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Albert-Ludwigs-Universität Freiburg Institut für Biochemie

Overview
Works: 17 works in 17 publications in 2 languages and 114 library holdings
Roles: Contributor
Publication Timeline
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Most widely held works by Albert-Ludwigs-Universität Freiburg
Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (respiratory complex I) by Doris Kreuzer Dekovic( )

1 edition published in 2016 in English and held by 18 WorldCat member libraries worldwide

Über die Assemblierung des respiratorischen Komplex I in Escherichia coli by Sabrina Burschel( )

1 edition published in 2017 in German and held by 17 WorldCat member libraries worldwide

Structural characterisation of the methyltransferases SgvM and MrsA and the polyphosphate kinase MrPPK2-III by Florian Kemper( )

1 edition published in 2016 in English and held by 17 WorldCat member libraries worldwide

Resolving the ligand-binding to pattern recognition receptor for advanced glycation end products (RAGE) by Roya Tadayon( )

1 edition published in 2016 in English and held by 14 WorldCat member libraries worldwide

Abstract: The Receptor for Advanced Glycation Endproducts (RAGE) is a pattern recognition receptor and key in the innate immune response. It is a type 2 membrane protein with an ectodomain consisting of three immunoglobulin-like domains, V, C1, and C2 domain. RAGE activation triggers the initiation and perpetuation of the inflammatory response. Hyper-activation of RAGE is associated with chronic inflammatory disorders, diabetic complications, tumor outgrowth and neurodegenerative disorders. Wide varieties of structurally diverse ligands bind to RAGE and trigger intracellular signal cascades. The cellular response evoked upon RAGE-ligand interaction is dependent on the nature of the ligand, its concentration, and affinity towards the receptor. <br>In order to understand the molecular basis of receptor activation, I was studying the interaction of this unique receptor with several of its ligands. Key ligands of RAGE are Danger-Associated Molecular Pattern molecules (DAMPs) like e.g. S100A9, S100A12 and S100A8/A9. Using isothermal calorimetry, I have characterized binding of S100A9 to RAGE-VC1 tandem domain. Only the Ca2+- and Zn2+-bound form of S100A9 interacts with VC1. Analysis of the binding data suggests that the interaction at a Kd of 4 µM is largely entropy driven. Further I have characterized the interaction of S100 proteins with RAGE applying surface plasmon resonance and microscale thermophoresis. The X-ray structure of S100A9 in complex with Ca2+- and Zn2+ revealed drastic metal ion-induced conformational changes exposing hydrophobic pocket required for high-affinity RAGE binding. <br>Blocking the interaction of S100A9 with RAGE represents a promising pharmaceutical approach in the therapy of chronic inflammatory diseases. Therefore, I characterized the binding of new compounds which block S100A9-receptor interaction. I have analyzed a series of compounds from the Quinoline-3-carboxamides family (Q-compounds) by ITC and X-ray crystallography. Strikingly, all different compounds bound to the hydrophobic pocket of S100A9. The structural data presented here give first insights into the molecular mechanism of inhibition and provide the basis for the development of more potent and specific drugs in the future
The alternative NrfA of Campylobacter rectus by Simon Lukas Netzer( )

1 edition published in 2017 in English and held by 13 WorldCat member libraries worldwide

Phytoene Desaturase from Oryza sativa Oligomeric Assembly, Membrane Association and Preliminary 3D-Analysis by Sandra Sina Ellen Gemmecker( )

1 edition published in 2015 in English and held by 4 WorldCat member libraries worldwide

Abstract: Recombinant phytoene desaturase (PDS-His6) from rice was purified to near-homogeneity and shown to be enzymatically active in a biphasic, liposome-based assay system. The protein contains FAD as the sole protein-bound redox-cofactor. Benzoquinones, not replaceable by molecular oxygen, serve as a final electron acceptor defining PDS as a 15-cis-phytoene (donor):plastoquinone oxidoreductase. The herbicidal PDS-inhibitor norflurazon is capable of arresting the reaction by stabilizing the intermediary FADred, while an excess of the quinone acceptor relieves this blockage, indicating competition. The enzyme requires its homo-oligomeric association for activity. The sum of data collected through gel permeation chromatography, non-denaturing polyacrylamide electrophoresis, chemical cross-linking, mass spectrometry and electron microscopy techniques indicate that the high-order oligomers formed in solution are the basis for an active preparation. Of these, a tetramer consisting of dimers represents the active unit. This is corroborated by our preliminary X-ray structural analysis that also revealed similarities of the protein fold with the sequence-inhomologous bacterial phytoene desaturase CRTI and other oxidoreductases of the GR2-family of flavoproteins. This points to an evolutionary relatedness of CRTI and PDS yielding different carotene desaturation sequences based on homologous protein folds
Identification of a spin-coupled Mo(III) in the nitrogenase iron-molybdenum cofactor by Ragnar Björnsson( )

1 edition published in 2014 in English and held by 3 WorldCat member libraries worldwide

Abstract: Nitrogenase is the enzyme responsible for the catalytic reduction of dinitrogen (N2) to ammonia. In contrast to the industrial Haber-Bosch process that reacts N2 and H2 at high temperature and pressure, the biological reduction proceeds at ambient temperature and pressure using a complex multicomponent protein system, which utilizes eight electrons, eight protons and 16 MgATP molecules.1,2 Unraveling the structural and mechanistic details of how nature activates the strong bond of dinitrogen is of fundamental importance and this knowledge could aid in the design of better catalysts
Preparation data of the bromodomains BRD3(1), BRD3(2), BRD4(1), and BRPF1B and crystallization of BRD4(1)-inhibitor complexes by Martin Hügle( )

1 edition published in 2016 in English and held by 3 WorldCat member libraries worldwide

Abstract: This article presents detailed purification procedures for the bromodomains BRD3(1), BRD3(2), BRD4(1), and BRPF1B. In addition we provide crystallization protocols for apo BRD4(1) and BRD4(1) in complex with numerous inhibitors. The protocols described here were successfully applied to obtain affinity data by isothermal titration calorimetry (ITC) and by differential scanning fluorimetry (DSF) as well as structural characterizations of BRD4(1) inhibitor complexes (PDB codes: PDB: 4LYI, PDB: 4LZS, PDB: 4LYW, PDB: 4LZR, PDB: 4LYS, PDB: 5D24, PDB: 5D25, PDB: 5D26, PDB: 5D3H, PDB: 5D3J, PDB: 5D3L, PDB: 5D3N, PDB: 5D3P, PDB: 5D3R, PDB: 5D3S, PDB: 5D3T). These data have been reported previously and are discussed in more detail elsewhere
Comparative electronic structures of nitrogenase FeMoco and FeVco by Julian A Rees( )

1 edition published in 2017 in English and held by 3 WorldCat member libraries worldwide

Abstract: An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed
The Fe-V cofactor of vanadium nitrogenase contains an interstitial carbon atom by Julian A Rees( )

1 edition published in 2015 in English and held by 3 WorldCat member libraries worldwide

Plant-type phytoene desaturase: Functional evaluation of structural implications by Julian Koschmieder( )

1 edition published in 2017 in English and held by 3 WorldCat member libraries worldwide

The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry by Ragnar Björnsson( )

1 edition published in 2015 in English and held by 3 WorldCat member libraries worldwide

Abstract: Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe 7 MoS 9 C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evo- lution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system
Structural and functional analysis of latex clearing protein (Lcp) provides insight into the enzymatic cleavage of rubber by Lorena Ilcu( )

1 edition published in 2017 in English and held by 3 WorldCat member libraries worldwide

Abstract: Latex clearing proteins (Lcps) are rubber oxygenases that catalyse the extracellular cleavage of poly (cis-1,4-isoprene) by Gram-positive rubber degrading bacteria. Lcp of Streptomyces sp. K30 (LcpK30) is a b-type cytochrome and acts as an endo-type dioxygenase producing C20 and higher oligo-isoprenoids that difer in the number of isoprene units but have the same terminal functions, CHO-CH2- and -CH2- COCH3. Our analysis of the LcpK30 structure revealed a 3/3 globin fold with additional domains at the N- and C-termini and similarities to globin-coupled sensor proteins. The haem group of LcpK30 is ligated to the polypeptide by a proximal histidine (His198) and by a lysine residue (Lys167) as the distal axial ligand. The comparison of LcpK30 structures in a closed and in an open state as well as spectroscopic and biochemical analysis of wild type and LcpK30 muteins provided insights into the action of the enzyme during catalysis
Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement by Thomas Spatzal( )

1 edition published in 2016 in English and held by 3 WorldCat member libraries worldwide

Abstract: The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S=3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the recently revised oxidation state assignment for the molybdenum ion, providing the first spatially resolved picture of the resting-state electron distribution within FeMoco. This might provide the long-sought experimental basis for a generally accepted theoretical description of the cluster that is in line with available spectroscopic and functional data
Substrate pathways in the nitrogenase MoFe protein by experimental identification of small molecule binding sites by Christine N Morrison( )

1 edition published in 2015 in English and held by 3 WorldCat member libraries worldwide

Abstract: In the nitrogenase molybdenum-iron (MoFe) protein, we have identified five potential substrate access pathways from the protein surface to the FeMo-cofactor (the active site) or the P-cluster using experimental structures of Xe pressurized into MoFe protein crystals from Azotobacter vinelandii and Clostridium pasteurianum. Additionally, all published structures of the MoFe protein, including those from Klebsiella pneumoniae, were analyzed for the presence of nonwater, small molecules bound to the protein interior. Each pathway is based on identification of plausible routes from buried small molecule binding sites to both the protein surface and a metallocluster. Of these five pathways, two have been previously suggested as substrate access pathways. While the small molecule binding sites are not conserved among the three species of MoFe protein, residues lining the pathways are generally conserved, indicating that the proposed pathways may be accessible in all three species. These observations imply that there is unlikely a unique pathway utilized for substrate access from the protein surface to the active site; however, there may be preferred pathways such as those described here
Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking by Tobias Rumpf( )

1 edition published in 2015 in English and held by 2 WorldCat member libraries worldwide

Abstract: Sirtuins constitute a family of NAD(+)-dependent enzymes that catalyse the cleavage of various acyl groups from the epsilon-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. To date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2-ADPR-indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future
Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis by Julia Clarissa Netzer( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Abstract: Background<br><br>Methionine adenosyltransferases catalyse the synthesis of S-adenosylmethionine, a cofactor abundant in all domains of life. In contrast to the enzymes from bacteria and eukarya that show high sequence similarity, methionine adenosyltransferases from archaea diverge on the amino acid sequence level and only few conserved residues are retained.<br><br>Results<br><br>We describe the initial characterisation and the crystal structure of the methionine adenosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis. As described for other archaeal methionine adenosyltransferases the enzyme is a dimer in solution and shows high temperature stability. The overall structure is very similar to that of the bacterial and eukaryotic enzymes described, with some additional features that might add to the stability of the enzyme. Compared to bacterial and eukaryotic structures, the active site architecture is largely conserved, with some variation in the substrate/product-binding residues. A flexible loop that was not fully ordered in previous structures without ligands in the active side is clearly visible and forms a helix that leaves an entrance to the active site open.<br><br>Conclusions<br><br>The similar three-dimensional structures of archaeal and bacterial or eukaryotic methionine adenosyltransferases support that these enzymes share an early common ancestor from which they evolved independently, explaining the low similarity in their amino acid sequences. Furthermore, methionine adenosyltransferase from T. kodakarensis is the first structure without any ligands bound in the active site where the flexible loop covering the entrance to the active site is fully ordered, supporting a mechanism postulated earlier for the methionine adenosyltransferase from E. coli. The structure will serve as a starting point for further mechanistic studies and permit the generation of enzyme variants with different characteristics by rational design.<br><br>Keywords<br><br>S-Adenosylmethionine synthase - S-Adenosylmethionine - Thermostable enzyme - Archaea
 
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Alternative Names
Albert-Ludwigs-Universität Freiburg Fakultät für Chemie und Pharmazie Institut für Biochemie

Institut für Biochemie

University of Freiburg Faculty for Chemistry and Pharmacy Institute of Biochemistry

Languages
English (16)

German (1)