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  • 1
    ISSN: 1432-1327
    Keywords: Key words Site-directed mutagenesis ; Iron-sulfur ; Ligand exchange ; Cluster conversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Cysteine is the ubiquitous ligand of iron-sulfur clusters in proteins, although chemical models have indicated that functional groups other than thiolates can coordinate iron in iron-sulfur compounds. Only a small number of naturally occurring examples of hydroxyl, histidinyl or carboxyl coordination have been clearly established but many others are suspected. Quite a few site-directed mutagenesis experiments have been aimed at replacing the cysteine ligands of iron-sulfur centers by other amino acids in various systems. The available data set shows that substituting one ligand, even by another functional residue, is very often destabilizing enough to impair cluster assembly; in some cases, the apoprotein cannot even be detected. One for one replacements have been demonstrated, but they have been so far almost exclusively confined to clusters with no more than one or two iron atoms. In contrast, changes of the cluster nuclearity or recruitment of free cysteine residues seem preferred ways for proteins containing larger clusters to cope with removal of a ligand, rather than using coordinating amino acids bearing different chemical functions. Furthermore, the possibility of replacing cysteines by other residues as ligands in iron-sulfur proteins does not uniquely depend on the ability of the cluster to accept other kinds of coordination than cysteinate; other factors such as the local flexibility of the polypeptide chain, the accessibility of the solvent and the electronic distribution on the active centers may also play a prominent role.
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  • 2
    ISSN: 1432-1327
    Keywords: Key words207Pb NMR ; Calmodulin ; Parvalbumin ; Helix-loop-helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The high-affinity Ca2+–binding sites of carp (pI 4.25) and pike (pI 5.0) parvalbumins, as well as those of mammalian calmodulin (CaM) and its C-terminal tryptic half-molecule (TR2C), were analyzed by 207Pb NMR spectroscopy. For the parvalbumins, two 207Pb signals were observed ranging in chemical shift from ≈750 to ≈1260 ppm downfield of aqueous Pb(NO3)2, corresponding to 207Pb2+ bound to the two high-affinity helix-loop-helix Ca2+–binding sites in each of these proteins. Four 207Pb signals, which fall in the same chemical shift window, could be discerned for CaM. Experiments on TR2C permitted the assignment of each signal as due to 207Pb2+ occupying a helix-loop-helix site in either the N- or the C-lobe of the intact protein. 207Pb and 1H NMR titration studies on CaM provided evidence that Pb2+ binding to all four sites occurs simultaneously, in contrast to the behavior of this protein in the presence of Ca2+. Titrations of the 207Pb2+–forms of CaM and TR2C with the antipsychotic drug trifluoperazine demonstrated that drug binding to the exposed hydrophobic surfaces in CaM causes substantial conformational changes and proceeds in a sequential manner – first the C-lobe and subsequently the N-lobe. Finally, the field dependence of CaM-bound 207Pb signals was examined. The 207Pb signal linewidths exhibited a sharp dependence on the square of the external magnetic field, a trend characteristic of relaxation via chemical shift anisotropy. Relaxation studies on TR2C demonstrated that chemical exchange also contributes to the observed linewidths. The large chemical shift dispersion observed for the 207Pb signals of the three proteins studied here illustrates the remarkable sensitivity of this parameter to subtle differences in the chemical environment of the protein-bound 207Pb nucleus. To our knowledge, the data presented in this article comprise the first ever published example of the application of 207Pb NMR spectroscopy to metalloproteins.
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  • 3
    ISSN: 1432-1327
    Keywords: Key words Rubrerythrin ; Desulfovibrio vulgaris ; Ferroxidase ; Diiron-oxo protein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Rubrerythrin (Rr) is the trivial name given to a non-heme iron protein of unknown function which has been found in anaerobic sulfate-reducing bacteria. Rr is unique in containing both rubredoxin-type FeS4 and diiron-oxo sites in the same protein. The results described here demonstrate for the recombinant protein that: (a) Rr catalyzes oxidation of Fe2+ to Fe3+ by O2, i.e., Rr has ferroxidase activity, (b) both FeS4 and diiron domains of the Rr protein are required for ferroxidase activity, (c) with excess Fe2+ and O2 the initial rate of this oxidation appears to be first order in [Rr] and independent of starting [Fe2+] above 30 μM, (d) the Fe3+ is produced in a form which is capable of rapid incorporation into the iron-binding site of ovotransferrin, and (e) the ferroxidase activity of Rr is comparable to that of published ferroxidase activities of apoferritins on a subunit basis. Ferroxidase activity of Rr was monitored either by the rate of increase in absorbance at 315 nm (which lies near an isosbestic point for oxidized and reduced Rr) or by using apoovotransferrin as Fe3+ acceptor, and measuring the rate and extent of diferric transferrin formation at 460 nm. No polyironoxyhydroxide aggregates appeared to associate with Rr after the ferroxidase reaction. A truncated form of Rr containing only the diiron domain had little or no ferroxidase activity. Rr could function as one component of a set of enzymes which channels the reaction products of O2 and Fe2+ onto a non-toxic pathway during transient exposure of the bacteria to air.
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  • 4
    ISSN: 1432-1327
    Keywords: Key wordsNε-Hydroxy-l-lysine ; Nω-Hydroxy-indospicine ; Arginase ; Mn(II) ligands ; Nδ-Hydroxy-l-ornithine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The effects of various compounds bearing an N-OH group such as N-hydroxy-guanidines, amidoximes, and hydroxylamines, on bovine and rat liver arginases was studied. Some of these compounds with an l-α-amino acid function at an appropriate distance from the N-OH group acted as strong competitive liver arginase inhibitors, displaying Ki values between 4 and 150 μM. Two compounds, N ε-hydroxy-l-lysine and N ω-hydroxy-d,l-indospicine, which exhibited Ki values of 4 and 20 μM (at pH 7.4), were the most potent inhibitors of arginase described to date. The distance between the α-amino acid and N-OH functions appeared to be crucial for potent inhibition of arginase, as N δ-hydroxy-l-ornithine, which has one -CH2 group less than N ε-hydroxy-l-lysine, exhibited a 37-fold higher Ki value than N ε-hydroxy-l-lysine. Based on these results, a model for the interaction of N ω-hydroxyamino-l-α-amino acids with the arginase active site is proposed. This model involves the binding of the N-OH group of the inhibitors to the arginase Mn(II) center and suggests that N ε-hydroxy-l-lysine is a good transition state analog of arginase.
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  • 5
    ISSN: 1432-1327
    Keywords: Key words Solution structure ; Paramagnetic biomolecules ; NMR ; Cytochrome c
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The availability of NOE constraints and of the relative solution structure of a paramagnetic protein permits the use of pseudocontact shifts as further structural constraints. We have developed a strategy based on: (1) determination of the χ tensor anisotropy parameters from the starting structure; (2) recalculation of a new structure by using NOE and pseudocontact shift constraints simultaneously; (3) redetermination of the χ tensor anisotropy parameters from the new structure, and so on until self-consistency. The system investigated is the cyanide derivative of a variant of the oxidized Saccharomyces cerevisiae iso-1-cytochrome c containing the Met80Ala mutation. The structure has been substantially refined. It is shown that the analysis of the deviation of the experimental pseudocontact shifts from those calculated using the starting structure may be unsound, as may the simple structure refinement based on the pseudocontact shift constraints only.
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  • 6
    ISSN: 1432-1327
    Keywords: Key words Cofactor biosynthesis ; Homocitrate ; Vanadium(V) alkoxides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Initial investigations into the possible roles of homocitric acid in the biosynthesis and function of the active site cofactor of nitrogenase resulted in the isolation and characterization of the dinuclear vanadium(V) species [K2(H2O)5][(VO2)2(R,S-C7H8O7)2]·H2O ( 1). Complex 1 represents the first synthetic structurally characterized transition metal homocitrate complex and may represent an early mobilized precursor in the biosynthesis of VFeco. Compound 1 was characterized by a variety of physical methods, including X-ray crystallography. Crystal data: space group P * (#2), with a = 10.292 (3) Å, b = 16.663 (3) Å, c = 8.343 (1) Å, α = 95.93 (1)°, β = 105.74 (2)°, γ = 90.86 (2)°, V = 1386 (1) Å3, and Z = 2. The homocitrate ligand is coordinated to the vanadium(V) atoms in a bidentate fashion via the deprotonated bridging hydroxyl group and a carboxylate donor. This unique coordination mode accurately mimics the coordination of homocitrate to the cofactor of nitrogenase.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    JBIC 1 (1996), S. 169-169 
    ISSN: 1432-1327
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
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  • 8
    ISSN: 1432-1327
    Keywords: Key words TFIIB ; Metalloprotein ; Zinc finger ; Gene transcription ; X-ray absorption spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The gene for an archaeal homolog of the eukaryotic transcription factor TFIIB has been cloned from the marine hyperthermophilic archaeon Pyrococcus furiosus and overexpressed in Escherichia coli. This TFB gene displays a sequence that is identical to a gene sequence in P. woesei. A gene for the 49-residue N-terminal domain of TFB that contains a putative C-X2-C-X15-C-X2-C metal-binding motif was subcloned and overexpressed as TFB-NTD. Purification of the TFB-NTD gene product yields Zn- and Fe-containing forms, which have been characterized by mass spectrometry and UV-visible, electron paramagnetic resonance, and X-ray absorption (XAS) spectroscopies. Only the Zn form of the TFB holoprotein has been (partially) purified, and it has been characterized by XAS. All spectroscopic characteristics are consistent with a nearly tetrahedral MS4 metal-binding site made up of the four cysteine residues in the N-terminal domain. The relatively greater thermal stability of the Zn form suggests that TFB may be a Zn-containing protein involved in archaeal transcription.
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  • 9
    ISSN: 1432-1327
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Covariance between J and B parameters and indetermination of the actual symmetry suggest caution in making general statements about their values in FenSn centers. The Fe4S4 3+ case is further complicated by electronic isomerism and lack of information on the actual symmetry. Electronic ground states and relative J and B values are discussed in the light of hyperfine coupling values.
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  • 10
    ISSN: 1432-1327
    Keywords: Key words Intramolecular electron transfer ; Amine oxidase ; Copper ; Arthrobacter P1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The intramolecular electron-transfer rate constant for the Cu(II)–topaNH2⇌ Cu(I)–topaSQ equilibrium in methylamine oxidase has been measured by temperature-jump relaxation techniques. At pH 7.0 the estimated kobs = 150±30 s–1 for both methylamine and benzylamine; assuming the equilibrium constant is ≈0.7–1 at pH 7.0 and 296 K, this would correspond to a forward electron-transfer rate constant kET≈ 60–75 s–1. Although substantially slower than the previously determined kET≈ 20 000 s–1 for pea seedling amine oxidase [5] steady-state kinetics measurements established that kET 〉 kcat≈ 4–10 s–1. Thus the Cu(I)-semiquinone state is a viable intermediate in methylamine oxidase turnover.
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