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Journal articles on the topic 'Non-OR copper binding site'

Author: Grafiati

Published: 14 March 2023

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1

Erales, Jenny, Brigitte Gontero, Julian Whitelegge, and Frédéric Halgand. "Mapping of a copper-binding site on the small CP12 chloroplastic protein of Chlamydomonas reinhardtii using top-down mass spectrometry and site-directed mutagenesis." Biochemical Journal 419, no. 1 (2009): 75–86. http://dx.doi.org/10.1042/bj20082004.

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CP12 is a small chloroplastic protein involved in the Calvin cycle that was shown to bind copper, a metal ion that is involved in the transition of CP12 from a reduced to an oxidized state. In order to describe CP12's copper-binding properties, copper-IMAC experiments and site-directed mutagenesis based on computational modelling, were coupled with top-down MS [electrospray-ionization MS and MS/MS (tandem MS)]. Immobilized-copper-ion-affinity-chromatographic experiments allowed the primary characterization of the effects of mutation on copper binding. Top-down MS/MS experiments carried out und

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2

McArdle, H. J., S. M. Gross, D. M. Danks, and A. G. Wedd. "Role of albumin's copper binding site in copper uptake by mouse hepatocytes." American Journal of Physiology-Gastrointestinal and Liver Physiology 258, no. 6 (1990): G988—G991. http://dx.doi.org/10.1152/ajpgi.1990.258.6.g988.

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It is possible, in vitro, to label albumin with copper either exclusively on the specific binding site or partly on the specific site and also on other sites by altering the pH at which the two ligands are mixed. Copper attached exclusively to the specific site is taken up more rapidly than copper attached to that site and others on albumin. The effect is proportional to the amount of copper on the specific site. Additional histidine stimulates uptake irrespective of the copper binding site on albumin. The effect is related to the histidine on position 3 of the albumin, since it is not seen wh

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3

Cater, Michael A., Sharon La fontaine, and Julian F. B. Mercer. "Copper binding to the N-terminal metal-binding sites or the CPC motif is not essential for copper-induced trafficking of the human Wilson protein (ATP7B)." Biochemical Journal 401, no. 1 (2006): 143–53. http://dx.doi.org/10.1042/bj20061055.

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The Wilson protein (ATP7B) is a copper-translocating P-type ATPase that mediates the excretion of excess copper from hep-atocytes into bile. Excess copper causes the protein to traffic from the TGN (trans-Golgi network) to subapical vesicles. Using site-directed mutagenesis, mutations known or predicted to abrogate catalytic activity (copper translocation) were introduced into ATP7B and the effect of these mutations on the intracellular traf-ficking of the protein was investigated. Mutation of the critical aspartic acid residue in the phosphorylation domain (DKTGTIT) blocked copper-induced red

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4

Calabrese, L., and M. Carbonaro. "An e.p.r. study of the non-equivalence of the copper sites of caeruloplasmin." Biochemical Journal 238, no. 1 (1986): 291–95. http://dx.doi.org/10.1042/bj2380291.

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The two Type 1 (blue) copper-binding sites of caeruloplasmin were spectroscopically differentiated by the kinetic analysis of the e.p.r. spectra during the redox cycle. One blue copper, with a hyperfine splitting constant (A parallel) of 6.8 mT, which was rapidly reduced, was not reoxidized by oxygen, whereas it was reoxidized by H2O2. The other blue copper (A parallel = 5.8 mT), which was reduced slowly, was rapidly reoxidized by either oxygen or H2O2. A conformational change of the Type 2 copper was concomitant with the fast reduction of Type 1 copper, whereas its reduction occurred during t

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5

Sinopoli, Alessandro, Antonio Magrì, Danilo Milardi, et al. "The role of copper(ii) in the aggregation of human amylin." Metallomics 6, no. 10 (2014): 1841–52. http://dx.doi.org/10.1039/c4mt00130c.

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Copper(ii) coordination to human amylin has an influence on the aggregation and cytotoxic features of the polypeptide. Comparative investigations, carried out on a model peptide encompassing the 17–29 aminoacid region of amylin containing the putative metal binding site, support the non-fibrillar nature of the copper(ii) complexes.

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6

Kekez, Ivana, Mihovil Faletar, Mario Kekez, et al. "Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori." Molecules 27, no. 11 (2022): 3387. http://dx.doi.org/10.3390/molecules27113387.

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Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, r

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7

NAKAMURA, Motoyoshi, Tasuku NAKAJIMA, Yasunori OHBA, Seigo YAMAUCHI, Byung Rho LEE, and Eiji ICHISHIMA. "Identification of copper ligands in Aspergillus oryzae tyrosinase by site-directed mutagenesis." Biochemical Journal 350, no. 2 (2000): 537–45. http://dx.doi.org/10.1042/bj3500537.

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Copper ligands of the recombinant tyrosinase from the fungus Aspergillus oryzae expressed in Saccharomyces cerevisiae or Escherichia coli were identified by site-directed mutagenesis. The recombinant protyrosinases expressed in S. cerevisiae were assayed for catalytic activities of mono-oxygenase and L-dopa oxidase at pH 5.5 after acid shock at pH 3.0. Replacements of His-63, His-84, His-93, His-290, His-294, His-332 or His-333 with asparagine resulted in mutant enzymes exhibiting no activities. The site-directed mutant Cys82Ala showed that Cys-82 was also an essential residue for the activity

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8

Maghool, Shadi, Michael T. Ryan, and Megan J. Maher. "What Role Does COA6 Play in Cytochrome C Oxidase Biogenesis: A Metallochaperone or Thiol Oxidoreductase, or Both?" International Journal of Molecular Sciences 21, no. 19 (2020): 6983. http://dx.doi.org/10.3390/ijms21196983.

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Complex IV (cytochrome c oxidase; COX) is the terminal complex of the mitochondrial electron transport chain. Copper is essential for COX assembly, activity, and stability, and is incorporated into the dinuclear CuA and mononuclear CuB sites. Multiple assembly factors play roles in the biogenesis of these sites within COX and the failure of this intricate process, such as through mutations to these factors, disrupts COX assembly and activity. Various studies over the last ten years have revealed that the assembly factor COA6, a small intermembrane space-located protein with a twin CX9C motif,

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9

D’Angelo, Paola, Stefano Della Longa, Alessandro Arcovito, et al. "Effects of the Pathological Q212P Mutation on Human Prion Protein Non-Octarepeat Copper-Binding Site." Biochemistry 51, no. 31 (2012): 6068–79. http://dx.doi.org/10.1021/bi300233n.

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10

Eakin, Catherine M., Jefferson D. Knight, Charles J. Morgan, Michael A. Gelfand та Andrew D. Miranker. "Formation of a Copper Specific Binding Site in Non-Native States of β-2-Microglobulin†". Biochemistry 41, № 34 (2002): 10646–56. http://dx.doi.org/10.1021/bi025944a.

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11

Attar, Narsis, Oscar A. Campos, Maria Vogelauer, et al. "The histone H3-H4 tetramer is a copper reductase enzyme." Science 369, no. 6499 (2020): 59–64. http://dx.doi.org/10.1126/science.aba8740.

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Eukaryotic histone H3-H4 tetramers contain a putative copper (Cu2+) binding site at the H3-H3′ dimerization interface with unknown function. The coincident emergence of eukaryotes with global oxygenation, which challenged cellular copper utilization, raised the possibility that histones may function in cellular copper homeostasis. We report that the recombinant Xenopus laevis H3-H4 tetramer is an oxidoreductase enzyme that binds Cu2+ and catalyzes its reduction to Cu1+ in vitro. Loss- and gain-of-function mutations of the putative active site residues correspondingly altered copper binding and

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12

Watmough, Nicholas J., Sarah J. Field, Ross J. L. Hughes, and David J. Richardson. "The bacterial respiratory nitric oxide reductase." Biochemical Society Transactions 37, no. 2 (2009): 392–99. http://dx.doi.org/10.1042/bst0370392.

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The two-subunit cytochrome bc complex (NorBC) isolated from membranes of the model denitrifying soil bacterium Paracoccus denitrificans is the best-characterized example of the bacterial respiratory nitric oxide reductases. These are members of the super-family of haem-copper oxidases and are characterized by the elemental composition of their active site, which contains non-haem iron rather than copper, at which the reductive coupling of two molecules of nitric oxide to form nitrous oxide is catalysed. The reaction requires the presence of two substrate molecules at the active site along with

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13

DiSpirito, Alan A., Jeremy D. Semrau, J. Colin Murrell, Warren H. Gallagher, Christopher Dennison, and Stéphane Vuilleumier. "Methanobactin and the Link between Copper and Bacterial Methane Oxidation." Microbiology and Molecular Biology Reviews 80, no. 2 (2016): 387–409. http://dx.doi.org/10.1128/mmbr.00058-15.

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SUMMARYMethanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a

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14

Marx, G., and M. Chevion. "Site-specific modification of albumin by free radicals. Reaction with copper(II) and ascorbate." Biochemical Journal 236, no. 2 (1986): 397–400. http://dx.doi.org/10.1042/bj2360397.

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Exposure of albumin to Cu(II) (10-100 microM) and ascorbate (0.1-2 mM) results in extensive molecular modifications, indicated by decreased fluorescence and chain breaks. The rate of utilization of molecular oxygen and ascorbate as a function of Cu(II) concentration is non-linear at copper/albumin ratios of greater than 1. It appears that Cu(II) bound to the tightest albumin-binding site is less available to the ascorbate than the more loosely bound cation. SDS/polyacrylamide-gel electrophoresis reveals new protein bands corresponding to 50, 47, 22, 18 and 3 kDa. For such a cleavage pattern, r

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15

SOLANO, Francisco, Celia JIMÉNEZ-CERVANTES, José H. MARTÍNEZ-LIARTE, José C. GARCÍA-BORRÓN, José R. JARA, and José A. LOZANO. "Molecular mechanism for catalysis by a new zinc-enzyme, dopachrome tautomerase." Biochemical Journal 313, no. 2 (1996): 447–53. http://dx.doi.org/10.1042/bj3130447.

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Dopachrome tautomerase (DCT; EC 5.3.3.12) catalyses the conversion of L-dopachrome into 5,6-dihydroxyindole-2-carboxylic acid in the mammalian eumelanogenic biosynthetic pathway. This enzyme, also named TRP2, belongs to a family of three metalloenzymes termed the tyrosinase-related proteins (TRPs). It is well known that tyrosinase has copper in its active site. However, the nature of the metal ion in the active site of DCT is under discussion. Whereas theoretical predictions based on similarity between the protein sequences of the TRPs suggest the presence of copper, the different inhibition p

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16

Percival, S. S., and E. D. Harris. "Regulation of Cu,Zn superoxide dismutase with copper. Caeruloplasmin maintains levels of functional enzyme activity during differentiation of K562 cells." Biochemical Journal 274, no. 1 (1991): 153–58. http://dx.doi.org/10.1042/bj2740153.

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K562 cells, a human erythroleukaemic cell line blocked for differentiation, commit towards erythrocytes when exposed to haemin (20 microM). The cells synthesize fetal haemoglobins and show site-specific binding of caeruloplasmin, a plasma copper protein. These events are set into motion by haemin. On the assumption that the binding of caeruloplasmin could reflect a greater need for copper, we sought to determine whether the transfer of 67Cu from caeruloplasmin was accelerated in haemin-induced compared with non-induced K562 cells. Cu,Zn superoxide dismutase (CuZnSOD) was the recipient. Haemin

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17

Giangregorio, Nicola, Annamaria Tonazzi, Lara Console, et al. "Effect of Copper on the Mitochondrial Carnitine/Acylcarnitine Carrier Via Interaction with Cys136 and Cys155. Possible Implications in Pathophysiology." Molecules 25, no. 4 (2020): 820. http://dx.doi.org/10.3390/molecules25040820.

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The effect of copper on the mitochondrial carnitine/acylcarnitine carrier (CAC) was studied. Transport function was assayed as [3H]carnitine/carnitine antiport in proteoliposomes reconstituted with the native protein extracted from rat liver mitochondria or with the recombinant CAC over-expressed in E. coli. Cu2+ (as well as Cu+) strongly inhibited the native transporter. The inhibition was reversed by GSH (reduced glutathione) or by DTE (dithioerythritol). Dose-response analysis of the inhibition of the native protein was performed from which an IC50 of 1.6 µM for Cu2+ was derived. The mechan

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18

Jaenicke, Elmar, Kay Büchler, Jürgen Markl, Heinz Decker, and Thomas R. M. Barends. "Cupredoxin-like domains in haemocyanins." Biochemical Journal 426, no. 3 (2010): 373–78. http://dx.doi.org/10.1042/bj20091501.

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Haemocyanins are multimeric oxygen transport proteins, which bind oxygen to type 3 copper sites. Arthropod haemocyanins contain 75-kDa subunits, whereas molluscan haemocyanins contain 350–400-kDa subunits comprising seven or eight different 50 kDa FUs (functional units) designated FU-a to FU-h, each with an active site. FU-h possesses a tail of 100 amino acids not present in the other FUs. In the present study we show by X-ray crystallography that in FU-h of KLH1 (keyhole-limpet-haemocyanin isoform 1) the structure of the tail domain is cupredoxin-like but contains no copper. The copper-free d

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19

Martins, Lucas Sousa, Jerônimo Lameira, Hendrik G. Kruger, Cláudio Nahum Alves, and José Rogério A. Silva. "Evaluating the Performance of a Non-Bonded Cu2+ Model Including Jahn−Teller Effect into the Binding of Tyrosinase Inhibitors." International Journal of Molecular Sciences 21, no. 13 (2020): 4783. http://dx.doi.org/10.3390/ijms21134783.

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Tyrosinase (TYR) is a metalloenzyme classified as a type-3 copper protein, which is involved in the synthesis of melanin through a catalytic process beginning with the conversion of the amino acid l-Tyrosine (l-Tyr) to l-3,4-dihydroxyphenylalanine (l-DOPA). It plays an important role in the mechanism of melanogenesis in various organisms including mammals, plants, and fungi. Herein, we used a combination of computational molecular modeling techniques including molecular dynamic (MD) simulations and the linear interaction energy (LIE) model to evaluate the binding free energy of a set of analog

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20

Khalil, Abdelouahed, та Tamàs Fülöp. "A comparison of the kinetics of low-density lipoprotein oxidation induced by copper or by γ-rays: Influence of radiation dose-rate and copper concentration". Canadian Journal of Physiology and Pharmacology 79, № 2 (2001): 114–21. http://dx.doi.org/10.1139/y00-080.

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The oxidation of low-density lipoproteins is the first step in the complex process leading to atherosclerosis. The aim of our study was to compare the kinetics of low density lipoprotein oxidation induced by copper ions or by oxygen free radicals generated by60Co γ-rays. The effects of copper concentration and irradiation dose-rate on LDL peroxidation kinetics were also studied. The oxidation of LDL was followed by the measurement of conjugated diene, hydroperoxides, and thiobarbituric acid reactive substance formation as well as α-tocopherol disappearance. In the case of gamma irradiation, th

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21

Varfolomeeva, Larisa A., Anastasia Yu Solovieva, Nikolai S. Shipkov, et al. "Probing the Role of a Conserved Phenylalanine in the Active Site of Thiocyanate Dehydrogenase." Crystals 12, no. 12 (2022): 1787. http://dx.doi.org/10.3390/cryst12121787.

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Copper-containing enzymes catalyze a broad spectrum of redox reactions. Thiocyanate dehydrogenase (TcDH) from Thioalkalivibrio paradoxus Arh1 enables the bacterium to use thiocyanate as a unique source of energy and nitrogen. Oxidation of thiocyanate takes place in the trinuclear copper center of TcDH with peculiar organization. Despite the TcDH crystal structure being established, a role of some residues in the enzyme active site has yet to be obscured. F436 residue is located in the enzyme active site and conserved among a number of TcDH homologs, however, its role in the copper center forma

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22

Baek, Seung-Hun, Angela Hartsock, and James P. Shapleigh. "Agrobacterium tumefaciens C58 Uses ActR and FnrN To Control nirK and nor Expression." Journal of Bacteriology 190, no. 1 (2007): 78–86. http://dx.doi.org/10.1128/jb.00792-07.

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ABSTRACT Agrobacterium tumefaciens can grow anaerobically via denitrification. To learn more about how cells regulate production of nitrite and nitric oxide, experiments were carried out to identify proteins involved in regulating expression and activity of nitrite and nitric oxide reductase. Transcription of NnrR, required for expression of these two reductases, was found to be under control of FnrN. Insertional inactivation of the response regulator actR significantly reduced nirK expression and Nir activity but not nnrR expression. Purified ActR bound to the nirK promoter but not the nor or

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23

Brouwer, M., T. Hoexum-Brouwer, and R. E. Cashon. "A putative glutathione-binding site in CdZn-metallothionein identified by equilibrium binding and molecular-modelling studies." Biochemical Journal 294, no. 1 (1993): 219–25. http://dx.doi.org/10.1042/bj2940219.

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Glutathione (GSH) has been found to form a complex with both vertebrate and invertebrate copper-metallothionein (CuMT) [Freedman, Ciriolo and Peisach (1989) J. Biol. Chem. 264, 5598-5605; Brouwer and Brouwer-Hoexum (1991) Arch. Biochem. Biophys. 290, 207-213]. In this paper we report on the interaction of GSH with CdZnMT-I and CdZnMT-II from rabbit liver and with CdMT-I from Blue crab hepatopancreas. Ultrafiltration experiments showed that all three MTs combined with GSH. The measured binding data for the three MTs could be described by a single binding isotherm. The GSH/MT stoichiometry was 1

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Georgieva, Dessislava Nikolova, Stanka Stoeva, Wolfgang Voelter, and Nicolay Genov. "Viviparus ater Hemocyanin: Investigation of the Dioxygen-Binding Site and Stability of the Oxy- and Apo-Forms." Zeitschrift für Naturforschung C 56, no. 9-10 (2001): 843–47. http://dx.doi.org/10.1515/znc-2001-9-1027.

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Abstract The active site of Viviparus ater (mollusc) hemocyanin was investigated using the fact that the binding of dioxygen to the binuclear copper-containing sites of hemocyanins is connected with the appearance of specific dichroic bands which are very sensitive to changes in the structrure and polarity of the environment. Oxy-Viviparus ater hemocyanin exhibits near UV and visible circular dichroism spectra different from those of other molluscan and arthropo-dan hemocyanins. These differences are due probably to variations in the geometry or charge distribution in the dioxygen binding site

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25

Boyd, Stefanie D., Morgan S. Ullrich, Jenifer S. Calvo, Fatemeh Behnia, Gabriele Meloni, and Duane D. Winkler. "Mutations in Superoxide Dismutase 1 (Sod1) Linked to Familial Amyotrophic Lateral Sclerosis Can Disrupt High-Affinity Zinc-Binding Promoted by the Copper Chaperone for Sod1 (Ccs)." Molecules 25, no. 5 (2020): 1086. http://dx.doi.org/10.3390/molecules25051086.

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Zinc (II) ions (hereafter simplified as zinc) are important for the structural and functional activity of many proteins. For Cu, Zn superoxide dismutase (Sod1), zinc stabilizes the native structure of each Sod1 monomer, promotes homo-dimerization and plays an important role in activity by “softening” the active site so that copper cycling between Cu(I) and Cu(II) can rapidly occur. Previously, we have reported that binding of Sod1 by its copper chaperone (Ccs) stabilizes a conformation of Sod1 that promotes site-specific high-affinity zinc binding. While there are a multitude of Sod1 mutations

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26

Wang, Jiou, Hilda Slunt, Victoria Gonzales, et al. "Copper-binding-site-null SOD1 causes ALS in transgenic mice: aggregates of non-native SOD1 delineate a common feature." Human Molecular Genetics 12, no. 21 (2003): 2753–64. http://dx.doi.org/10.1093/hmg/ddg312.

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Wakabayashi, Hironao, Qian Zhou, Keiji Nogami, and Philip J. Fay. "Effects of Single Point Mutations within Proposed Copper Binding Sites on Specific Activity and Inter-Chain Affinity of Factor VIII." Blood 104, no. 11 (2004): 1730. http://dx.doi.org/10.1182/blood.v104.11.1730.1730.

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Abstract Copper ions appear important for the structural integrity and the function of factor VIII. Reconstitution studies have shown that Cu2+ increases specific activity of factor VIII as well as increases affinity between heavy chain (HC) and light chain (LC). Based on the ceruloplasmin homology, the existence of three Cu2+ binding sites has been proposed. These include a type 1 site in HC (A1 domain) coordinated by C310, H315, H267, and M320, a type 1 site in LC (A3 domain) coordinated by C2000, H1954, H2005, and M2010, and type 2 site spanning A1 and A3 domains coordinated by H99 and H195

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28

Brauchli, Sven Y., Frederik J. Malzner, Edwin C. Constable, and Catherine E. Housecroft. "Copper(i)-based dye-sensitized solar cells with sterically demanding anchoring ligands: bigger is not always better." RSC Advances 5, no. 60 (2015): 48516–25. http://dx.doi.org/10.1039/c5ra07449e.

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DSC performances of [Cu(N⁁N<sub>anchor</sub>)(N⁁N<sub>ancillary</sub>)]<sup>+</sup> dyes with Ph or Me groups adjacent to the copper-binding site in N⁁N<sub>anchor</sub> are compared; electrodes with dyes that bleach are regenerated by reimmersion in dye baths containing N⁁N<sub>anchor</sub>.

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Faraco, Vincenza, Paola Giardina, and Giovanni Sannia. "Metal-responsive elements in Pleurotus ostreatus laccase gene promoters." Microbiology 149, no. 8 (2003): 2155–62. http://dx.doi.org/10.1099/mic.0.26360-0.

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Fungal laccase gene transcription is strongly induced by copper ions; notably, some laccase promoters contain multiple putative metal-responsive elements (MREs). Previously, it has been demonstrated that the Pleurotus ostreatus laccase genes poxc and poxa1b are transcriptionally induced by copper, and several putative MREs were found in the promoter regions of these genes, which extend for about 400 nt upstream of the start codon (ATG). Identification of MRE sequences, which are protected by protein binding in the poxc and poxa1b promoter regions, has been achieved by footprinting analyses. El

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CATER, Michael A., John FORBES, Sharon La FONTAINE, Diane COX, and Julian F. B. MERCER. "Intracellular trafficking of the human Wilson protein: the role of the six N-terminal metal-binding sites." Biochemical Journal 380, no. 3 (2004): 805–13. http://dx.doi.org/10.1042/bj20031804.

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The Wilson protein (ATP7B) is a copper-transporting CPx-type ATPase defective in the copper toxicity disorder Wilson disease. In hepatocytes, ATP7B delivers copper to apo-ceruloplasmin and mediates the excretion of excess copper into bile. These distinct functions require the protein to localize at two different subcellular compartments. At the trans-Golgi network, ATP7B transports copper for incorporation into apo-ceruloplasmin. When intracellular copper levels are increased, ATP7B traffics to post-Golgi vesicles in close proximity to the canalicular membrane to facilitate biliary copper excr

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31

Jureschi, Monica, Brindusa Alina Petre, Laura Ion, Catalina Ionica Ciobanu, Ion Sandu, and Gabi Drochioiu. "Synthesis of Different Analogs of Ab(9-16) Peptide Mass spectrometric evidence for heavy metal binding." Revista de Chimie 70, no. 9 (2019): 3348–53. http://dx.doi.org/10.37358/rc.19.9.7547.

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Amyloid-b (Ab) peptides are proteins associated with Alzheimer�s disease (AD), because the extracellular Ab deposits are the main cause of this disorder. The aggregation of Ab has been shown to depend on the interactions with metal ions, such as copper, zinc, aluminum or iron. The N-terminal sequence of Ab(1-42) or Ab(1-40) peptides, namely Ab(1-16) peptide fragment, is considered the metal binding site involved in AD neurodegeneration and amyloidogenesis. Therefore, we have investigated different peptide sequences to understand the role played by some amino acid residues in metal binding. In

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Pirota, Valentina, Enrico Lunghi, Alessandra Benassi, Emmanuele Crespan, Mauro Freccero, and Filippo Doria. "Selective Binding and Redox-Activity on Parallel G-Quadruplexes by Pegylated Naphthalene Diimide-Copper Complexes." Molecules 26, no. 16 (2021): 5025. http://dx.doi.org/10.3390/molecules26165025.

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G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against COVID-19, have triggered the ever-increasing need to develop selective molecules able to interact with parallel G4s. Naphthalene diimides (NDIs) are widely exploited as G4 ligands, being able to induce and strongly stabilize these structures. Sometimes, a reversible NDI-G4 interaction is also associated with an irreversible one, due to the cleavag

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Pfeuffer, I., S. Klein-Hessling, A. Heinfling, et al. "Octamer factors exert a dual effect on the IL-2 and IL-4 promoters." Journal of Immunology 153, no. 12 (1994): 5572–85. http://dx.doi.org/10.4049/jimmunol.153.12.5572.

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Abstract The promoters of IL-2 and IL-4 genes contain multiple binding sites for octamer factors. In peripheral T lymphocytes and several T cell lines, both the ubiquitous Oct factor Oct-1 and the lymphocyte-specific factor Oct-2 are expressed and bind to the IL-2 and IL-4 promoters. Prominent octamer binding sites of IL-2 and IL-4 promoters are their upstream promoter sites (UPS) which share 14 identical nucleotides. Multiple copies of the IL-2 and IL-4 UPS act as inducible enhancers in T cells, and their induction is inhibited by the immunosuppressant cyclosporin A (CsA). Closely linked to t

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ABRAHAM, Zelda H. L., Barry E. SMITH, Barry D. HOWES, David J. LOWE, and Robert R. EADY. "pH-dependence for binding a single nitrite ion to each type-2 copper centre in the copper-containing nitrite reductase of Alcaligenes xylosoxidans." Biochemical Journal 324, no. 2 (1997): 511–16. http://dx.doi.org/10.1042/bj3240511.

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The first quantitative characterization of the interaction of NO2- with the Cu-containing dissimilatory nitrite reductase (NiR) of Alcaligenes xylosoxidansusing steady-state kinetics, equilibrium gel filtration and EPR spectroscopy is described. Each molecule of this protein consists of three equivalent subunits, each containing a type-1 Cu atom and also a type-2 Cu atom at each subunit interface. Enzyme activity increased in a biphasic manner with decreasing pH, having an optimum at pH 5.2 and a plateau between pH 6.1 and 5.8. Equilibrium gel filtration showed that binding of NO2- to the oxid

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35

Shcheglovitov, Aleksandr, Iuliia Vitko, Roman M. Lazarenko, Peihan Orestes, Slobodan M. Todorovic, and Edward Perez-Reyes. "Molecular and biophysical basis of glutamate and trace metal modulation of voltage-gated Cav2.3 calcium channels." Journal of General Physiology 139, no. 3 (2012): 219–34. http://dx.doi.org/10.1085/jgp.201110699.

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Here, we describe a new mechanism by which glutamate (Glu) and trace metals reciprocally modulate activity of the Cav2.3 channel by profoundly shifting its voltage-dependent gating. We show that zinc and copper, at physiologically relevant concentrations, occupy an extracellular binding site on the surface of Cav2.3 and hold the threshold for activation of these channels in a depolarized voltage range. Abolishing this binding by chelation or the substitution of key amino acid residues in IS1–IS2 (H111) and IS2–IS3 (H179 and H183) loops potentiates Cav2.3 by shifting the voltage dependence of a

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36

Naro, Fabio, Maria G. Tordi, Giorgio M. Giacometti, Francesco Tomei, Anna M. Timperio, and Lello Zolla. "Metal Binding to Pseudomonas aeruginosa Azurin: a Kinetic Investigation." Zeitschrift für Naturforschung C 55, no. 5-6 (2000): 347–54. http://dx.doi.org/10.1515/znc-2000-5-609.

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The interaction between azurin from Pseudomonas aeruginosa and Ag(I), Cu(II), Hg(II), was investigated as a function of protein state, i.e. apo-, reduced and oxidised azurin. Two different metal binding sites, characterized by two different spectroscopic absorbancies, were detected: one is accessible to Ag(I) and Cu(II) but not to Hg(II); the other one binds Ag(I) and Hg(II) but not copper. When added in stoichiometric amount, Ag(I) shows high affinity for the redox center of apo-azurin, to which it probably binds by the -SH group of Cys112; it can displace Cu(I) from reducedazurin, while it d

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Teodori, Laura, Marjan Omer, Anders Märcher, et al. "Site-specific nanobody-oligonucleotide conjugation for super-resolution imaging." Journal of Biological Methods 9, no. 1 (2022): e159. http://dx.doi.org/10.14440/jbm.2022.381.

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Camelid single-domain antibody fragments, also called nanobodies, constitute a class of binders that are small in size (~15 kDa) and possess antigen-binding properties similar to their antibody counterparts. Facile production of recombinant nanobodies in several microorganisms has made this class of binders attractive within the field of molecular imaging. Particularly, their use in super-resolution microscopy has improved the spatial resolution of molecular targets due to a smaller linkage error. In single-molecule localization microscopy techniques, the effective spatial resolution can be fu

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Scala, David J., and Lee J. Kerkhof. "Diversity of Nitrous Oxide Reductase (nosZ) Genes in Continental Shelf Sediments." Applied and Environmental Microbiology 65, no. 4 (1999): 1681–87. http://dx.doi.org/10.1128/aem.65.4.1681-1687.1999.

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ABSTRACT Diversity of the nitrous oxide reductase (nosZ) gene was examined in sediments obtained from the Atlantic Ocean and Pacific Ocean continental shelves. Approximately 1,100 bp of thenosZ gene were amplified via PCR, using nosZgene-specific primers. Thirty-seven unique copies of thenosZ gene from these marine environments were characterized, increasing the nosZ sequence database fourfold. The average DNA similarity for comparisons between all 49 variants of the nosZ gene was 64% ± 10%. Alignment of the derived amino acid sequences confirmed the conservation of important structural motifs

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Abbas, Ioana M., Marija Vranic, Holger Hoffmann, et al. "Investigations of the Copper Peptide Hepcidin-25 by LC-MS/MS and NMR." International Journal of Molecular Sciences 19, no. 8 (2018): 2271. http://dx.doi.org/10.3390/ijms19082271.

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Hepcidin-25 was identified as the main iron regulator in the human body, and it by binds to the sole iron-exporter ferroportin. Studies showed that the N-terminus of hepcidin is responsible for this interaction, the same N-terminus that encompasses a small copper(II)-binding site known as the ATCUN (amino-terminal Cu(II)- and Ni(II)-binding) motif. Interestingly, this copper-binding property is largely ignored in most papers dealing with hepcidin-25. In this context, detailed investigations of the complex formed between hepcidin-25 and copper could reveal insight into its biological role. The

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Sen, Kakali, Sam Horrell, Demet Kekilli, et al. "Active-site protein dynamics and solvent accessibility in nativeAchromobacter cycloclastescopper nitrite reductase." IUCrJ 4, no. 4 (2017): 495–505. http://dx.doi.org/10.1107/s2052252517007527.

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Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCATand HisCAT) involved in the nitrite-reductio

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Goto, Yoshio, and Judith P. Klinman. "Binding of Dioxygen to Non-Metal Sites in Proteins: Exploration of the Importance of Binding Site Size versus Hydrophobicity in the Copper Amine Oxidase fromHansenula polymorpha†." Biochemistry 41, no. 46 (2002): 13637–43. http://dx.doi.org/10.1021/bi0204591.

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Frank, L. H., H. K. Cheung, and R. S. Cohen. "Identification and characterization of Drosophila female germ line transcriptional control elements." Development 114, no. 2 (1992): 481–91. http://dx.doi.org/10.1242/dev.114.2.481.

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The highly organized structure of the Drosophila ovary makes it an ideal system for studying mechanisms of differential gene expression. Here we report the identification of a 171 bp sequence from the 5' end of the hsp26 gene that functions as a female germ-line-specific transcriptional regulator when linked in two copies to a basal promoter. The regulator is active only in nondividing cells of the germ line, i.e., only in nurse cells and oocytes. It is not active in any examined tissue or cell type outside of the female germ line. Copper nuclease footprinting studies show that the germ line r

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Maniak, Halina, Michał Talma, Konrad Matyja, Anna Trusek, and Mirosław Giurg. "Synthesis and Structure-Activity Relationship Studies of Hydrazide-Hydrazones as Inhibitors of Laccase from Trametes versicolor." Molecules 25, no. 5 (2020): 1255. http://dx.doi.org/10.3390/molecules25051255.

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A series of hydrazide-hydrazones 1–3, the imine derivatives of hydrazides and aldehydes bearing benzene rings, were screened as inhibitors of laccase from Trametes versicolor. Laccase is a copper-containing enzyme which inhibition might prevent or reduce the activity of the plant pathogens that produce it in various biochemical processes. The kinetic and molecular modeling studies were performed and for selected compounds, the docking results were discussed. Seven 4-hydroxybenzhydrazide (4-HBAH) derivatives exhibited micromolar activity Ki = 24–674 µM with the predicted and desirable competiti

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Olczak, Teresa, Dabney White Dixon, and Caroline Attardo Genco. "Binding Specificity of the Porphyromonas gingivalis Heme and Hemoglobin Receptor HmuR, Gingipain K, and Gingipain R1 for Heme, Porphyrins, and Metalloporphyrins." Journal of Bacteriology 183, no. 19 (2001): 5599–608. http://dx.doi.org/10.1128/jb.183.19.5599-5608.2001.

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ABSTRACT Previous genetic and biochemical studies have confirmed that hemoglobin and hemin utilization in Porphyromonas gingivalis is mediated by the outer membrane hemoglobin and heme receptor HmuR, as well as gingipain K (Kgp), a lysine-specific cysteine protease, and gingipain R1 (HRgpA), one of two arginine-specific cysteine proteases. In this study we report on the binding specificity of the recombinant P. gingivalis HmuR protein and native gingipains for hemoglobin, hemin, various porphyrins, and metalloporphyrins as assessed by spectrophotometric assays, by affinity chromatography, and

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Banci, Lucia, Ivano Bertini, Vito Calderone, et al. "Copper(I)-mediated protein–protein interactions result from suboptimal interaction surfaces." Biochemical Journal 422, no. 1 (2009): 37–42. http://dx.doi.org/10.1042/bj20090422.

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The homoeostasis of metal ions in cells is the result of the contribution of several cellular pathways that involve transient, often weak, protein–protein interactions. Metal transfer typically implies the formation of adducts where the metal itself acts as a bridge between proteins, by co-ordinating residues of both interacting partners. In the present study we address the interaction between the human copper(I)-chaperone HAH1 (human ATX1 homologue) and a metal-binding domain in one of its partners, namely the P-type copper-transporting ATPase, ATP7A (ATPase, Cu+ transporting, α polypeptide).

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Das, Dola, Nisha Tapryal, Shyamal K. Goswami, Paul L. Fox, and Chinmay K. Mukhopadhyay. "Regulation of ceruloplasmin in human hepatic cells by redox active copper: identification of a novel AP-1 site in the ceruloplasmin gene." Biochemical Journal 402, no. 1 (2007): 135–41. http://dx.doi.org/10.1042/bj20060963.

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Cp (ceruloplasmin), a copper containing plasma protein, mainly synthesized in the liver, is known to be functional between the interface of iron and copper metabolism. We have reported previously that Cp is regulated by cellular iron status, but the process of the regulation of Cp by copper still remains a subject for investigation. In the present paper, we show that PDTC (pyrrolidine dithiocarbamate), a thiol compound widely known to increase intracellular redox copper, regulates Cp expression in hepatic cells by a copper-dependent transcriptional mechanism. To find out the mechanism of induc

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47

Urresti, Saioa, Alan Cartmell, Feng Liu, Paul H. Walton, and Gideon J. Davies. "Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum." Acta Crystallographica Section F Structural Biology Communications 74, no. 8 (2018): 496–505. http://dx.doi.org/10.1107/s2053230x18006842.

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The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment. It was sought to analyse whether the GH124 metal-io

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Varela-Nallar, Lorena, Enrique M. Toledo, Luis F. Larrondo, Ana L. B. Cabral, Vilma R. Martins, and Nibaldo C. Inestrosa. "Induction of cellular prion protein gene expression by copper in neurons." American Journal of Physiology-Cell Physiology 290, no. 1 (2006): C271—C281. http://dx.doi.org/10.1152/ajpcell.00160.2005.

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Prion diseases are caused by the conformational transition of the native α-helical cellular prion protein (PrPC) into a β-sheet pathogenic isoform. However, the normal physiological function of PrPC remains elusive. We report herein that copper induces PrPC expression in primary hippocampal and cortical neurons. PrPC induced by copper has a normal glycosylation pattern, is proteinase K-sensitive and reaches the cell surface attached by a glycosyl phosphatidylinositol anchor. Immunofluorescence analysis revealed that copper induces PrPC levels in the cell surface and in an intracellular compart

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49

Huo, Chunheng, Tinghong Ming, Yan Wu, et al. "Structural and Biochemical Characterization of Silver/Copper Binding by Dendrorhynchus zhejiangensis Ferritin." Polymers 15, no. 5 (2023): 1297. http://dx.doi.org/10.3390/polym15051297.

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Ferritin with a highly symmetrical cage-like structure is not only key in the reversible storage of iron in efficient ferroxidase activity; it also provides unique coordination environments for the conjugation of heavy metal ions other than those associated with iron. However, research regarding the effect of these bound heavy metal ions on ferritin is scarce. In the present study, we prepared a marine invertebrate ferritin from Dendrorhynchus zhejiangensis (DzFer) and found that it could withstand extreme pH fluctuation. We then demonstrated its capacity to interact with Ag+ or Cu2+ ions usin

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50

Goumakos, William, Jean-Pierre Laussac, and Bibudhendra Sarkar. "Binding of cadmium(II) and zinc(II) to human and dog serum albumins. An equilibrium dialysis and 113Cd-NMR study." Biochemistry and Cell Biology 69, no. 12 (1991): 809–20. http://dx.doi.org/10.1139/o91-121.

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The binding of Cd(II) and Zn(II) to human serum albumin (HSA) and dog serum albumin (DSA) has been studied by equilibrium dialysis and 113Cd(II)-NMR techniques at physiological pH. Scatchard analysis of the equilibrium dialysis data indicate the presence of at least two classes of binding sites for Cd(II) and Zn(II). On analysis of the high-affinity class of sites, HSA is shown to bind 2.08 ± 0.09 (log K = 5.3 ± 0.6) and 1.07 ± 0.12 (log K = 6.4 ± 0.8) moles of Cd(II) and Zn(II) per mole of protein, respectively. DSA bound 2.02 ± 0.19 (log K = 5.1 ± 0.8), and 1.06 ± 0.15 (log K = 6.0 ± 0.2) mo

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