concentration of 1185.0 mg L-1. A concomitant removal of 97% of nitrate was observed for a mean influent concentration of 423.4 mg L-1. The independent removal of each hydrocarbon demonstrated that these contaminants can be biodegraded separately, without the need for a compound to be the primary substrate for the degradation of another. This study proposes the application of the system for treatment of areas contaminated with these compounds, with substitution and formation of a biofilm in a 30-day period.

Anaerobiosis↗
PubMed2000

Tyr(30) of amicyanin is not critical for electron transfer to cytochrome c-551i: implications for predicting electron transfer pathways.

A Pathways analysis of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein electron transfer (ET) complex predicts two sets of ET pathways of comparable efficiency from the type I copper of amicyanin to the heme of cytochrome c-551i. In one pathway, the electron exits copper via the Cys(92) copper ligand, and in the other, it exits via the Met(98) copper ligand. If the Pathways algorithm is modified to include contributions from the anisotropy of metal-ligand coupling, independent of differences in copper-ligand bond length, then the pathways via Cys(92) are predicted to be at least 100-fold more strongly coupled than the pathways via any of the other copper ligands. All of the favored pathways via Cys(92) include a through-space jump from Cys(92) to the side chain of Tyr(30). To determine whether or not the pathways via Cys(92) are preferentially used for ET, Tyr(30) was changed to other amino acid residues by site-directed mutagenesis. Some mutant proteins were very unstable suggesting a role for Tyr(30) in stabilizing the protein structure. Y30F and Y30I mutant amicyanins could be isolated and analyzed. For the Y30I mutant, the modified Pathways analysis which favors ET via Cys(92) predicts a decrease in ET rate of at least two orders of magnitude, whereas the standard Pathways analysis predicts no change in ET rate since ET via Met(98) is not affected. Experimentally, the ET rates of the Y30I and Y30F mutants were indistinguishable from that of wild-type amicyanin. Likely explanations for these observations are discussed as are their implications for predicting pathways for ET reactions of metalloproteins.

Algorithms↗
PubMed2000

The role of the D- and K-pathways of proton transfer in the function of the haem-copper oxidases.

The X-ray structures of several haem-copper oxidases now at hand have given important constraints on how these enzymes function. Yet, dynamic data are required to elucidate the mechanisms of electron and proton transfer, the activation of O(2) and its reduction to water, as well as the still enigmatic mechanism by which these enzymes couple the redox reaction to proton translocation. Here, some recent observations will be briefly reviewed with special emphasis on the functioning of the so-called D- and K-pathways of proton transfer. It turns out that only one of the eight protons taken up by the enzyme during its catalytic cycle is transferred via the K-pathway. The D-pathway is probably responsible for the transfer of all other protons, including the four that are pumped across the membrane. The unique K-pathway proton may be specifically required to aid O-O bond scission by the haem-copper oxidases.

Binding Sites↗
PubMed1984

Nitrous oxide reductase and the 120,000 MW copper protein of N2-producing denitrifying bacteria are different entities.

Zumft and Matsubara [1982) FEBS Lett. 148, 107-112) isolated a 120,000 MW copper protein from certain denitrifying bacteria which were capable of producing N2. The presence of this protein correlated with a nutritional requirement of copper for growth on and reduction of N2O by the bacteria. The copper protein was alleged by these workers to be nitrous oxide reductase. However, it is shown that the copper protein and nitrous oxide reductase have different molecular weights and exhibit different behavior upon anion exchange chromatography. The copper protein is therefore not nitrous oxide reductase.

Copper↗
PubMed1998

Intrinsic uncoupling of cytochrome c oxidase may cause the maternally inherited mitochondrial diseases MELAS and LHON.

Mutations in the human mtDNA gene encoding subunit III of cytochrome c oxidase (CO) have been reported to cause MELAS and LHON. Poracoccus denitrificans cells expressing substitutions homologous to these MELAS- and LHON-causing mutations had lower growth yield than wild type cells and lower efficiency of proton pumping by CO (e.g. lower H+/e ratio and lower deltapsi), but had similar CO activity. These results indicate that both substitutions (F263L > A212T) cause intrinsic uncoupling, which may be the direct cause of the diseases. These results also suggest that subunit III is involved in proton pumping.

Ascorbic Acid↗