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Journal of Biological Inorganic Chemistry: JBIC

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https://www.readbyqxmd.com/read/29350298/contribution-of-m%C3%A3-ssbauer-spectroscopy-to-the-investigation-of-fe-s-biogenesis
#1
REVIEW
Ricardo Garcia-Serres, Martin Clémancey, Jean-Marc Latour, Geneviève Blondin
Fe/S cluster biogenesis involves a complex machinery comprising several mitochondrial and cytosolic proteins. Fe/S cluster biosynthesis is closely intertwined with iron trafficking in the cell. Defects in Fe/S cluster elaboration result in severe diseases such as Friedreich ataxia. Deciphering this machinery is a challenge for the scientific community. Because iron is a key player, 57Fe-Mössbauer spectroscopy is especially appropriate for the characterization of Fe species and monitoring the iron distribution...
January 19, 2018: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29349663/ibandronate-metal-complexes-solution-behavior-and-antiparasitic-activity
#2
Bruno Demoro, Santiago Rostán, Mauricio Moncada, Zhu-Hong Li, Roberto Docampo, Claudio Olea Azar, Juan Diego Maya, Julia Torres, Dinorah Gambino, Lucía Otero
To face the high costs of developing new drugs, researchers in both industry and academy are looking for ways to repurpose old drugs for new uses. In this sense, bisphosphonates that are clinically used for bone diseases have been studied as agents against Trypanosoma cruzi, causative parasite of Chagas disease. In this work, the development of first row transition metal complexes (M = Co2+, Mn2+, Ni2+) with the bisphosphonate ibandronate (iba, H4iba representing the neutral form) is presented. The in-solution behavior of the systems containing iba and the selected 3d metal ions was studied by potentiometry...
January 18, 2018: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29349662/roles-and-maturation-of-iron-sulfur-proteins-in-plastids
#3
REVIEW
Jonathan Przybyla-Toscano, Mélanie Roland, Frédéric Gaymard, Jérémy Couturier, Nicolas Rouhier
One reason why iron is an essential element for most organisms is its presence in prosthetic groups such as hemes or iron-sulfur (Fe-S) clusters, which are notably required for electron transfer reactions. As an organelle with an intense metabolism in plants, chloroplast relies on many Fe-S proteins. This includes those present in the electron transfer chain which will be, in fact, essential for most other metabolic processes occurring in chloroplasts, e.g., carbon fixation, nitrogen and sulfur assimilation, pigment, amino acid, and vitamin biosynthetic pathways to cite only a few examples...
January 18, 2018: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29299674/kinetic-and-spectroscopic-characterization-of-tungsten-substituted-dmso-reductase-from-rhodobacter-sphaeroides
#4
Josué Pacheco, Dimitri Niks, Russ Hille
We have examined the kinetic and spectroscopic properties of a tungsten-substituted form of DMSO reductase from Rhodobacter sphaeroides, an enzyme that normally possesses molybdenum. Partial reduction with sodium dithionite yields a well-resolved W(V) EPR signal of the so-called "high-g split" type that exhibits markedly greater g-anisotropy than the corresponding Mo(V) signal of the native form of the enzyme, with the g values shifted to higher magnetic field by as much as Δgave = 0.056. Deuteration of the enzyme confirms that the coupled proton is solvent-exchangeable, allowing us to accurately simulate the tungsten hyperfine coupling...
January 3, 2018: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29290009/the-ph-dependent-activation-mechanism-of-ser102-in-escherichia-coli-alkaline-phosphatase-a-theoretical-study
#5
Hao Zhang, Ling Yang, Wanjian Ding, Yingying Ma
The accepted catalytic mechanism of alkaline phosphatases was established on the hypothesis that Mg-coordinated water is a readily available hydroxide ion that functions as a general base and accepts a proton from the Ser102 hydroxyl group. The roles of the two distinctive residues Asp153 and Lys328 in Escherichia coli alkaline phosphatase (ECAP), which distinguish it from the mammalian enzymes, are elusive. Based on the crystal structures of ECAP in the absence and presence of inorganic phosphate, we have investigated the activation of Ser102 for nucleophilic attack and the subsequent formation of a covalent phosphoseryl intermediate using hybrid density functional theory (DFT) with the B3LYP functional...
December 30, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29282552/combined-qm-mm-and-monte-carlo-study-for-redox-leveling-in-mn-and-fe-superoxide-dismutase
#6
Muhamed Amin, Zainab Mohamed, Mohamed El-Sayed, Asmaa Samy, Afnan Sultan, Mahmoud Bassuoni, Mohamed H Alkordi
Superoxide dismutases (SOD) are vital enzymes for disproportionation of superoxide molecules in mammals. Despite the high similarity between the Mn-SOD and Fe-SOD, they are inactive if the metals in the active sites are exchanged. Here, we use DFT, QM/MM and Monte Carlo sampling to optimize the crystal structure and to calculate the mid-point potential for the native and substituted Mn/Fe-SOD. The optimized DFT and QM/MM structures of the Mn-SOD show a major conformational change for the conserved TYR34 compared to the X-ray structure...
December 27, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29280002/iron-sulfur-clusters-biogenesis-by-the-suf-machinery-close-to-the-molecular-mechanism-understanding
#7
REVIEW
J Pérard, Sandrine Ollagnier de Choudens
Iron-sulfur clusters (Fe-S) are amongst the most ancient and versatile inorganic cofactors in nature which are used by proteins for fundamental biological processes. Multiprotein machineries (NIF, ISC, SUF) exist for Fe-S cluster biogenesis which are mainly conserved from bacteria to human. SUF system (sufABCDSE operon) plays a general role in many bacteria under conditions of iron limitation or oxidative stress. In this mini-review, we will summarize the current understanding of the molecular mechanism of Fe-S biogenesis by SUF...
December 26, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29270817/the-crystal-structure-of-z-dna-with-untypically-coordinated-ca2-ions
#8
Zhipu Luo, Zbigniew Dauter
DNA oligomer duplexes with alternating cytosines and guanines in their sequence tend to form helices of the Z-DNA type, where the sugar and phosphate backbone forms a left-handed helix in a zigzag fashion with a repeat of two successive Watson-Crick pairs of nucleotides. Z-DNA duplexes often crystallize in complexes with diverse metal ions interacting with polar DNA atoms in various ways. This work describes the high-resolution crystal structure of a Z-DNA d(CGCGCG)2 duplex in complex with Ca2+ ions, unusually coordinated as an approximate pentagonal bipyramid by two neighboring guanines through their O6 and N7 atoms and a water molecule in the equatorial plane and a phosphate oxygen atom and another water molecule in the apical positions...
December 21, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29264659/investigation-of-glutathione-derived-electrostatic-and-hydrogen-bonding-interactions-and-their-role-in-defining-grx5-2fe-2s-cluster-optical-spectra-and-transfer-chemistry
#9
Sambuddha Sen, Claudia Bonfio, Sheref S Mansy, J A Cowan
Human glutaredoxin 5 (Grx5) is one of the core components of the Isc (iron-sulfur cluster) assembly and trafficking machinery, and serves as an intermediary cluster carrier, putatively delivering cluster from the Isu scaffold protein to target proteins. The tripeptide glutathione is intimately involved in this role, providing cysteinyl coordination to the iron center of the Grx5-bound [2Fe-2S] cluster. Grx5 has a well-defined glutathione-binding pocket with protein amino acid residues providing many ionic and hydrogen binding contacts to the bound glutathione...
December 20, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29260327/cytotoxicity-in-vitro-cellular-uptake-localization-and-apoptotic-mechanism-studies-induced-by-ruthenium-ii-complex
#10
Jincan Chen, Yao Zhang, Guodong Li, Fa Peng, Xinming Jie, Ji She, Guangzhi Dongye, Zhilin Zou, Shiwen Rong, Lanmei Chen
Ruthenium-based complexes have been regarded as one of the most potential metal-based candidates for anticancer therapy. Herein, two ruthenium (II) methylimidazole complexes [Ru(MeIm)4(4npip)]2+ (complex 1) and [Ru(MeIm)4(4mopip)]2+ (complex 2) were synthesized and evaluated for their in vitro anticancer activities. The results showed that these ruthenium (II) methylimidazole complexes exhibited moderate antitumor activity comparable with cisplatin against A549, NCI-H460, MCF-7 and HepG2 human cancer cells, but with less toxicity to a human normal cell line HBE...
December 19, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218642/porphyrin-polymer-nanocompartments-singlet-oxygen-generation-and-antimicrobial-activity
#11
Angelo Lanzilotto, Myrto Kyropoulou, Edwin C Constable, Catherine E Housecroft, Wolfgang P Meier, Cornelia G Palivan
A new water-soluble photocatalyst for singlet oxygen generation is presented. Its absorption extends to the red part of the spectrum, showing activity up to irradiation at 660 nm. Its efficiency has been compared to that of a commercial analogue (Rose Bengal) for the oxidation of L-methionine. The quantitative and selective oxidation was promising enough to encapsulate the photocatalyst in polymersomes. The singlet oxygen generated in this way can diffuse and remain active for the oxidation of L-methionine outside the polymeric compartment...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218641/mixed-guanine-adenine-base-quartets-possible-roles-of-protons-and-metal-ions-in-their-stabilization
#12
Dominik A Megger, Patrick M Lax, Jeroen Paauwe, Célia Fonseca Guerra, Bernhard Lippert
Structural variations of the well-known guanine quartet (G4) motif in nucleic acid structures, namely substitution of two guanine bases (G) by two adenine (A) nucleobases in mutual trans positions, are discussed and studied by density functional theory (DFT) methods. This work was initiated by three findings, namely (1) that GA mismatches are compatible with complementary pairing patterns in duplex-DNA structures and can, in principle, be extended to quartet structures, (2) that GA pairs can come in several variations, including with a N1 protonated adeninium moiety (AH), and (3) that cross-linking of the major donor sites of purine nucleobases (N1 and N7) by transition metal ions of linear coordination geometries produces planar purine quartets, as demonstrated by some of us in the past...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218640/oxoiron-iv-complexes-as-synthons-for-the-assembly-of-heterobimetallic-centers-such-as-the-fe-mn-active-site-of-class-ic-ribonucleotide-reductases
#13
Ang Zhou, Patrick M Crossland, Apparao Draksharapu, Andrew J Jasniewski, Scott T Kleespies, Lawrence Que
Nonheme oxoiron(IV) complexes can serve as synthons for generating heterobimetallic oxo-bridged dimetal complexes by reaction with divalent metal complexes. The formation of FeIII-O-CrIII and FeIII-O-MnIII complexes is described herein. The latter complexes may serve as models for the FeIII-X-MnIII active sites of an emerging class of Fe/Mn enzymes represented by the Class 1c ribonucleotide reductase from Chlamydia trachomatis and the R2-like ligand-binding oxidase (R2lox) found in Mycobacterium tuberculosis...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218639/histidine-tracts-in-human-transcription-factors-insight-into-metal-ion-coordination-ability
#14
Aleksandra Hecel, Joanna Wątły, Magdalena Rowińska-Żyrek, Jolanta Świątek-Kozłowska, Henryk Kozłowski
Consecutive histidine repeats are chosen both by nature and by molecular biologists due to their high affinity towards metal ions. Screening of the human genome showed that transcription factors are extremely rich in His tracts. In this work, we examine two of such His-rich regions from forkhead box and MAFA proteins-MB3 (contains 18 His) and MB6 (with 21 His residues), focusing on the affinity and binding modes of Cu2+ and Zn2+ towards the two His-rich regions. In the case of Zn2+ species, the availability of imidazole nitrogen donors enhances metal complex stability...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218638/celebrating-helmut-sigel
#15
EDITORIAL
Eva Freisinger, Roland K O Sigel
No abstract text is available yet for this article.
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218637/specific-phosphorothioate-substitution-within-domain-6-of-a-group-ii-intron-ribozyme-leads-to-changes-in-local-structure-and-metal-ion-binding
#16
Michèle C Erat, Emina Besic, Michael Oberhuber, Silke Johannsen, Roland K O Sigel
Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218636/incorporation-of-second-coordination-sphere-d-amino-acids-alters-cd-ii-geometries-in-designed-thiolate-rich-proteins
#17
Leela Ruckthong, Aniruddha Deb, Lars Hemmingsen, James E Penner-Hahn, Vincent L Pecoraro
We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) n -G-NH2], where n = 4 is TRI and n = 5 is GRAND, one L-Leu may be substituted by L-Cys to generate a planar tris-thiolate array capable of metal binding...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218635/long-range-paramagnetic-nmr-data-can-provide-a-closer-look-on-metal-coordination-in-metalloproteins
#18
Linda Cerofolini, Tommaso Staderini, Stefano Giuntini, Enrico Ravera, Marco Fragai, Giacomo Parigi, Roberta Pierattelli, Claudio Luchinat
Paramagnetic NMR data can be profitably incorporated in structural refinement protocols of metalloproteins or metal-substituted proteins, mostly as distance or angle restraints. However, they could in principle provide much more information, because the magnetic susceptibility of a paramagnetic metal ion is largely determined by its coordination sphere. This information can in turn be used to evaluate changes occurring in the coordination sphere of the metal when ligands (e.g.: inhibitors) are bound to the protein...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218634/walking-the-seven-lines-binuclear-copper-a-in-cytochrome-c-oxidase-and-nitrous-oxide-reductase
#19
REVIEW
Peter M H Kroneck
The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N2O to N2 in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O2 to H2O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu1...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218633/characterization-of-the-one-electron-oxidized-cu-ii-salen-complexes-with-a-side-chain-aromatic-ring-the-effect-of-the-indole-ring-on-the-cu-ii-phenoxyl-radical-species
#20
Hiromi Oshita, Takayoshi Yoshimura, Seiji Mori, Fumito Tani, Yuichi Shimazaki, Osamu Yamauchi
To gain insights into the role of the proximal indole ring in the redox-active metal center as seen in galactose oxidase, we prepared the Cu(II)-salen-type complexes having a pendent indol-3-ylmethyl (1), methyl (2) or benzyl (3) group substituted on the ethylenediamine moiety and investigated the structures and redox properties by various physicochemical methods and theoretical calculations. Neutral complexes 1, 2, and 3 showed no significant difference in the UV-Vis-NIR and EPR spectra. One-electron oxidation of 1, 2, and 3 by addition of 1 equiv...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
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