Zinc binding of Tim10: evidence for existence of an unstructured binding intermediate for a zinc finger protein

Zinc-finger proteins are among the most abundant proteins in eukaryotic genomes. Tim10 and all the small Tim proteins of the mitochondrial intermembrane space contain a consensus twin CX(3)C zinc-finger motif. Zn(2+) can bind to the reduced Tim10, but not disulphide bonded (oxidized) protein. However, the zinc-binding reaction of Tim10 and of zinc-finger proteins, in general, is ill-defined. In this study, the thermodynamic and kinetic properties of zinc-binding to reduced Tim10 were investigated using circular dichroism (CD), fluorescence spectrometry, and stopped-flow fluorescence techniques. At equilibrium, coupled with the use of protein fluorescence and metal chelators, the zinc-binding affinity was determined for Tim10 to be about 8 x 10(-10)M. Then, far UV CD was used to investigate the secondary structure change upon zinc-binding of the same set of protein samples at various free Zn(2+) concentrations. Comparison between the results of CD and fluorescence studies showed that the zinc-binding reaction is not a simple one-step process. It involves formation of a binding intermediate that is structurally as unfolded as the apoTim10; subsequently, a degree of folding is induced at increased zinc concentrations in the final complex. Next, the stopped-flow fluorescence technique was used to investigate the kinetic process of the binding reaction. Data analysis shows that the reaction has a single kinetic phase at a low free Zn(2+) concentration ( approximately 1 nM), and a double kinetic phase at a high free Zn(2+) concentration. The kinetic result is consistent with that of the studies at equilibrium. Therefore, a two-step reaction model mechanism is proposed, in which zinc-binding is regulated by the initial selective-binding of Zn(2+) to Cys followed by folding. Implication of the two-step zinc-binding mechanism for Zn(2+) trafficking in the cell is discussed.     

Novel Zinc-binding Site in the E2 Domain Regulates Amyloid Precursor-like Protein 1 (APLP1) Oligomerization

The amyloid precursor protein (APP) and the APP-like proteins 1 and 2 (APLP1 and APLP2) are a family of multidomain transmembrane proteins possessing homo- and heterotypic contact sites in their ectodomains. We previously reported that divalent metal ions dictate the conformation of the extracellular APP E2 domain (Dahms, S. O., Könnig, I., Roeser, D., Gührs, K.-H., Mayer, M. C., Kaden, D., Multhaup, G., and Than, M. E. (2012) J. Mol. Biol. 416, 438–452), but unresolved is the nature and functional importance of metal ion binding to APLP1 and APLP2. We found here that zinc ions bound to APP and APLP1 E2 domains and mediated their oligomerization, whereas the APLP2 E2 domain interacted more weakly with zinc possessing a less surface-exposed zinc-binding site, and stayed monomeric. Copper ions bound to E2 domains of all three proteins. Fluorescence resonance energy transfer (FRET) analyses examined the effect of metal ion binding to APP and APLPs in the cellular context in real time. Zinc ions specifically induced APP and APLP1 oligomerization and forced APLP1 into multimeric clusters at the plasma membrane consistent with zinc concentrations in the blood and brain. The observed effects were mediated by a novel zinc-binding site within the APLP1 E2 domain as APLP1 deletion mutants revealed. Based upon its cellular localization and its dominant response to zinc ions, APLP1 is mainly affected by extracellular zinc among the APP family proteins. We conclude that zinc binding and APP/APLP oligomerization are intimately linked, and we propose that this represents a novel mechanism for regulating APP/APLP protein function at the molecular level.     

Cytosolic zinc buffering and muffling: their role in intracellular zinc homeostasis

Our knowledge of the molecular mechanisms of intracellular homeostatic control of zinc ions is now firmly grounded on experimental findings gleaned from the study of zinc proteomes and metallomes, zinc transporters, and insights from the use of computational approaches. A cell's repertoire of zinc homeostatic molecules includes cytosolic zinc-binding proteins, transporters localized to cytoplasmic and organellar membranes, and sensors of cytoplasmic free zinc ions. Under steady state conditions, a primary function of cytosolic zinc-binding proteins is to buffer the relatively large zinc content found in most cells to a cytosolic zinc(ii) ion concentration in the picomolar range. Under non-steady state conditions, zinc-binding proteins and transporters act in concert to modulate transient changes in cytosolic zinc ion concentration in a process that is called zinc muffling. For example, if a cell is challenged by an influx of zinc ions, muffling reactions will dampen the resulting rise in cytosolic zinc ion concentration and eventually restore the cytosolic zinc ion concentration to its original value by shuttling zinc ions into subcellular stores or by removing zinc ions from the cell. In addition, muffling reactions provide a potential means to control changes in cytosolic zinc ion concentrations for purposes of cell signalling in what would otherwise be considered a buffered environment not conducive for signalling. Such intracellular zinc ion signals are known to derive from redox modifications of zinc-thiolate coordination environments, release from subcellular zinc stores, and zinc ion influx via channels. Recently, it has been discovered that metallothionein binds its seven zinc ions with different affinities. This property makes metallothionein particularly well positioned to participate in zinc buffering and muffling reactions. In addition, it is well established that metallothionein is a source of zinc ions under conditions of redox signalling. We suggest that the biological functions of transient changes in cytosolic zinc ion concentrations (presumptive zinc signals) complement those of calcium ions in both spatial and temporal dimensions.     

Zinc-binding property of the major yolk protein in the sea urchin - implications of its role as a zinc transporter for gametogenesis

Major yolk protein (MYP), a transferrin superfamily protein that forms yolk granules in sea urchin eggs, is also contained in the coelomic fluid and nutritive phagocytes of the gonad in both sexes. MYP in the coelomic fluid (CFMYP; 180 kDa) has a higher molecular mass than MYP in eggs (EGMYP; 170 kDa). Here we show that MYP has a zinc-binding capacity that is diminished concomitantly with its incorporation from the coelomic fluid into the gonad in the sea urchin Pseudocentrotus depressus. Most of the zinc in the coelomic fluid was bound to CFMYP, whereas zinc in eggs was scarcely bound to EGMYP. Both CFMYP and EGMYP were present in nutritive phagocytes, where CFMYP bound more zinc than EGMYP. Saturation binding assays revealed that CFMYP has more zinc-binding sites than EGMYP. Labeled CFMYP injected into the coelom was incorporated into ovarian and testicular nutritive phagocytes and vitellogenic oocytes, and the molecular mass of part of the incorporated CFMYP shifted to 170 kDa. Considering the fact that the digestive tract is a major production site of MYP, we propose that CFMYP transports zinc, essential for gametogenesis, from the digestive tract to the ovary and testis through the coelomic fluid, after which part of the CFMYP is processed to EGMYP with loss of zinc-binding site(s).     

Myelin Basic Protein Is a Zinc-Binding Protein in Brain: Possible Role in Myelin Compaction

The zinc-binding proteins (ZnBPs) in porcine brain were characterized by the radioactive zinc-blot technique. Three ZnBPs of molecular weights about 53 kDa, 42 kDa, and 21 kDa were identified. The 53 kDa and 42 kDa ZnBPs were found in all subcellular fractions while the 21 kDa ZnBP was mainly associated with particulate fractions. This 21 kDa ZnBP was identified by internal protein sequence data as the myelin basic protein. Further characterization of its electrophoretic properties and cyanogen bromide cleavage pattern with the authentic protein confirmed its identity. The zinc binding properties of myelin basic protein are metal specific, concentration dependent and pH dependent. The zinc binding property is conferred by the histidine residues since modification of these residues by diethyl-pyrocarbonate would abolish this activity. Furthermore, zinc ion was found to potentiate myelin basic protein-induced phospholipid vesicle aggregation. It is likely that zinc plays an important role in myelin compaction by interacting with myelin basic protein.     

Human papillomavirus type 18 E7 protein requires intact Cys-X-X-Cys motifs for zinc binding, dimerization, and transformation but not for Rb binding.

Human papillomavirus type 18 (HPV-18) E7 proteins bind zinc through Cys-X-X-Cys repeats located at the C terminus of the protein. In order to examine the role of these cysteine motifs in E7 function, we expressed the HPV-18 E7 protein in bacteria and found that purified E7 forms a dimer through interactions with zinc. Mutants with single mutations within the Cys-X-X-Cys motifs bound a reduced level of zinc in a zinc blot assay, while a double mutant lost all zinc-binding activity. When expressed in vivo, none of the mutants cooperated with an activated ras oncogene to transform primary rat embryo fibroblasts, but all mutants retained nearly wild-type Rb-binding activity. The results indicate that the cysteine motifs play an important role in transformation by HPV-18 E7 but do not contribute to Rb binding.     

Biochemical alteration of a metallothionein-like protein in developing rat brain

Zinc participates extensively in the metabolism of carbohydrates, lipids, proteins, and nucleic acids and therefore is essential for the growth and development of all organs, including the brain. The concentrations of zinc in various regions of developing rat brain are nonuniform, and either remain the same or decline dramatically. Studies involving gel permeation chromatography on Sephadex G-75 have shown that unlike the hepatic metallothionein, the concentration of a metallothionein-like protein increases postnatally in the brain from 0.2 μg in 1 d after birth to 3.60 μg zinc/mg protein in 50 d after birth. Furthermore, high-performance liquid chromatographic studies have shown that the adult rat brain contains three small-molecular-weight zinc-binding proteins, one of which is stimulated following intracerebroventricular administration of zinc, producing metallothionein-like isoforms I and II, with retention times of 17.32 and 18.64 min, respectively. All three zinc-binding proteins are absent in the brains of newborn rats. It is proposed that the developmental alteration in the concentration of brain metallothionein-like protein may be related to zinc-mediated functions associated with the development and the maturation of brain.     

Identification of zinc-binding sites of proteins: zinc binds to the amino-terminal region of tubulin

The discovery that certain proteins may require zinc for their activity, and the fact that several of them cannot be purified in large amounts, has led us to develop a rapid, sensitive method to detect these proteins in samples. This method is based on the fractionation of the proteins by gel electrophoresis, blotting onto nitrocellulose paper, and overlaying with 65Zn. We have tested the procedure with well-characterized zinc-binding proteins. In the case of tubulin, we have used this method to localize its zinc-binding site. It was found that zinc binds to the first 150 amino acids of both alpha- and beta-tubulin subunits.     

Accumulation of the major yolk protein and zinc in the agametogenic sea urchin gonad

Sea urchins of both sexes store the nutrients necessary for gametogenesis in nutritive phagocytes of the agametogenic gonad. A zinc-binding protein termed the major yolk protein (MYP) is stored here as two isoforms: the egg-type (predominant in egg yolk granules) and the coelomic fluid-type (a precursor with greater zinc-binding capacity). MYP is used during gametogenesis as material for synthesizing gametic proteins and other components. We investigated its accumulation and relationship to zinc contents in gonads during the non-reproductive season in Pseudocentrotus depressus. MYP constituted most of the protein in coelomic fluid and gonads. Both ovaries and testes grew gradually, accumulating MYP and zinc during the year. Total zinc contents and the ratio of coelomic fluid-type to egg-type protein were higher in ovaries than in testes as gametogenesis approached. Most of the zinc in the coelomic fluid was bound to MYP, and the concentrations of MYP and zinc were elevated toward the onset of oogenesis in the female coelomic fluid. Thus, MYP accumulates in the agametogenic ovaries and testes during the non-reproductive season, playing a role as a carrier to transport zinc to the gonad. Transportation of zinc by MYP is more active in females than in males.     

Zinc uptake of Curtobacterium possessing ω-cyclohexyl fatty acids and zinc-binding activity of its membrane

Abstract The immobilization of zinc taken up by Curtobacterium pusillum strain Z-96 possessing ω-cyclohexyl fatty acids and the zinc-binding activity of the membrane were investigated. The zinc taken up was immobilized in the membrane fraction to a great extent; little zinc was found in the cytoplasmic fraction. Zinc-binding activity of membranes was comparable to the amount of zinc immobilized by the intact cells. The level of ω-cyclohexyl fatty acids and the zinc-binding activity of the membrane were increased by the addition of zinc to the culture medium. The amount of bound zinc was approximately proportional to the level of ω-cyclohexyl fatty acids. In addition, the zinc-binding activity was not appreciably influenced by acidic or high-temperature treatment of membranes.     

Role of zinc metallothionein-3 (ZnMt3) in epidermal growth factor (EGF)-induced c-Abl protein activation and actin polymerization in cultured astrocytes

Recent evidence indicates that zinc plays a major role in neurochemistry. Of the many zinc-binding proteins, metallothionein-3 (Mt3) is regarded as one of the major regulators of cellular zinc in the brain. However, biological functions of Mt3 are not yet well characterized. Recently, we found that lysosomal dysfunction in metallothionein-3 (Mt3)-null astrocytes involves down-regulation of c-Abl. In this study, we investigated the role of Mt3 in c-Abl activation and actin polymerization in cultured astrocytes following treatment with epidermal growth factor (EGF). Compared with wild-type (WT) astrocytes, Mt3-null cells exhibited a substantial reduction in the activation of c-Abl upon treatment with EGF. Consistent with previous studies, activation of c-Abl by EGF induced dissociation of c-Abl from F-actin. Mt3 added to astrocytic cell lysates bound F-actin, augmented F-actin polymerization, and promoted the dissociation of c-Abl from F-actin, suggesting a possible role for Mt3 in this process. Conversely, Mt3-deficient astrocytes showed significantly reduced dissociation of c-Abl from F-actin following EGF treatment. Experiments using various peptide fragments of Mt3 showed that a fragment containing the N-terminal TCPCP motif (peptide 1) is sufficient for this effect. Removal of zinc from Mt3 or pep1 with tetrakis(2-pyridylmethyl)ethylenediamine abrogated the effect of Mt3 on the association of c-Abl and F-actin, indicating that zinc binding is necessary for this action. These results suggest that ZnMt3 in cultured astrocytes may be a normal component of c-Abl activation in EGF receptor signaling. Hence, modulation of Mt3 levels or distribution may prove to be a useful strategy for controlling cytoskeletal mobilization following EGF stimulation in brain cells.     

Zinc through the three domains of life

Zinc is one of the metal ions essential for life, as it is required for the proper functioning of a large number of proteins. Despite its importance, the annotation of zinc-binding proteins in gene banks or protein domain databases still has significant room for improvement. In the present work, we compiled a list of known zinc-binding protein domains and of known zinc-binding sequence motifs (zinc-binding patterns), and then used them jointly to analyze the proteome of 57 different organisms to obtain an overview of zinc usage by archaeal, bacterial, and eukaryotic organisms. Zinc-binding proteins are an abundant fraction of these proteomes, ranging between 4% and 10%. The number of zinc-binding proteins correlates linearly with the total number of proteins encoded by the genome of an organism, but the proportionality constant of Eukaryota (8.8%) is significantly higher than that observed in Bacteria and Archaea (from 5% to 6%). Most of this enrichment is due to the larger portfolio of regulatory proteins in Eukaryota.     

Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone.

The crystal structure of recombinant TroA, a zinc-binding protein component of an ATP-binding cassette transport system in Treponema pallidum, was determined at a resolution of 1.8 A. The organization of the protein is largely similar to other periplasmic ligand-binding proteins (PLBP), in that two independent globular domains interact with each other to create a zinc-binding cleft between them. The structure has one bound zinc pentavalently coordinated to residues from both domains. Unlike previous PLBP structures that have an interdomain hinge composed of beta-strands, the N- and C-domains of TroA are linked by a single long backbone helix. This unique backbone helical conformation was possibly adopted to limit the hinge motion associated with ligand exchange.     

A Zinc Site in the C-Terminal Domain of RAG1 Is Essential for DNA Cleavage Activity

The recombination-activating protein, RAG1, a key component of the V(D)J recombinase, binds multiple Zn²⁺ ions in its catalytically required core region. However, the role of zinc in the DNA cleavage activity of RAG1 is not well resolved. To address this issue, we determined the stoichiometry of Zn²⁺ ions bound to the catalytically active core region of RAG1 under various conditions. Using metal quantitation methods, we determined that core RAG1 can bind up to four Zn²⁺ ions. Stripping the full complement of bound Zn²⁺ ions to produce apoprotein abrogated DNA cleavage activity. Moreover, even partial removal of zinc-binding equivalents resulted in a significant diminishment of DNA cleavage activity, as compared to holo-Zn²⁺ core RAG1. Mutants of the intact core RAG1 and the isolated core RAG1 domains were studied to identify the location of zinc-binding sites. Significantly, the C-terminal domain in core RAG1 binds at least two Zn²⁺ ions, with one zinc-binding site containing C902 and C907 as ligands (termed the CC zinc site) and H937 and H942 coordinating a Zn²⁺ ion in a separate site (HH zinc site). The latter zinc-binding site is essential for DNA cleavage activity, given that the H937A and H942A mutants were defective in both in vitro DNA cleavage assays and cellular recombination assays. Furthermore, as mutation of the active-site residue E962 reduces Zn²⁺ coordination, we propose that the HH zinc site is located in close proximity to the DDE active site. Overall, these results demonstrate that Zn²⁺ serves an important auxiliary role for RAG1 DNA cleavage activity. Furthermore, we propose that one of the zinc-binding sites is linked to the active site of core RAG1 directly or indirectly by E962.     

Inhibitory zinc sites in enzymes

Several pathways increase the concentrations of cellular free zinc(II) ions. Such fluctuations suggest that zinc(II) ions are signalling ions used for the regulation of proteins. One function is the inhibition of enzymes. It is quite common that enzymes bind zinc(II) ions with micro- or nanomolar affinities in their active sites that contain catalytic dyads or triads with a combination of glutamate (aspartate), histidine and cysteine residues, which are all typical zinc-binding ligands. However, for such binding to be physiologically significant, the binding constants must be compatible with the cellular availability of zinc(II) ions. The affinity of inhibitory zinc(II) ions for receptor protein tyrosine phosphatase β is particularly high (K _i = 21 pM, pH 7.4), indicating that some enzymes bind zinc almost as strongly as zinc metalloenzymes. The competitive pattern of zinc inhibition for this phosphatase implicates its active site cysteine and nearby residues in the coordination of zinc. Quantitative biophysical data on both affinities of proteins for zinc and cellular zinc(II) ion concentrations provide the basis for examining the physiological significance of inhibitory zinc-binding sites in proteins and the role of zinc(II) ions in cellular signalling. Regulatory functions of zinc(II) ions add a significant level of complexity to biological control of metabolism and signal transduction and embody a new paradigm for the role of transition metal ions in cell biology.     

Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures

In a recent sequence-analysis study it was concluded that up to 10% of the human proteome could be comprised of zinc proteins, quite varied in the functional spread. The native structures of only few of the proteins are actually established. The elucidation of rest of the sequences of not just human but even other actively investigated genomes may benefit from knowledge of the structural consensus of the zinc-binding centers of the currently known zinc proteins. Nearly four hundred X-ray and NMR structures in the database of zinc-protein structures available as of April 2007 were investigated for geometry and conformation in the zinc-binding centers; separately for the structural and catalytic proteins and individually in the zinc centers coordinated to three and four amino-acid ligands. Enhanced cysteine involvement in agreement with the observation in human proteome has been detected in contrast with previous reports. Deviations from ideal coordination geometries are detected, possible underlying reasons are investigated, and correlations of geometry and conformation in zinc-coordination centers with protein function are established, providing possible benchmarks for putative zinc-binding patterns of the burgeoning genome data.     

Functional characterization of iron-substituted neural zinc finger factor 1: metal and DNA binding

Neural zinc finger factor 1 (NZF-1) is a nonclassical zinc finger protein involved in neuronal development. NZF-1 contains multiple copies of a unique CCHHC zinc-binding domain that recognize a promoter element in the β-retinoic acid receptor gene termed β-retinoic acid receptor element (β-RARE). Previous studies have established that a two-domain fragment of NZF-1 bound with zinc is sufficient for specific DNA binding. Proper functioning of the nervous system relies heavily on iron and misregulation of this highly redox active metal has serious consequences. Several classes of zinc finger proteins have been shown to bind other metal ions, including iron. To determine if ferrous iron can coordinate to the metal-binding sites of NZF-1 and assess the functional consequences of such coordination, a fragment of NZF-1 that contains two zinc-binding domains, NZF-1 double finger (NZF-1-DF), was prepared. UV–vis spectroscopy experiments demonstrated that Fe(II) is capable of binding to NZF-1-DF. Upon reconstitution with either Fe(II) or Zn(II), NZF-1-DF binds selectively and tightly (nanomolar affinity) to its target β-RARE DNA sequence, whereas apo-NZF-1-DF does not bind to DNA and instead aggregates.     

The role of zinc in the S100 proteins: insights from the X-ray structures

We here aim to summarise the present knowledge on zinc binding by S100 proteins. While the importance of modulation of the function of the S100 family of EF-hand proteins by calcium is well established, a substantial proportion is also regulated by zinc or copper. Indeed regulation by zinc in addition to calcium was suggested almost as soon as the first S100 protein was discovered and has been confirmed for many family members by numerous experiments. For the first, “His-Zn”, group, zinc-binding sites composed of three histidines and an aspartic acid were first proposed based on sequence comparisons and later confirmed by structural studies. A second, “Cys-Zn”, group lacks such well-defined zinc-binding motifs and for these cysteines were suggested as the main zinc ligands. There is no three-dimensional structure for a Cys-Zn S100 in the presence of zinc. However, analysis of their sequences together with their X-ray structures in the absence of zinc suggests the possibility of two zinc-binding sites: a conserved site with a degree of similarity to those of the His-Zn group and a less-defined site with a Cys interdimer-binding motif. Some S100 protein-mediated events, such as signalling in the extracellular space, where the levels of calcium are already high, are most unlikely to be calcium regulated. Therefore, a broader knowledge of the role of zinc in the functioning of the S100 proteins will add significantly to the understanding how they propagate their signals.