ChemBioChem

Cover image for ChemBioChem

September 23, 2013

Volume 14, Issue 14

Pages 1669–1906

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Review
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Review
    1. You have free access to this content
      Cover Picture: Multi-phosphorylation of the Intrinsically Disordered Unique Domain of c-Src Studied by In-Cell and Real-Time NMR Spectroscopy (ChemBioChem 14/2013) (page 1669)

      Dr. Irene Amata, Mariano Maffei, Dr. Ana Igea, Dr. Marina Gay, Dr. Marta Vilaseca, Dr. Angel R. Nebreda and Prof. Dr. Miquel Pons

      Article first published online: 14 SEP 2013 | DOI: 10.1002/cbic.201390050

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      The cover picture shows an artist's view of the phosphorylation–dephosphorylation processes affecting various potential sites (shown as red spheres) of an intrinsically disordered protein domain in the cytoplasm of living cells. The article by A. R. Nebreda, M. Pons, et al. on p. 1820 ff. of this issue shows that the phosphorylation pattern of the unique domain of c-Src, a prototypical oncogene, depends on the steady-state balance between the activities of kinases and phosphatases. Intrinsically disordered domains are often found in eukaryotic proteins and are essential regulatory elements that participate in dynamic interactions with other cell components. Post-translation modifications, including phosphorylation (shown as orange spheres in the scheme), are an important part of the regulation process. These processes can be monitored in vivo and in real time by NMR spectroscopy. Xenopus laevis oocytes, into which isotopically labelled protein can be microinjected, are shown in the background.

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      Inside Cover: Superoxide Reductase: Different Interaction Modes with its Two Redox Partners (ChemBioChem 14/2013) (page 1670)

      Dr. Rui M. Almeida, Prof. Paola Turano, Prof. Isabel Moura, Prof. José J. G. Moura and Dr. Sofia R. Pauleta

      Article first published online: 14 SEP 2013 | DOI: 10.1002/cbic.201390051

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      The inside cover picture shows superoxide reductase, which is used by anaerobic bacteria to detoxify ROS, without producing O2, by accepting an electron from rubredoxin or desulforedoxin. On p. 1858 ff., S. R. Pauleta et al. characterize the interaction of superoxide reductase from Desulfovibrio gigas with both electron donors by steady-state kinetics, 2D NMR titrations, and backbone-relaxation measurements‥

  2. Editorial

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    3. Editorial
    4. Graphical Abstract
    5. Corrigendum
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    7. Review
    8. Highlight
    9. Communications
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    11. Book Review
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      Magnetic Resonance Spectroscopy in Bio(in)organic Chemistry and in Mechanistic Systems Biology: A Tribute to Ivano Bertini (pages 1671–1675)

      Prof. Dr. Harald Schwalbe and Prof. Dr. Joshua Telser

      Article first published online: 9 SEP 2013 | DOI: 10.1002/cbic.201300451

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      This special issue of ChemBioChem is dedicated to the memory of the noted Italian scientist Ivano Bertini, who died in July 2012. He was known for his many contributions to both bioinorganic chemistry and magnetic resonance spectroscopy (NMR and EPR); this issue features articles by leading groups on these general topics.

  3. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Review
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Review
    1. Graphical Abstract: ChemBioChem 14/2013 (pages 1677–1684)

      Article first published online: 14 SEP 2013 | DOI: 10.1002/cbic.201390052

  4. Corrigendum

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    3. Editorial
    4. Graphical Abstract
    5. Corrigendum
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    11. Book Review
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      Corrigendum: Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis (page 1684)

      Dr. Veronika Papoušková, Dr. Pavel Kadeřávek, Olga Otrusinová, Alžbeta Rabatinová, Dr. Hana Šanderová, Jiří Nováček, Dr. Libor Krásný, Prof. Vladimír Sklenář and Dr. Lukáš Žídek

      Article first published online: 14 SEP 2013 | DOI: 10.1002/cbic.201300497

      This article corrects:

      Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis

      Vol. 14, Issue 14, 1772–1779, Article first published online: 18 JUL 2013

  5. News

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    11. Book Review
  6. Review

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    1. Biophysical Studies of the Amyloid β-Peptide: Interactions with Metal Ions and Small Molecules (pages 1692–1704)

      Dr. Sebastian Wärmländer, Dr. Ann Tiiman, Axel Abelein, Jinghui Luo, Dr. Jyri Jarvet, Dr. Kajsa L. Söderberg, Dr. Jens Danielsson and Prof. Astrid Gräslund

      Article first published online: 26 AUG 2013 | DOI: 10.1002/cbic.201300262

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      Self-aggregation of amyloid beta (Aβ) peptides is generally considered to be the cause of Alzheimer's disease. This review focuses on biophysical studies of Aβ peptide properties, including their aggregation pathways, intermediate molecular structures, and interactions with aggregation-modulating small molecules and metal ions.

  7. Highlight

    1. Top of page
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    5. Corrigendum
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    11. Book Review
    1. Detecting Intracellular Cysteine Redox States by in-Cell NMR Spectroscopy (pages 1705–1707)

      Dr. Robert Silvers and Prof. Dr. Harald Schwalbe

      Article first published online: 24 JUL 2013 | DOI: 10.1002/cbic.201300379

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      An in-cell perspective: Nowadays, in-cell NMR spectroscopy has proven to be a thrilling alternative for the investigation of biomacromolecules under physiological conditions at atomic resolution. A recent example demonstrating significant progress in in-cell NMR was published by the groups of Banci and Aricescu that investigated the post-translational maturation of human superoxide dismutase 1 (SOD1) in living human cells.

  8. Communications

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    11. Book Review
    1. A Computational Study of the Effects of 13C–13C Scalar Couplings on 13C CEST NMR Spectra: Towards Studies on a Uniformly 13C-Labeled Protein (pages 1709–1713)

      Dr. Pramodh Vallurupalli, Dr. Guillaume Bouvignies and Prof. Lewis E. Kay

      Article first published online: 19 JUN 2013 | DOI: 10.1002/cbic.201300230

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      Read the label: The NMR CEST experiment can be used to reconstruct spectra of sparsely populated, transiently formed protein conformers so long as they exchange with a highly populated ground state with rates of 20–300 s−1. Here we establish that accurate 13C chemical shifts of side-chain carbon nuclei can be obtained from uniformly 13C-labeled samples, without interference from the coupled 13C spin network.

    2. Spectroscopic and Electrochemical Characterization of the [NiFeSe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F: Reversible Redox Behavior and Interactions between Electron Transfer Centers (pages 1714–1719)

      Dr. Jana Riethausen, Dr. Olaf Rüdiger, Prof. Dr. Wolfgang Gärtner, Prof. Dr. Wolfgang Lubitz and Dr. Hannah S. Shafaat

      Article first published online: 3 SEP 2013 | DOI: 10.1002/cbic.201300120

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      Characterizing a new hydrogenase: The newly isolated [NiFeSe] hydrogenase from Desulfovibrio vulgaris Miyazaki F displays catalytic properties distinct from other hydrogenase proteins. Here we apply site-specific spectroscopic and electrochemical techniques to characterize these unique features at the molecular level.

    3. A Single-Stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme (pages 1720–1723)

      Phuong Nguyen, Dr. Xuesong Shi, Prof. Snorri Th. Sigurdsson, Prof. Daniel Herschlag and Prof. Peter Z. Qin

      Article first published online: 30 JUL 2013 | DOI: 10.1002/cbic.201300376

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      Rigid spinning: Site-directed spin-labeling studies using a rigid nitroxide spin label (Ç) reveal that both length and sequence of a single-stranded junction (J1/2) modulate nanosecond motional ordering of the substrate-recognition duplex (P1) of the 120 kD group I ribozyme. The studies demonstrate an approach for experimental measurements of nanosecond dynamics in high-molecular-weight RNA complexes.

  9. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Review
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Review
    1. Evolutionary Origins of the Photosynthetic Water Oxidation Cluster: Bicarbonate Permits Mn2+ Photo-oxidation by Anoxygenic Bacterial Reaction Centers (pages 1725–1731)

      Dr. Andrei Khorobrykh, Jyotishman Dasgupta, Dr. Derrick R. J. Kolling, Dr. Vasily Terentyev, Prof. Dr. Vyacheslav V. Klimov and Prof. Dr. G. Charles Dismukes

      Article first published online: 4 SEP 2013 | DOI: 10.1002/cbic.201300355

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      Having a bicarbonate complex: EPR spectroscopy reveals that Mn2+ can be photo-oxidized by native type II anoxygenic bacterial reaction centers (bRCs) only when it is complexed to bicarbonate, as the reaction is enabled by thermodynamic stabilization of the product, Mn3+(CO32-)bRC2. A model is proposed for how this chemistry enabled evolution of the oxygenic reaction center.

    2. Heparin Modulates the Mitogenic Activity of Fibroblast Growth Factor by Inducing Dimerization of its Receptor. A 3D View by Using NMR (pages 1732–1744)

      Dr. Lidia Nieto, Dr. Ángeles Canales, Dr. Israel S. Fernández, Dr. Elena Santillana, Dr. Rocío González-Corrochano, Dr. Mariano Redondo-Horcajo, Prof. F. Javier Cañada, Dr. Pedro Nieto, Prof. Manuel Martín-Lomas, Prof. Guillermo Giménez-Gallego and Prof. Jesús Jiménez-Barbero

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300313

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      Held together with a hairpin: A structural explanation of the modulation of FGF-driven mitogenesis by heparin and heparan sulfate is given. Full enhancement occurs when heparin is previously incubated with the receptors, which then dimerize and adopt the relative conformation present in the complete signaling complex.

    3. A Caged, Destabilized, Free Radical Intermediate in the Q-Cycle (pages 1745–1753)

      Dr. Preethi R. Vennam, Dr. Nicholas Fisher, Dr. Matthew D. Krzyaniak, Prof. David M. Kramer and Prof. Michael K. Bowman

      Article first published online: 5 SEP 2013 | DOI: 10.1002/cbic.201300265

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      Semiquinone in the Q-cycle: Formation of semiquinone in cytochrome bc1 complexes removes both substrate protons in the initial oxidation step during conformational changes of the semiquinone and Qo proteins. The resulting radical anion is kinetically trapped in a nonpolar “bottle”, conserving redox energy to drive electron transfer to cytochrome bL.

    4. Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of α-Synuclein (pages 1754–1761)

      Dr. Julien Roche, Dr. Jinfa Ying, Dr. Alexander S. Maltsev and Dr. Ad Bax

      Article first published online: 28 JUN 2013 | DOI: 10.1002/cbic.201300244

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      Feeling the pressure? The impact of variation in hydrostatic pressure, over a range of 1–2500 bar, on α-synuclein was probed at the residue-specific level by multinuclear two- and three-dimensional NMR spectroscopy. The results indicate that pressure only has minor effects on the structural propensity and dynamic behavior of the protein.

    5. Copper(II)-bis-Histidine Coordination Structure in a Fibrillar Amyloid β-Peptide Fragment and Model Complexes Revealed by Electron Spin Echo Envelope Modulation Spectroscopy (pages 1762–1771)

      Dr. Jessica Hernández-Guzmán, Dr. Li Sun, Dr. Anil K. Mehta, Dr. Jijun Dong, Prof. David G. Lynn and Prof. Kurt Warncke

      Article first published online: 6 SEP 2013 | DOI: 10.1002/cbic.201300236

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      Truncated and mutated amyloid β-peptides (Aβ) have been used to study the molecular origins of metal ion effects on Aβ aggregation rates, types of aggregate structures formed, and cytotoxicity. The 3D geometry of bis-histidine imidazole coordination of CuII in fibrils, revealed by ESEEM spectroscopy, provides possible explanations for the acceleration of fibrillization by CuII.

    6. Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis (pages 1772–1779)

      Dr. Veronika Papoušková, Dr. Pavel Kadeřávek, Olga Otrusinová, Alžbeta Rabatinová, Dr. Hana Šanderová, Jiří Nováček, Dr. Libor Krásný, Prof. Vladimír Sklenář and Dr. Lukáš Žídek

      Article first published online: 18 JUL 2013 | DOI: 10.1002/cbic.201300226

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      All in order: The structure of the ordered N-terminal domain of the RNA polymerase δ subunit was determined by using distance restraints. The structure is color-coded according to contacts with a paramagnetic label placed at cysteine 99 in the disordered C-terminal domain. The color scale ranges from blue (no contact) to orange (strongest contact).

    7. The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations (pages 1780–1788)

      Dr. Lorna J. Smith, Dr. Alice M. Bowen, Dr. Alexandre Di Paolo, Prof. Dr. André Matagne and Prof. Dr. Christina Redfield

      Article first published online: 25 JUN 2013 | DOI: 10.1002/cbic.201300193

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      Flexible lips: NMR studies, complemented by MD simulations, showed that the upper and lower lip regions in λ lysozyme are dynamic in solution containing fluctuating regions of secondary structure. This might allow the enzyme to access a range of different conformers needed for substrate binding and enzyme activity.

    8. Characterization of a Cyclic Nucleotide-Activated K+ Channel and its Lipid Environment by Using Solid-State NMR Spectroscopy (pages 1789–1798)

      Dr. Abhishek Cukkemane and Prof. Dr. Marc Baldus

      Article first published online: 16 AUG 2013 | DOI: 10.1002/cbic.201300182

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      Size does matter: By using solid-state NMR spectroscopy (ssNMR), we have structurally characterized a 4×355 residue channel, its lipid environment, and polymorphic states that might be relevant to function. This study highlights the potential of ssNMR to characterize large membrane proteins and their environments in native lipid conditions.

    9. Kinase in Motion: Insights into the Dynamic Nature of p38α by High-Pressure NMR Spectroscopic Studies (pages 1799–1806)

      Dr. Gerd Nielsen, Dr. Hendrik R. A. Jonker, Dr. Navratna Vajpai, Prof. Dr. Stephan Grzesiek and Prof. Dr. Harald Schwalbe

      Article first published online: 10 JUL 2013 | DOI: 10.1002/cbic.201300170

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      Kinase under pressure: Structural flexibility and the accessibility of excited-energy conformations throughout the structure of activated p38α are probed by a combination of high pressure and NMR spectroscopy. High pressure is shown to induce biologically relevant conformations previously only associated with binding of allosteric DFG-out ligands.

    10. Ligand Binding Promiscuity of Human Liver Fatty Acid Binding Protein: Structural and Dynamic Insights from an Interaction Study with Glycocholate and Oleate (pages 1807–1819)

      Filippo Favretto, Dr. Michael Assfalg, Dr. Mariana Gallo, Prof. Daniel Oscar Cicero, Dr. Mariapina D'Onofrio and Prof. Henriette Molinari

      Article first published online: 11 JUN 2013 | DOI: 10.1002/cbic.201300156

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      Fabulous living: Human liver FABP, an abundant cytosolic lipid carrier, has the ability to bind a variety of amphipathic molecules. NMR studies showed specific binding for glycocholate and provided structural and dynamic determinants of a promiscuous binding capability.

    11. Multi-phosphorylation of the Intrinsically Disordered Unique Domain of c-Src Studied by In-Cell and Real-Time NMR Spectroscopy (pages 1820–1827)

      Dr. Irene Amata, Mariano Maffei, Dr. Ana Igea, Dr. Marina Gay, Dr. Marta Vilaseca, Dr. Angel R. Nebreda and Prof. Dr. Miquel Pons

      Article first published online: 6 JUN 2013 | DOI: 10.1002/cbic.201300139

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      The interplay between kinases and phosphatases, in particular physiological states, determines the phosphorylation pattern of the intrinsically disordered (ID) “unique domain” of c-Src. The non-invasive character of NMR and the favorable properties of ID regions allow real-time monitoring of multiple phosphorylation events in living cells or cell extracts.

    12. Structural Characterization of Nitrosomonas europaea Cytochrome c-552 Variants with Marked Differences in Electronic Structure (pages 1828–1838)

      Dr. Mehmet Can, Jolanta Krucinska, Dr. Giorgio Zoppellaro, Dr. Niels H. Andersen, Prof. Joseph E. Wedekind, Dr. Hans-Petter Hersleth, Prof. K. Kristoffer Andersson and Prof. Kara L. Bren

      Article first published online: 31 JUL 2013 | DOI: 10.1002/cbic.201300118

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      Many roles for one residue: X-ray crystal structures of N. europaea cytochrome c-552 and of a single-deletion mutant demonstrate that one heme pocket residue influences axial ligand conformation, heme conformation, and access of water to the heme, with significant consequences for electronic structure.

    13. Mechanistic Aspects of hSOD1 Maturation from the Solution Structure of CuI-Loaded hCCS Domain 1 and Analysis of Disulfide-Free hSOD1 Mutants (pages 1839–1844)

      Prof. Lucia Banci, Dr. Francesca Cantini, Dr. Tatiana Kozyreva and Dr. Jeffrey T. Rubino

      Article first published online: 26 APR 2013 | DOI: 10.1002/cbic.201300042

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      Growing up: Superoxide dismutase 1 (SOD1), which protects cells from radical oxygen species, requires a chaperone, CCS, for maturation. The solution structure of CuI-loaded hCCS domain 1 and analysis of NMR titrations of an hSOD1 disulfide-free mutant with CuI-hCCS reveal important aspects of CCS-dependent SOD1 maturation.

    14. Investigations of Two Bidirectional Carbon Monoxide Dehydrogenases from Carboxydothermus hydrogenoformans by Protein Film Electrochemistry (pages 1845–1851)

      Vincent C.-C. Wang, Prof. Dr. Stephen W. Ragsdale and Prof. Dr. Fraser A. Armstrong

      Article first published online: 3 SEP 2013 | DOI: 10.1002/cbic.201300270

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      Electrocatalysis of CO2 reduction with minimum overpotential: CODH ICh and CODH IICh catalyse reversible and rapid interconversion between CO and CO2 on the PGE electrode. Several substrate-mimic inhibitors selectively target different redox states of the active site in CODH.

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      EPR Characterisation of the Ferrous Nitrosyl Complex Formed within the Oxygenase Domain of NO Synthase (pages 1852–1857)

      Dr. Jérôme Santolini, Dr. Amandine Maréchal, Dr. Alain Boussac and Dr. Pierre Dorlet

      Article first published online: 13 AUG 2013 | DOI: 10.1002/cbic.201300233

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      NO change: We studied the effects of temperature on the {FeNO}7 EPR spectra of two isozymes of NO synthase. Two different forms, axial and rhombic, coexist over a large range of temperature; their interconversion is not obvious, although the rhombic form exhibit clear variation of g anisotropy with temperature.

    16. Superoxide Reductase: Different Interaction Modes with its Two Redox Partners (pages 1858–1866)

      Dr. Rui M. Almeida, Prof. Paola Turano, Prof. Isabel Moura, Prof. José J. G. Moura and Dr. Sofia R. Pauleta

      Article first published online: 22 AUG 2013 | DOI: 10.1002/cbic.201300196

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      One way or another: Superoxide reductase is used by anaerobic bacteria to detoxify reactive oxygen species, reducing O2.− to H2O2 without producing molecular oxygen. The interaction of superoxide reductase from Desulfovibrio gigas with electron donors rubredoxin and desulforedoxin was characterized by using steady-state kinetics, 2D NMR titrations, and backbone relaxation measurements.

    17. The Topology, in Model Membranes, of the Core Peptide Derived from the T-Cell Receptor Transmembrane Domain (pages 1867–1875)

      Erez Matalon, Omri Faingold, Dr. Miriam Eisenstein, Prof. Yechiel Shai and Prof. Daniella Goldfarb

      Article first published online: 24 JUL 2013 | DOI: 10.1002/cbic.201300191

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      Core peptide membrane topology: We have characterized the core peptide (CP) derived from the TCRα trans-membrane domain by CD, ATR-FTIR, and EPR methods. The CP, in model membranes, was shown to be helical and to form oligomers (mostly dimers) that are parallel to the membrane plane.

    18. The Heterogeneous Structural Behavior of E7 from HPV16 Revealed by NMR Spectroscopy (pages 1876–1882)

      Eduardo O. Calçada, Prof. Isabella C. Felli, Tomáš Hošek and Prof. Roberta Pierattelli

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300172

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      Coming into focus: NMR studies of the full E7 oncoprotein construct from HPV16 reveal very heterogeneous structural and dynamic properties with a highly flexible N-terminal module and a more structured C terminus. This will enable detailed studies of the molecular basis of the highly oncogenic potential of E7 and its ability to interact with a large number of targets.

    19. EPR Relaxation-Enhancement-Based Distance Measurements on Orthogonally Spin-Labeled T4-Lysozyme (pages 1883–1890)

      Sahand Razzaghi, Evan K. Brooks, Dr. Enrica Bordignon, Prof. Dr. Wayne L. Hubbell, Dr. Maxim Yulikov and Prof. Dr. Gunnar Jeschke

      Article first published online: 14 JUN 2013 | DOI: 10.1002/cbic.201300165

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      Watch your distance: A systematic nanometer-range-distance measurement approach, applicable to diamagnetic bio-macromolecules is presented. The approach is based on orthogonal site-directed spin labeling and inversion-recovery electron paramagnetic resonance as a detection technique. Relaxation enhancement data were verified by reference distance measurements with GdIII–nitroxide double electron–electron resonance.

    20. Formation Kinetics and Structural Features of Beta-Amyloid Aggregates by Sedimented Solute NMR (pages 1891–1897)

      Prof. Dr. Ivano Bertini, Gianluca Gallo, Magdalena Korsak, Prof. Claudio Luchinat, Dr. Jiafei Mao and Dr. Enrico Ravera

      Article first published online: 2 JUL 2013 | DOI: 10.1002/cbic.201300141

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      Aβ Construction: Solid-state NMR spectroscopy was used to study sediments of soluble beta-amyloid (Aβ) assemblies obtained by ultracentrifugation (SedNMR) from a solution of free monomers. This method can be applied to address the kinetics of formation and to reveal atomic-level structural features of soluble Aβ assemblies.

    21. Theoretical Spectroscopy of the NiII Intermediate States in the Catalytic Cycle and the Activation of [NiFe] Hydrogenases (pages 1898–1905)

      Dr. Tobias Krämer, Dr. Mario Kampa, Prof. Dr. Dr. Wolfgang Lubitz, Dr. Maurice van Gastel and Prof. Dr. Frank Neese

      Article first published online: 22 MAY 2013 | DOI: 10.1002/cbic.201300104

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      Building bridges: Candidates for the Ni-SIr, Ni-SIa, and Ni-R states have been identified. The Ni-SIr and Ni-SIa states feature a water molecule loosely bound to nickel and a formally vacant bridge. For reduced Ni-R two models emerged: H2 coordinates side-on to nickel, or a hydride bridge and a protonated thiolate.

  10. Book Review

    1. Top of page
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    3. Editorial
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Review
    8. Highlight
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    10. Full Papers
    11. Book Review
    1. NMR of Biomolecules: Towards Mechanistic Systems Biology. Edited by Ivano Bertini, Kathleen S. McGreevy and Giacomo Parigi. (page 1906)

      John Christodoulou and Christopher A. Waudby

      Article first published online: 22 APR 2013 | DOI: 10.1002/cbic.201300209

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      Wiley-Blackwell, Weinheim 2012, XXXVIII+612 pp., softcover, € 99.00.—ISBN 978-3-527-32850-5

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