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  • Biochemistry and Biotechnology  (3)
  • X-ray absorption spectroscopy  (3)
  • 1
    ISSN: 1432-1327
    Keywords: Key words α-Ketoglutarate dioxygenase ; TfdA ; X-ray absorption spectroscopy ; Extended X-ray absorption fine structure ; 2 ; 4-Dichlorophenoxyacetic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The first step in the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by Ralstonia eutropha JMP134 is catalyzed by the α-ketoglutarate (α-KG)-dependent dioxygenase TfdA. Previously, EPR and ESEEM studies on inactive Cu(II)-substituted TfdA suggested a mixture of nitrogen/oxygen coordination with two imidazole-like ligands. Differences between the spectra for Cu TfdA and α-KG- and 2,4-D-treated samples were interpreted as a rearrangement of the g–tensor principal axis system. Herein, we report the use of X-ray absorption spectroscopy (XAS) to further characterize the metal coordination environment of Cu TfdA as well as that in the active, wild-type Fe(II) enzyme. The EXAFS data are interpreted in terms of four N/O ligands (two imidazole-like) in the Cu TfdA sample and six N/O ligands (one or two imidazole-like) in the Fe TfdA sample. Addition of α-KG results in no significant structural change in coordination for Cu or Fe TfdA. However, addition of 2,4-D results in a decrease in the number of imidazole ligands in both Cu and Fe TfdA. Since this change is seen both in the Fe and Cu EXAFS, loss of one histidine ligand upon 2,4-D addition best describes the phenomenon. These XAS data clearly demonstrate that changes occur in the atomic environment of the metallocenter upon substrate binding.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-1327
    Keywords: Key words Transcription factor IIB ; Metalloprotein ; Zinc finger ; Gene transcription ; X-ray absorption spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract X-ray absorption spectroscopy has been used to compare the metal coordination of the N-terminal zinc binding domain of eukaryal human transcription factor (TF) IIB to the previously reported structure of archaeal Pyrococcus furiosus (Pf) TFB. Full length and N-terminal fragments for both PfTFBand human TFIIB were cloned, expressed, and purified. The [C10H] variant of PfTFB was constructed to resemble the metal binding motif of higher eukaryal TFIIB proteins by mutating the second cysteine ligand to a histidine. All five proteins bind zinc in a 1 :1 ratio. Zn X-ray absorption spectroscopy of human TFIIB and [C10H]PfTFB mutant are consistent with ZnS3(N,O) ligation, and further suggest that the N/O ligand is an imidazole.
    Type of Medium: Electronic Resource
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  • 3
    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.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0887-3585
    Keywords: interleukin-4 ; circular dichroism spectroscopy ; site-directed mutagenesis ; protein structure modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of human interleukin 4 (IL-4) was predicted utilizing a series of experimental and theoretical techniques. Circular Dichroism (CD) spectroscopy indicated that IL-4 belonged to the all α-helix class of protein structures. Secondary structure prediction, site-directed mutagenesis, and CD spectroscopy suggested a predominantly α-helical structure, consistent with a four-helix bundle structural motif. A human/mouse IL-4 chimera was constructed to qualitatively evaluate alternative secondary structure predictions. The four predicted helices were assembled into tertiary structures using established algorithms. The mapping of three disulfide bridges in IL-4 provided additional constraints on possible tertiary structures. Using accessible surface contact area as a criterion, the most suitable structures were right handed all antiparallel four-helix bundles with two overhand loop connections. Successful loop closure and incorporation of the three disulfide constraints were possible while maintaining the expected shape, solvent accessibility, and steric interactions between loops and helices. Lastly, energy minimization was used to regularize the chain.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Journal of Bioluminescence and Chemiluminescence 4 (1989), S. 507-511 
    ISSN: 0884-3996
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Advent of the multichannel plate and position sensitive detector has made possible true single photon counting imaging tubes. We have investigated the application of these detectors in studies of the ultraweak light emission of biological materials. Initially, we focussed our efforts on two objectives: (1) obtaining single photon counting images of living tissues using only the light (chemiluminescence) emitted by the specimen and (2) developing means of obtaining well-resolved spectra of weakly emitting sources. We have obtained a variety of images. One striking result of this work is the first observation of tissue specific localization of photon emission in situ. Using this detector we have also obtained the first well-resolved spectra of some important ultraweak emission processes. These results illustrate the potential use of single photon imaging in bioluminescence and chemiluminescence research.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 3190-3198 
    ISSN: 0173-0835
    Keywords: Wheat ; Proteins ; Buffers ; Gliadins ; Capillary electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Studies were conducted to produce faster, simpler, more rugged protocols for separating wheat proteins by high performance capillary electrophoresis (HPCE). Three areas were targeted for improvement: initial capillary equilibration procedures, buffer composition, and post-separation rinsing procedures. For the initial equilibration of capillaries, a brief rinse with a hydroxypropylmethylcellulose (HPMC) solution was the most critical factor for successful separation of wheat proteins. To reduce separation time and maintain resolution, β-alanine and glycine were each used in place of sodium phosphate as buffer ions. Two isoelectric buffers, aspartic acid and iminodiacetic acid (IDA) were also tested. Each of these four buffer systems generated substantially lower currents, and provided faster separations, than sodium phosphate-based buffers. Finally, post-separation rinsing procedures were re-examined with the goal of reducing the time necessary to rinse the capillary after each separation. A critical factor in achieving this goal was removal of albumins and globulins prior to separation. These proteins bind to the capillary wall and cause rising baselines and excessive peak tailing. Once these proteins were removed, capillaries could be rinsed with buffer for only 2 min between separations. Capillary equilibration procedures were shortened from 90 min to 30 min. Likewise, separation times were reduced by ∼ 40% (25 min to 15 min) by using glycine in place of sodium phosphate in the separation buffer. Finally, post-separation times were reduced by 80% (10 min to 2 min). Overall, these factors resulted in a reduction in total separation time of 50% (35 to 17 min) and maintained high resolution separations and good run-to-run repeatability.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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