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  • 1
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    Protein carbon-13 spin systems by a single two-dimensional nuclear magnetic resonance experiment (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-05-13
    Description: By applying a two-dimensional double-quantum carbon-13 nuclear magnetic resonance experiment to a protein uniformly enriched to 26 percent carbon-13, networks of directly bonded carbon atoms were identified by virtue of their one-bond spin-spin couplings and were classified by amino acid type according to their particular single- and double-quantum chemical shift patterns. Spin systems of 75 of the 98 amino acid residues in a protein, oxidized Anabaena 7120 ferredoxin (molecular weight 11,000), were identified by this approach, which represents a key step in an improved methodology for assigning protein nuclear magnetic resonance spectra. Missing spin systems corresponded primarily to residues located adjacent to the paramagnetic iron-sulfur cluster.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oh, B H -- Westler, W M -- Darba, P -- Markley, J L -- RR02301/RR/NCRR NIH HHS/ -- RR02781/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1988 May 13;240(4854):908-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3129784" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids ; Carbon Isotopes ; Cyanobacteria/analysis ; *Ferredoxins ; *Magnetic Resonance Spectroscopy ; Oxidation-Reduction ; Spectrum Analysis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Safeguarding the integrity of protein archive (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-30
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456675/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456675/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berman, Helen M -- Kleywegt, Gerard J -- Nakamura, Haruki -- Markley, John L -- Burley, Stephen K -- P41 LM005799/LM/NLM NIH HHS/ -- England -- Nature. 2010 Jan 28;463(7280):425. doi: 10.1038/463425c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110969" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Protein/*ethics/*standards ; Ethics, Research ; Reproducibility of Results ; Scientific Misconduct
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Structural basis for the photoconversion of a phytochrome to the activated Pfr form (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-16
    Description: Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red-light-absorbing, ground state (Pr) and a far-red-light-absorbing, photoactivated state (Pfr). Although the structures of several phytochromes as Pr have been determined, little is known about the structure of Pfr and how it initiates signalling. Here we describe the three-dimensional solution structure of the bilin-binding domain as Pfr, using the cyanobacterial phytochrome from Synechococcus OSB'. Contrary to predictions, light-induced rotation of the A pyrrole ring but not the D ring is the primary motion of the chromophore during photoconversion. Subsequent rearrangements within the protein then affect intradomain and interdomain contact sites within the phytochrome dimer. On the basis of our models, we propose that phytochromes act by propagating reversible light-driven conformational changes in the bilin to altered contacts between the adjacent output domains, which in most phytochromes direct differential phosphotransfer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807988/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ulijasz, Andrew T -- Cornilescu, Gabriel -- Cornilescu, Claudia C -- Zhang, Junrui -- Rivera, Mario -- Markley, John L -- Vierstra, Richard D -- P41 RR002301/RR/NCRR NIH HHS/ -- P41 RR002301-237748/RR/NCRR NIH HHS/ -- U54 GM074901/GM/NIGMS NIH HHS/ -- U54 GM074901-05/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 14;463(7278):250-4. doi: 10.1038/nature08671.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075921" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry/metabolism/radiation effects ; Bacterial Proteins/*chemistry/genetics/metabolism/*radiation effects ; Bile Pigments/chemistry/metabolism/radiation effects ; Binding Sites ; *Light ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Phytochrome/*chemistry/genetics/metabolism/*radiation effects ; Protein Kinases/*chemistry/genetics/metabolism/*radiation effects ; Protein Structure, Tertiary/radiation effects ; Rotation ; Synechococcus/*chemistry/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
    Electronic Resource
    Electronic Resource
    Location and mobility of ubiquinones of different chain lengths in artificial membrane vesicles (1985)
    s.l. : American Chemical Society
    Biochemistry 24 (1985), S. 2501-2508 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00331a016
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  • 5
    Electronic Resource
    Electronic Resource
    Amino acid residues in Anabaena ferredoxin crucial to interaction with ferredoxin-NADP+ reductase: Site-directed mutagenesis and laser flash photolysis (1993)
    s.l. : American Chemical Society
    Biochemistry 32 (1993), S. 9346-9354 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00087a013
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  • 6
    Electronic Resource
    Electronic Resource
    Structure of the trigonal form of recombinant oxidized flavodoxin from Anabaena 7120 at 1.40 Å resolution (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 318-330 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The oxidized recombinant flavodoxin from the cyanobacterium Anabaena 7120 has been crystallized in a trigonal form. The recombinant protein has an identical primary structure to that purified directly from Anabaena, which functions as a substitute for ferredoxin in an iron-deficient environment for electron transfer from photosystem I to ferredoxin–NADP+ reductase. X-ray data to 1.40 Å were collected on a Siemens area detector. Of the 311 379 reflections collected, 36069 reflections were unique in space group P3121 (a = 55.36, c = 102.59 Å) with an Rmerge of 3.8%. The structure was solved by molecular replacement using coordinates from the wild-type monoclinic structure previously solved in this laboratory [Rao, Shaffie, Yu, Satyshur, Stockman & Markley (1992). Protein Sci. 1, 1413–1427]. The structure was refined with X-PLOR and SHELXL93 to a crystallographic R-factor of 13.9% for 32963 reflections with I〉 2σ(I). The final structure contains 2767 atoms including 31 flavin mononucleotide (FMN) atoms, 299 water molecules, and one sulfate ion. The protein is comprised of a central five-stranded β-sheet surrounded by five helices and binds a single molecule of FMN at the C-terminus of the sheet. The trigonal protein structure and the crystal packing are compared with the monoclinic wild-type protein. Helix α3 in this structure is less distorted than in the monoclinic structure and shows additional hydrogen bonds in the N-terminal portion of the helix. The trigonal structure is extensively hydrogen bonded in three major areas with neighboring molecules compared with five regions in the monoclinic structure, but using significantly fewer hydrogen bonds to stabilize the lattice. There are several hydrogen bonds to the amide groups from water molecules several of which stabilize and extend the ends of the β-sheet.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994011716
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  • 7
    Electronic Resource
    Electronic Resource
    Detailed Analysis of Protein Structure and Function by NMR Spectroscopy: Survey of Resonance Assignments (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 13 (1984), S. 493-521 
    Details
    ISSN: 0084-6589
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.13.060184.002425
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  • 8
    Electronic Resource
    Electronic Resource
    NMR Spectroscopic Studies of Paramagnetic Proteins: Iron-Sulfur Proteins (1995)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 209-237 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bb.24.060195.001233
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  • 9
    Electronic Resource
    Electronic Resource
    Intramolecular deuterium distributions reveal disequilibrium of chloroplast phosphoglucose isomerase (1999)
    Oxford, UK : Blackwell Publishing Ltd
    Plant, cell & environment 22 (1999), S. 0 
    Details
    ISSN: 1365-3040
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: 
D, deuterium
δD(NMR), chemical shift axis in a deuterium NMR spectrum
F6P, fructose-6-phosphate
G6P, glucose-6-phosphate
IRMS, isotope ratio mass spectrometry
NMR, nuclear magnetic resonance
PGI, phosphoglucose isomerase

Intramolecular deuterium distributions of the carbon-bound hydrogens of glucose were measured using deuterium nuclear magnetic resonance. Glucose isolated from leaf starch of common bean (Phaseolus vulgaris cv. Linden) or spinach (Spinacia oleracea cv. Giant nobel) was depleted in deuterium in the C(2) position, compared with glucose isolated from leaf sucrose or bean endosperm starch. In beans, the depletion of C(2) was independent of the light intensity during growth (150 or 700 μmol photons s–1 m–2). The ratio of glucose-6-phosphate to fructose-6-phosphate ([G6P]/[F6P]) in bean chloroplasts was 0·9 in high light, indicating that the phosphoglucose isomerase reaction was not in equilibrium ([G6P]/[F6P]) ≈ 3). This implies that the kinetic isotope effect of phosphoglucose isomerase depleted deuterium in the C(2) position of G6P. Because the depletion was the same, the chloroplastic ([G6P]/[F6P]) ratio was in disequilibrium irrespective of the light intensity. If the ([G6P]/[F6P]) ratio was in equilibrium, a large chloroplastic pool of G6P would be unavailable for regeneration of ribulose-1,5-bisphospate. We argue that chloroplast phosphoglucose isomerase activity is regulated to avoid this. The deuterium depletion of C(2) explains the known low overall deuterium abundance of leaf starch. This example shows that measurements of intramolecular deuterium distributions can be essential to understand overall deuterium abundances of plant material.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-3040.1999.00440.x
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  • 10
    Electronic Resource
    Electronic Resource
    The spatial distribution of chloroplast water in Acer platanoides sun and shade leaves (1993)
    Oxford, UK : Blackwell Publishing Ltd
    Plant, cell & environment 16 (1993), S. 0 
    Details
    ISSN: 1365-3040
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We evaluated a new, two-dimensional (2-D) nuclear magnetic resonance (NMR) imaging technique as a method for measuring the distribution of chloroplasts in leaves. NMR images that showed the distribution of chloroplast water and of total water as a function of depth into Acer platanoides sun and shade leaves were compared with the distribution of chlorophyll in the same leaf types (as measured by fluorescence microscopy), with the cellular structure (by scanning electron microscopy), and with published information. Results showed that the volume fraction of chloroplast water was much larger in shade than in sun leaves, and that it averaged about one-third larger in the palisade than in the spongy parenchyma region of both leaf types. Chlorophyll fluorescence was more intense in shade than in sun leaves. In sun leaves, fluorescence was maximal in the palisade region near the junction with the spongy parenchyma, while in shade leaves, fluorescence was maximal in the upper part of the spongy layer. We concluded that 2-D NMR imaging reliably indicates the location of chloroplast water.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-3040.1993.tb00492.x
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