The Experts below are selected from a list of 240 Experts worldwide ranked by ideXlab platform
Wolfgang Maret - One of the best experts on this subject based on the ideXlab platform.
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the biological inorganic chemistry of Zinc ions
Archives of Biochemistry and Biophysics, 2016Co-Authors: Artur Krezel, Wolfgang MaretAbstract:The solution and complexation chemistry of Zinc ions is the basis for Zinc biology. In living organisms, Zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in Proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human Proteins, Zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other Proteins Zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about Zinc Proteins, the coordination chemistry of the “mobile” Zinc ions in these processes, i.e. when not bound to Proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of Zinc ions is essential for understanding its cellular biology and for designing complexes that deliver Zinc to Proteins and chelating agents that remove Zinc from Proteins, for detecting Zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving Zinc ions and nanoparticles such as Zinc oxide (ZnO). In most investigations, reference is made to Zinc or Zn2+ without full appreciation of how biological Zinc ions are buffered and how the d-block cation Zn2+ differs from s-block cations such as Ca2+ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in Proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that Zinc ion speciation is important in Zinc biochemistry and for biological recognition as a variety of low molecular weight Zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol.
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Zinc biochemistry from a single Zinc enzyme to a key element of life
Advances in Nutrition, 2013Co-Authors: Wolfgang MaretAbstract:The nutritional essentiality of Zinc for the growth of living organisms had been recognized long before Zinc biochemistry began with the discovery of Zinc in carbonic anhydrase in 1939. Painstaking analytical work then demonstrated the presence of Zinc as a catalytic and structural cofactor in a few hundred enzymes. In the 1980s, the field again gained momentum with the new principle of "Zinc finger" Proteins, in which Zinc has structural functions in domains that interact with other biomolecules. Advances in structural biology and a rapid increase in the availability of gene/protein databases now made it possible to predict Zinc-binding sites from metal-binding motifs detected in sequences. This procedure resulted in the definition of Zinc proteomes and the remarkable estimate that the human genome encodes ∼3000 Zinc Proteins. More recent developments focus on the regulatory functions of Zinc(II) ions in intra- and intercellular information transfer and have tantalizing implications for yet additional functions of Zinc in signal transduction and cellular control. At least three dozen Proteins homeostatically control the vesicular storage and subcellular distribution of Zinc and the concentrations of Zinc(II) ions. Novel principles emerge from quantitative investigations on how strongly Zinc interacts with Proteins and how it is buffered to control the remarkably low cellular and subcellular concentrations of free Zinc(II) ions. It is fair to conclude that the impact of Zinc for health and disease will be at least as far-reaching as that of iron.
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Zinc and the Zinc proteome.
Metal ions in life sciences, 2012Co-Authors: Wolfgang MaretAbstract:Zinc(II) ions are catalytic, structural, and regulatory cofactors in Proteins. In contrast to painstakingly collecting the pieces by isolating and characterizing Zinc Proteins, ‘omics’ approaches are now allowing us to tease out information about Zinc Proteins from genomes and to piece together the information to a broader knowledge and appreciation of the role of Zinc in biology. Estimates for the number of Zinc Proteins in the human genome and in genomes of other organisms have been derived from a bioinformatics approach: mining sequence databases for homologies of known Zinc-coordination motifs with characteristic ligand signatures for metal binding and combining this information with the knowledge about metal-binding domains of Proteins. This approach resulted in an impressive number of almost 3000 human Zinc Proteins and made major contributions to our understanding of the composition of the Zinc proteome and the functions of Zinc Proteins. However, the impact of Zinc on protein science is even greater. Predictions do not include yet undiscovered ligand signatures, coordination environments that employ complex binding patterns with nonsequential binding of ligands and ligand bridges, Zinc/protein interactions at protein interfaces, and transient interactions of Zinc(II) ions with Proteins that are not known to be Zinc Proteins. All this information and recent discoveries of how cellular Zinc is controlled and how Zinc(II) ions function as signaling ions add an hitherto unrecognized dimension to the Zinc proteome of multicellular eukaryotic organisms. Zinc proteomics employs a combination of approaches from different disciplines, such as bioinformatics, biology, inorganic biochemistry, and significantly, analytical and structural chemistry. It provides crucial large-scale datasets for interpreting the roles of Zinc in health and disease at both a molecular and a global, systems biology, level.
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Redox biochemistry of mammalian metallothioneins
JBIC Journal of Biological Inorganic Chemistry, 2011Co-Authors: Wolfgang MaretAbstract:Metallothionein (MT) is a generic name for certain families of structurally rather variable metal-binding Proteins. While purely chemical or biological approaches failed to establish a single physiologic function for MTs in any species, a combination of chemical and biological approaches and recent progress in defining the low but significant concentrations of cytosolic free Zinc(II) ions have demonstrated that mammalian MTs function in cellular Zinc metabolism in specific ways that differ from conventional knowledge about any other metalloprotein. Their thiolate coordination environments make MTs redox-active Zinc Proteins that exist in different molecular states depending on the availability of cellular Zinc and the redox poise. The Zinc affinities of MTs cover a range of physiologic Zinc(II) ion concentrations and are modulated. Oxidative conditions make more Zinc available, while reductive conditions make less Zinc available. MTs move from the cytosol to cellular compartments, are secreted from cells, and are taken up by cells. They provide cellular Zinc ions in a chemically available form and participate in cellular metal muffling: the combination of physiologic buffering in the steady state and the cellular redistribution and compartmentalization of transiently elevated Zinc(II) ion concentrations in the pre-steady state. Cumulative evidence indicates that MTs primarily have a redox-dependent function in Zinc metabolism, rather than a Zinc-dependent function in redox metabolism.
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Metals on the move: Zinc ions in cellular regulation and in the coordination dynamics of Zinc Proteins
BioMetals, 2011Co-Authors: Wolfgang MaretAbstract:Homeostatic control maintains essential transition metal ions at characteristic cellular concentrations to support their physiological functions and to avoid adverse effects. Zinc is especially widely used as a catalytic or structural cofactor in about 3000 human Zinc Proteins. In addition, the homeostatic control of Zinc in eukaryotic cells permits functions of Zinc(II) ions in regulation and in paracrine and intracrine signaling. Zinc ions are released from Proteins through ligand-centered reactions in Zinc/thiolate coordination environments, and from stores in cellular organelles, where Zinc transporters participate in Zinc loading and release. Muffling reactions allow Zinc ions to serve as signaling ions (second messengers) in the cytosol that is buffered to picomolar Zinc ion concentrations at steady-state. Muffling includes Zinc ion binding to metallothioneins, cellular translocations of metallothioneins, delivery of Zinc ions to transporter Proteins, and Zinc ion fluxes through cellular membranes with the result of removing the additional Zinc ions from the cytosol and restoring the steady-state. Targets of regulatory Zinc ions are Proteins with sites for transient Zinc binding, such as membrane receptors, enzymes, protein–protein interactions, and sensor Proteins that control gene expression. The generation, transmission, targets, and termination of Zinc ion signals involve Proteins that use coordination dynamics in the inner and outer ligand spheres to control metal ion association and dissociation. These new findings establish critically important functions of Zinc ions and Zinc metalloProteins in cellular control.
Bert L. Vallee - One of the best experts on this subject based on the ideXlab platform.
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Zinc fingers, Zinc clusters, and Zinc twists in DNA-binding protein domains (transcription factors/steroid receptors/hormone receptors/GAL4/Zinc binding site)
2016Co-Authors: Bert L. Vallee, E Joseph, David S. AuldAbstract:We now recognize three distinct motifs of DNA-binding Zinc Proteins: (i) Zinc fingers, (ii) Zinc clusters, and (iii) Zinc twists. Until very recently, x-ray crystallographic or NMR three-dimensional structure analyses of DNA-binding Zinc Proteins have not been available to serve as standards of reference for the Zinc binding sites of these families of Proteins. Those of the DNA-binding domains of the fungal transcription factor GAL4 and the rat glucocorticoid receptor are the first to have been determined. Both Proteins contain two Zinc binding sites, and in both, cysteine residues are tie sole Zinc ligands. In GAL4, two Zinc atoms are bound to six cysteine residues which form a "Zinc cluster" akin to that of metallothionein; the distance between the two Zinc atoms of GAL4 is -3.5 A. In the glucocorticoid receptor, each Zinc atom is bound to four cysteine residues; the interatomic Zinc-Zinc distance is -13 A, and in this instance, a "Zinc twist" is represented by a helical DNA recognition site located between the two Zinc atoms. Zinc clusters and Zinc twists are here recognized as two distinctive motifs in DNA-binding Proteins containing multiple Zinc at- oms. For native "Zinc fingers," structural data do not exist as yet; consequently, the interatomic distances between Zinc at- oms are not known. As further structural data become avail- able, the structural and functional significance of these differ- ent motifs in their binding to DNA and other Proteins partic- ipating in the transmission of the genetic message will become apparent.
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Control of Zinc transfer between thionein, metallothionein, and Zinc Proteins
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: Claus Jacob, Wolfgang Maret, Bert L. ValleeAbstract:Metallothionein (MT), despite its high metal binding constant (KZn = 3.2 × 1013 M−1 at pH 7.4), can transfer Zinc to the apoforms of Zinc enzymes that have inherently lower stability constants. To gain insight into this paradox, we have studied Zinc transfer between Zinc enzymes and MT. Zinc can be transferred in both directions—i.e., from the enzymes to thionein (the apoform of MT) and from MT to the apoenzymes. Agents that mediate or enhance Zinc transfer have been identified that provide kinetic pathways in either direction. MT does not transfer all of its seven Zinc atoms to an apoenzyme, but apparently contains at least one that is more prone to transfer than the others. Modification of thiol ligands in MT Zinc clusters increases the total number of Zinc ions released and, hence, the extent of transfer. Aside from disulfide reagents, we show that selenium compounds are potential cellular enhancers of Zinc transfer from MT to apoenzymes. Zinc transfer from Zinc enzymes to thionein, on the other hand, is mediated by Zinc-chelating agents such as Tris buffer, citrate, or glutathione. Redox agents are asymmetrically involved in both directions of Zinc transfer. For example, reduced glutathione mediates Zinc transfer from enzymes to thionein, whereas glutathione disulfide oxidizes MT with enhanced release of Zinc and transfer of Zinc to apoenzymes. Therefore, the cellular redox state as well as the concentration of other biological chelating agents might well determine the direction of Zinc transfer and ultimately affect Zinc distribution.
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Coordination dynamics of biological Zinc "clusters" in metallothioneins and in the DNA-binding domain of the transcription factor Gal4.
Proceedings of the National Academy of Sciences of the United States of America, 1997Co-Authors: Wolfgang Maret, Kjeld S. Larsen, Bert L. ValleeAbstract:The almost universal appreciation for the importance of Zinc in metabolism has been offset by the considerable uncertainty regarding the Proteins that store and distribute cellular Zinc. We propose that some Zinc Proteins with so-called Zinc cluster motifs have a central role in Zinc distribution, since they exhibit the rather exquisite properties of binding Zinc tightly while remaining remarkably reactive as Zinc donors. We have used Zinc isotope exchange both to probe the coordination dynamics of Zinc clusters in metallothionein, the small protein that has the highest known Zinc content, and to investigate the potential function of Zinc clusters in cellular Zinc distribution. When mixed and incubated, metallothionein isoProteins-1 and -2 rapidly exchange Zinc, as demonstrated by fast chromatographic separation and radiometric analysis. Exchange kinetics exhibit two distinct phases (kfast ≃ 5000 min−1·M−1; kslow ≃ 200 min−1·M−1, pH 8.6, 25°C) that are thought to reflect exchange between the three-Zinc clusters and between the four-Zinc clusters, respectively. Moreover, we have observed and examined Zinc exchange between metallothionein-2 and the Gal4 protein (k ≃ 800 min−1·M−1, pH 8.0, 25°C), which is a prototype of transcription factors with a two-Zinc cluster. This reaction constitutes the first experimental example of intermolecular Zinc exchange between heterologous Proteins. Such kinetic reactivity distinguishes Zinc in biological clusters from Zinc in the coordination environment of Zinc enzymes, where the metal does not exchange over several days with free Zinc in solution. The molecular organization of these clusters allows Zinc exchange to proceed through a ligand exchange mechanism, involving molecular contact between the reactants.
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Vitellogenin and lipovitellin: Zinc Proteins of Xenopus laevis oocytes.
Biochemistry, 1995Co-Authors: Marcelo Montorzi, Kenneth H. Falchuk, Bert L. ValleeAbstract:Xenopus laevis vitellogenin is a plasma protein that contains a total of 5 mol of metal/440 kDa dimer, 2 mol of Zinc, and 3 mol of calcium (Montorzi et al. (1994) Biochem. Biophys. Res. Commun. 200, 1407-1413]. There are no other group IIB or transition metals in the molecule. The Zinc atoms are removed instantaneously by 1,10-phenanthroline (OP) (pK 4.8). Once internalized by receptor-mediated endocytosis, vitellogenin is cleaved into multiple polypeptides, i.e., the two lipovitellin subunits (1 and 2) plus phosvitin; these are then stored as microcrystals within yolk platelets. We here show by metal analysis of the individual Proteins generated by vitellogenin processing that Zinc and calcium occur in different domains of the vitellogenin polypeptide chain. All of the vitellogenin Zinc is present in lipovitellin, in amounts equal to 1 mol of Zinc/141 kDa. Calcium, in contrast, is detected exclusively in phosvitin which, in addition, contains 3 mol of magnesium/35 kDa, apparently acquired following vitellogenin entry into the oocyte. The Zinc in lipovitellin is removed by OP in a concentration-dependent manner with a pK of 4.8, identical to that obtained for vitellogenin, and by exposure to acidic conditions (below pH 5). Following removal of Zinc, the two lipovitellin subunits remain associated, suggesting that Zinc is not involved in their interaction. On exposure to 1% SDS, lipovitellin does dissociate into 106 and 33 kDa subunits. The presence of stoichiometric quantities of Zinc in both vitellogenin and lipovitellin calls for the study of the hitherto unrecognized biochemistry and functions of these Proteins in Zinc metabolism and development of the frog oocyte and embryo.
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The function of metallothionein
Neurochemistry international, 1995Co-Authors: Bert L. ValleeAbstract:Since its discovery in 1957 metallothionein (MT) has remained a protein in search of a function. After 40 years of frustrating efforts, three areas of research point to its Zinc cluster structure as the basis of its functional potential: (1) the regulation of MT gene expression by Zinc-dependent transcription factors, (2) neuronal growth inhibition in brain, and (3) interactions with glutathione and Zinc Proteins.
David S. Auld - One of the best experts on this subject based on the ideXlab platform.
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Zinc fingers, Zinc clusters, and Zinc twists in DNA-binding protein domains (transcription factors/steroid receptors/hormone receptors/GAL4/Zinc binding site)
2016Co-Authors: Bert L. Vallee, E Joseph, David S. AuldAbstract:We now recognize three distinct motifs of DNA-binding Zinc Proteins: (i) Zinc fingers, (ii) Zinc clusters, and (iii) Zinc twists. Until very recently, x-ray crystallographic or NMR three-dimensional structure analyses of DNA-binding Zinc Proteins have not been available to serve as standards of reference for the Zinc binding sites of these families of Proteins. Those of the DNA-binding domains of the fungal transcription factor GAL4 and the rat glucocorticoid receptor are the first to have been determined. Both Proteins contain two Zinc binding sites, and in both, cysteine residues are tie sole Zinc ligands. In GAL4, two Zinc atoms are bound to six cysteine residues which form a "Zinc cluster" akin to that of metallothionein; the distance between the two Zinc atoms of GAL4 is -3.5 A. In the glucocorticoid receptor, each Zinc atom is bound to four cysteine residues; the interatomic Zinc-Zinc distance is -13 A, and in this instance, a "Zinc twist" is represented by a helical DNA recognition site located between the two Zinc atoms. Zinc clusters and Zinc twists are here recognized as two distinctive motifs in DNA-binding Proteins containing multiple Zinc at- oms. For native "Zinc fingers," structural data do not exist as yet; consequently, the interatomic distances between Zinc at- oms are not known. As further structural data become avail- able, the structural and functional significance of these differ- ent motifs in their binding to DNA and other Proteins partic- ipating in the transmission of the genetic message will become apparent.
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The ins and outs of biological Zinc sites
Biometals : an international journal on the role of metal ions in biology biochemistry and medicine, 2009Co-Authors: David S. AuldAbstract:The inner shell coordination properties of Zinc Proteins have led to the identification of four types of Zinc binding sites: catalytic, cocatalytic, structural, and protein interface. Outer shell coordination can influence the stability of the Zinc site and its function as exemplified herein by the Zinc sites in carbonic anhydrase, promatrix metalloproteases and alcohol dehydrogenase. Agents that disrupt these interactions, can lead to increased off rate constants for Zinc. d-penicillamine is the first drug to inhibit a Zinc protease by catalyzing the removal of the metal. Since it can accept the released Zinc we have referred to it as a catalytic chelator. Agents that catalyze the release of the metal in the presence of a scavenger chelator will also inhibit enzyme catalysis and are referred to as enhanced dechelation inhibitors.
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Zinc coordination sphere in biochemical Zinc sites
Biometals, 2001Co-Authors: David S. AuldAbstract:Zinc is known to be indispensable to growth and development and transmission of the genetic message. It does this through a remarkable mosaic of Zinc binding motifs that orchestrate all aspects of metabolism. There are now nearly 200 three dimensional structures for Zinc Proteins, representing all six classes of enzymes and covering a wide range of phyla and species. These structures provide standards of reference for the identity and nature of Zinc ligands in other Proteins for which only the primary structure is known. Three primary types of Zinc sites are apparent from examination of these structures: structural, catalytic and cocatalytic. The most common amino acids that supply ligands to these sites are His, Glu, Asp and Cys. In catalytic sites Zinc generally forms complexes with water and any three nitrogen, oxygen and sulfur donors with His being the predominant amino acid chosen. Water is always a ligand to such sites. Structural Zinc sites have four protein ligands and no bound water molecule. Cys is the preferred ligand in such sites. Cocatalytic sites contain two or three metals in close proximity with two of the metals bridged by a side chain moiety of a single amino acid residue, such as Asp, Glu or His and sometimes a water molecule. Asp and His are the preferred amino acids for these sites. No Cys ligands are found in such sites. The scaffolding of the Zinc sites is also important to the function and reactivity of the bound metal. The influence of Zinc on quaternary protein structure has led to the identification of a fourth type of Zinc binding site, protein interface. In this case Zinc sites are formed from ligands supplied from amino acid residues residing in the binding surface of two Proteins. The resulting Zinc site usually has the coordination properties of a catalytic or structural Zinc binding site.
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Subunit Composition of the Zinc Proteins α- and β-Lipovitellin from Chicken
Journal of Protein Chemistry, 2000Co-Authors: Dieter Groche, Leonid G. Rashkovetsky, Kenneth H. Falchuk, David S. AuldAbstract:Chicken α- and β-lipovitellin are derived from parent vitellogenin Proteins and contain four subunits (125, 80, 40, and 30 kDa) and two subunits (125 and 30 kDa), respectively. Metal analyses demonstrate both are Zinc Proteins containing 2.1 ± 0.2 mol of Zinc/275 kDa per α-lipovitellin and 1.4 ± 0.2 mol of Zinc/155 kDa per β-lipovitellin, respectively. The subunits of β-lipovitellin, Lv 1 (MW 125 kDa) and Lv 2 (MW 30 kDa), are separated by gel exclusion chromatography in the presence of zwittergent 3–16. Zinc elutes with Lv 1, suggesting that this subunit binds Zinc in the absence of Lv 2. The subunits of α- and β-lipovitellin were separated by SDS-PAGE, digested with trypsin, and mapped by reverse-phase HPLC. The peptide maps of the 125-kDa subunits from α- and β-lipovitellin are essentially identical. Similar results are obtained for the 30-kDa subunits of both lipovitellins. The sequences of five and four peptides of the 125-kDa subunit of α- and β-Lv, respectively, and two peptides of the 30-kDa subunit of α- and β-lipovitellin were determined and match those predicted from the gene for vitellogenin II, Vtg II. Comparison of the amino acid composition of the 125- and 30-kDa subunits of α- and β-lipovitellin support the conclusion that they originate from the same gene. The sequences of peptides from the 80- and 40-kDa subunits of α-lipovitellin have not been found in the NCBI nonredundant data bank. The 27-amino acid N-terminal sequence of the 40-kDa protein is 56% similar to the last third of the Lv 1-coding region of the Vtg II gene, suggesting it may come from an analogous region of the Vtg I gene. We propose a scheme for the precursor—product relationship of Vtg I.
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Subunit composition of the Zinc Proteins alpha- and beta-lipovitellin from chicken.
Journal of protein chemistry, 2000Co-Authors: Dieter Groche, Leonid G. Rashkovetsky, Kenneth H. Falchuk, David S. AuldAbstract:Chicken α- and β-lipovitellin are derived from parent vitellogenin Proteins and contain four subunits (125, 80, 40, and 30 kDa) and two subunits (125 and 30 kDa), respectively. Metal analyses demonstrate both are Zinc Proteins containing 2.1 ± 0.2 mol of Zinc/275 kDa per α-lipovitellin and 1.4 ± 0.2 mol of Zinc/155 kDa per β-lipovitellin, respectively. The subunits of β-lipovitellin, Lv 1 (MW 125 kDa) and Lv 2 (MW 30 kDa), are separated by gel exclusion chromatography in the presence of zwittergent 3–16. Zinc elutes with Lv 1, suggesting that this subunit binds Zinc in the absence of Lv 2. The subunits of α- and β-lipovitellin were separated by SDS-PAGE, digested with trypsin, and mapped by reverse-phase HPLC. The peptide maps of the 125-kDa subunits from α- and β-lipovitellin are essentially identical. Similar results are obtained for the 30-kDa subunits of both lipovitellins. The sequences of five and four peptides of the 125-kDa subunit of α- and β-Lv, respectively, and two peptides of the 30-kDa subunit of α- and β-lipovitellin were determined and match those predicted from the gene for vitellogenin II, Vtg II. Comparison of the amino acid composition of the 125- and 30-kDa subunits of α- and β-lipovitellin support the conclusion that they originate from the same gene. The sequences of peptides from the 80- and 40-kDa subunits of α-lipovitellin have not been found in the NCBI nonredundant data bank. The 27-amino acid N-terminal sequence of the 40-kDa protein is 56% similar to the last third of the Lv 1-coding region of the Vtg II gene, suggesting it may come from an analogous region of the Vtg I gene. We propose a scheme for the precursor—product relationship of Vtg I.
Joseph E. Coleman - One of the best experts on this subject based on the ideXlab platform.
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Zinc as a structural and folding element of Proteins which interact with DNA
Inorganica Chimica Acta, 1998Co-Authors: Matthew Junker, Karla K. Rodgers, Joseph E. ColemanAbstract:Zinc Proteins involved in the control of gene expression include two types which contain Zinc binuclear clusters; fungal transcription factors containing DNA binding domains organized around a Zn2Cys6 cluster and the V(D)J recombination-activating Proteins, RAG1's, of higher eukaryotes in which the dimerization domains contain a Zn2Cys5His2 cluster. Two solution structures of Zn2Cys6 cluster domains are compared along with the crystal structure of the dimerization domain of RAG1. The dimerization domain of RAG1 contains four Zinc ions and is organized around a Zinc finger, a Zinc RING finger and a Zinc binuclear cluster. Protein folds stabilized by multiple Zinc sites are discussed.
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Zinc Proteins enzymes storage Proteins transcription factors and replication Proteins
Annual Review of Biochemistry, 1992Co-Authors: Joseph E. ColemanAbstract:In the past five years there has been a great expansion in our knowledge of the role of Zinc in the structure and function of Proteins. Not only is Zinc required for essential catalytic functions in enzymes (more than 300 are known at present), but also it stabilizes and even induces the folding of protein subdomains. The latter functions have been most dramatically illustrated by the discovery of the essential role of Zinc in the folding of the DNA-binding domains of eukaryotic transcription factors, including the Zinc finger transcription factors, the large family of hormone receptor Proteins, and the Zinc cluster transcription factors from yeasts. Similar functions are highly probable for the Zinc found in the RNA polymerases and the Zinc-containing accessory Proteins involved in nucleic acid replication. The rapid increase in the number and nature of the Proteins in which Zinc functions is not unexpected since Zinc is the second most abundant trace metal found in eukaryotic organisms, second only to iron. If one subtracts the amount of iron found in hemoglobin, Zinc becomes the most abundant trace metal found in the human body.
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Zinc fingers, Zinc clusters, and Zinc twists in DNA-binding protein domains
Proceedings of the National Academy of Sciences of the United States of America, 1991Co-Authors: Bert L. Vallee, Joseph E. Coleman, David S. AuldAbstract:Abstract We now recognize three distinct motifs of DNA-binding Zinc Proteins: (i) Zinc fingers, (ii) Zinc clusters, and (iii) Zinc twists. Until very recently, x-ray crystallographic or NMR three-dimensional structure analyses of DNA-binding Zinc Proteins have not been available to serve as standards of reference for the Zinc binding sites of these families of Proteins. Those of the DNA-binding domains of the fungal transcription factor GAL4 and the rat glucocorticoid receptor are the first to have been determined. Both Proteins contain two Zinc binding sites, and in both, cysteine residues are the sole Zinc ligands. In GAL4, two Zinc atoms are bound to six cysteine residues which form a "Zinc cluster" akin to that of metallothionein; the distance between the two Zinc atoms of GAL4 is approximately 3.5 A. In the glucocorticoid receptor, each Zinc atom is bound to four cysteine residues; the interatomic Zinc-Zinc distance is approximately 13 A, and in this instance, a "Zinc twist" is represented by a helical DNA recognition site located between the two Zinc atoms. Zinc clusters and Zinc twists are here recognized as two distinctive motifs in DNA-binding Proteins containing multiple Zinc atoms. For native "Zinc fingers," structural data do not exist as yet; consequently, the interatomic distances between Zinc atoms are not known. As further structural data become available, the structural and functional significance of these different motifs in their binding to DNA and other Proteins participating in the transmission of the genetic message will become apparent.
Artur Krężel - One of the best experts on this subject based on the ideXlab platform.
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Structural Zinc binding sites shaped for greater works: Structure-function relations in classical Zinc finger, hook and clasp domains.
Journal of inorganic biochemistry, 2019Co-Authors: Michał Padjasek, Anna Kocyła, Katarzyna Kluska, Olga Kerber, Józef Ba Tran, Artur KrężelAbstract:Abstract Metal ions are essential elements present in biological systems able to facilitate many cellular processes including proliferation, signaling, DNA synthesis and repair. Zinc ion (Zn(II)) is an important cofactor for numerous biochemical reactions. Commonly, structural Zinc sites demonstrate high Zn(II) affinity and compact architecture required for sequence-specific macromolecule binding. However, how Zn(II)-dependent Proteins fold, how their dissociation occurs, and which factors modulate Zinc protein affinity as well as stability remains not fully understood. The molecular rules governing precise regulation of Zinc Proteins function are hidden in the relationship between sequence and structure, and hence require deep understanding of their folding mechanism under metal load, reactivity and metal-to-protein affinity. Even though, this sequence-structure relationship has an impact on Zinc Proteins function, it has been shown that other biological factors including cellular localization and Zn(II) availability influence overall protein behavior. Taking into account all of the mentioned factors, in this review, we aim to describe the relationship between structure-function-stability of Zinc structural sites, found in a Zinc finger, Zinc hook and Zinc clasps, and reach far beyond a structural point of view in order to appreciate the balance between chemistry and biology that govern the protein world.
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Relationship between the architecture of Zinc coordination and Zinc binding affinity in Proteins – insights into Zinc regulation
Metallomics : integrated biometal science, 2015Co-Authors: Tomasz Kochańczyk, Agnieszka Drozd, Artur KrężelAbstract:Zinc Proteins are an integral component of the proteome of all domains of life. Zn(II), one of the most widespread transition elements, serves multiple functions in Proteins, such as a catalytic co-factor, a structural center and a signaling component. The mechanism by which Proteins associate with and dissociate from Zn(II) and the factors that modulate their affinity and stability remain incompletely understood. In this article, we aim to address how Zinc binding sites present in Proteins differ in their architecture and how their structural arrangement is associated with protein function, thermodynamic and kinetic stability, reactivity, as well as Zinc-dependent regulation. Here, we emphasize that the concentration-dependent functionality of the interprotein Zinc binding site may serve as another factor regulating the relationship between cellular Zn(II) availability and protein function.
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Metal binding properties of the Zinc finger metallome – insights into variations in stability
Metallomics : integrated biometal science, 2014Co-Authors: Anna Miłoch, Artur KrężelAbstract:Zinc is one of the most widespread metal ions found in biological systems. Of the expected 3000 Zinc Proteins in the human proteome, most contain Zinc in structural sites. Among these structures, the most important are Zinc fingers, which are well suited to facilitate interactions with DNA, RNA, Proteins and lipid molecules. Knowledge regarding their stability is a critical issue in understanding the function of Zinc fingers and their reactivity under fluxing cellular Zn(II) availability and different redox states. Zinc stability constants that have been determined using a variety of methods demonstrate wide diversity. Recent studies on the stability of consensus Zinc fingers have demonstrated that the known metal-ion affinities for Zinc fingers may have been underestimated by as much as three or more orders of magnitude. Here, using four natural ββα Zinc fingers, we compare in detail several different methods that have been used for the determination of Zinc finger stability constants, such as common reverse-titration, potentiometry, competition with metal chelators, and a new approach based on a three-step spectrophotometric titration. We discuss why the stabilities of Zinc fingers that are determined spectrophotometrically are frequently underestimated due to the lack of effective equilibrium competition, which leads to large errors during the processing of the titration data. The literature stability constants of many natural Zinc fingers have been underestimated, and they are significantly lower when compared with the consensus peptides. Our data show that in the cell, some naturally occurring Zinc fingers may potentially be unoccupied and are instead loaded transiently with Zn(II). Large variations in stability within the same class of Zinc fingers have demonstrated that the thermodynamic effects hidden in the sequence and structure are the key elements responsible for the differentiation of the stability of the Zinc finger metallome.
