Tight Metal Binding Research Articles

Effect of pH and denaturants on the fold and metal status of anthrax lethal factor

Anthrax lethal factor (LF) is a critical component of the anthrax toxin, and functions intracellularly as a zinc-dependent endopeptidase targeting proteins involved in maintaining critical host signaling pathways. To reach the cytoplasm, LF requires to be unfolded and guided through the narrow protective antigen pore in a pH-dependent process. The current study sought to address the question as to whether LF is capable of retaining its metal ion when exposed to a low-pH environment (similar to that found in late endosomes) and an unfolding stress (induced by urea). Using a combination of tryptophan fluorescence spectroscopy and chelation studies, we show that a decrease in the pH value (from 7.0 to 5.0) leads to a pronounced shift in the onset of structural alterations in LF to lower urea concentrations. More importantly, the enzyme was found to retain its Zn2+ ion beyond the unfolding transitions monitored by Trp fluorescence, a finding indicative of tight metal binding to LF in a non-native state. In addition, an analysis of red-edge excitation shift (REES) spectra suggests the protein to maintain residual structure (a feature necessary for metal binding) even at very high denaturant concentrations. Furthermore, studies using the chromophoric chelator 4-(2-pyridylazo)resorcinol (PAR) revealed LF's Zn2+ ion to become accessible to complexation at urea concentrations in between those required to cause structural changes and metal dissociation. This phenomenon likely originates from the conversion of a PAR-inaccessible (closed) to a PAR-accessible (open) state of LF at intermediate denaturant concentrations.

Contributions of primary coordination ligands and importance of outer sphere interactions in UFsc, a de novo designed protein with high affinity for metal ions

Metalloproteins constitute nearly half of all proteins and catalyze some of the most complex chemical reactions. Recently, we reported a design of 4G-UFsc (Uno Ferro single chain), a single chain four-helical bundle with extraordinarily high (30 pM) affinity for zinc. We evaluated the contribution of different side chains to binding of Co(II), Ni(II), Zn(II) and Mn(II) using systematic mutagenesis of the amino acids that constitute the primary metal coordination and outer spheres. The binding affinity of proteins for metals was then measured using isothermal titration calorimetry. Our results show that both primary metal coordination environment and side chains in the outer sphere of UFsc are highly sensitive to even slight changes and can be adapted to binding different 3d metals, including hard-to-tightly bind metal ions such as Mn(II). The studies on the origins of tight metal binding will guide future metalloprotein design efforts.

Ni(II) Sensing by RcnR Does Not Require an FrmR-Like Intersubunit Linkage.

E. coli RcnR (resistance to cobalt and nickel regulator) is a homotetrameric DNA binding protein that regulates the expression of a Ni(II) and Co(II) exporter (RcnAB) by derepressing expression of rcnA and rcnB in response to binding Co(II) or Ni(II). Prior studies have shown that the cognate metal ions, Ni(II) and Co(II), bind in six-coordinate sites at subunit interfaces and are distinguished from noncognate metals (Cu(I), Cu(II), and Zn(II)) by coordination number and ligand selection. In analogy with FrmR, a formaldehyde-responsive transcriptional regulator in the RcnR/CsoR family, the interfacial site allows the metal ions to "cross-link" the N-terminal domain of one subunit with the invariant Cys35 residue in another, which has been deemed to be key to mediating the allosteric response of the tetrameric protein to metal binding. Through the use of mutagenesis to disconnect one subunit from the metal-mediated cross-link, X-ray absorption spectroscopy (XAS) as a structural probe, LacZ reporter assays, and metal binding studies using isothermal titration calorimetry (ITC), the work presented here shows that neither the interfacial binding site nor the coordination number of Ni(II) is important to the allosteric response to binding of this cognate metal ion. The opposite is found for the other cognate metal ion, Co(II), with respect to the interfacial binding site, suggesting that the molecular mechanisms for transcriptional regulation by the two ions are distinct. The metal binding studies reveal that tight metal binding is maintained in the variant. XAS is further used to demonstrate that His33 is not a ligand for Co(II), Ni(II), or Zn(II) in WT-RcnR. The results are discussed in the context of the overall understanding of the molecular mechanisms of metallosensors.

Complex-forming properties of peat humic acids from a raised bog profiles

Humic substances (HS) belong to the most powerful complex-forming agents, significantly affecting major and trace element speciation in natural environment. Several authors have focused on humic–metal interactions, using differing methods and comparing humic substances on different sources. However, the intrinsic differences among the HS of different origin and the impact of humification degree on the complex formation between humic substances and metals have not received the necessary attention until now.The aim of this study is to determine the Cu(II) complexing capacity and stability constants of Cu(II) complexes of humic acids (HA) isolated from two well-characterized raised bog peat profiles in respect to the basic properties and humification characteristics of the studied peats and their humic acids. Elemental and functional analysis of the isolated HA were determined by elemental composition (C, H, N, O), UV spectrophotometry, and the total acidity method, as well as the copper (Cu2+) ion selective electrode was used in complexing analysis of humic acids and metal ions.The complex stability constants are within the range of stability constants of the humic substances isolated from other sources (soil, coal, water, and peat). The complex stability constants significantly changed within the bog profiles and are well correlated with the age and the degree of peat decomposition.A comparison of the complex stability constant and the actual copper concentration in peat humic acids shows significant correlation, indicating the importance of tight metal binding for the actual presence of metal in peat and peat humic acids. None of the basic characteristics of humic acids (concentration of carboxylic groups and total acidity, hydrophobicity, etc.) alone can fully explain the complex-forming capacity of humic acids, which suggests a contribution of other factors that are yet to be determined.

Multivalent, Sulfur-Rich PyBox Asterisk Ligands in Asymmetric Metal Catalysis (Eur. J. Org. Chem. 31/2012)

The cover picture shows white flowers of wild garlic (Allium ursinum), also called bear's garlic, with six petals and yellow pistils. Their bulbs are a favorite of brown bears and wild boars. In the old days, wild garlic was considered as a magic plant. It is also classified as a medicinal plant containing numerous sulfurated and odorous compounds, which is supposed to detoxify the body from heavy metals. The analogy to the PyBox asterisk ligand could not be better. Similarly, it also has six petals, contains sulfur, is able to bind heavy metals, and even has a yellow color originating from its (sulfurated) core. Additionally, the magic comes from the ability of a PyBox asterisk to modulate the enantioselectivity of a rhodium-catalyzed hydrosilylation reaction according to its metal content. Some competitive crossover experiments with other PyBox ligands and molecular modeling calculations indicated that six proximal sulfur atoms do not inhibit this enantiocatalytic process, even at a 1 % molar ratio. The enantioselectivity mainly comes from a tight metal binding to the PyBox petals (ligands). This work promotes new thoughts about multivalent ligands in metal-mediated catalysis. Details are discussed in the article by M. Gingras et al. on p. 6145 ff.

Insights into the Role of an Active Site Aspartate in Ty1 Reverse Transcriptase Polymerization

Long terminal repeat-containing retrotransposons encode reverse transcriptases (RTs) that replicate their RNA into integratable, double-stranded DNA. A mutant version of the RT from Saccharomyces cerevisiae retrotransposon Ty1, in which one of the three active site aspartates has been changed to asparagine (D211N), is still capable of in vitro polymerization, although it is blocked for in vivo transposition. We generated recombinant WT and D211N Ty1 RTs to study RT function and determine specific roles for the Asp(211) residue. Presteady-state kinetic analysis of the two enzymes shows that the D211N mutation has minimal effect on nucleotide binding but reduces the k(pol) by approximately 230-fold. The mutation reduces binding affinity for both Mn(2+) and Mg(2+), indicating that the Asp(211) side chain helps create a tight metal binding pocket. Although both enzymes are highly processive and tend to remain bound to their initial substrate, each shows distinctive patterns of pausing, attributable to interactions between metal ions and the active site residue. These results provide insights to specific roles for the Asp(211) residue during polymerization and indicate unusual enzymatic properties that bear on the Ty1 replication pathway.

Metal binding by humic acids isolated from water hyacinth plants ( Eichhornia crassipes [Mart.] Solm-Laubach: Pontedericeae) in the Nile Delta, Egypt

Humic acids (HAs) are animal and plant decay products that confer water retention, metal and organic solute binding functions and texture/workability in soils. HAs assist plant nutrition with minimal run-off pollution. Recent isolation of HAs from several live plants prompted us to investigate the HA content of the water hyacinth ( Eichhornia crassipes [Mart.] Solm-Laubach: Pontedericeae), a delicately flowered plant from Amazonian South America that has invaded temperate lakes, rivers and waterways with devastating economic effects. Hyacinth thrives in nutrient-rich and polluted waters. It has a high affinity for metals and is used for phytoremediation. In this work, HAs isolated from the leaves, stems and roots of live water hyacinth plants from the Nile Delta, Egypt were identified by chemical and spectral analysis and by comparison with authentic soil and plant derived HAs. Similar carbohydrate and amino acid distributions and tight metal binding capacities of the HAs and their respective plant components suggest that the presence of HAs in plants is related to their metal binding properties.

Fate of heavy metals in a strongly acidic shooting‐range soil: small‐scale metal distribution and its relation to preferential water flow

AbstractTo assess the mobility of Pb and associated metals in a highly contaminated shooting range soil (Losone, Ticino, Switzerland), we investigated the spatial distribution of the metals and their relation to preferential water flow paths. A 2.2 m2 plot located 40 m behind the stop butt was irrigated with a solution containing bromide and Brilliant Blue, a slightly sorbing dye. A soil profile 50 cm in width was sampled down to 80 cm with a spatial resolution of 2.5 cm, resulting in 626 samples. Concentrations of elements (12 ≤ Z ≤ 92) were determined by energy‐dispersive Xray fluorescence spectrometry, and Brilliant Blue concentrations were determined with a chromameter. In the acidic (pH 3), organic matter‐rich, well drained Dystric Cambisol, maximum concentrations of 80.9 g kg‐1 Pb, 4.0 g kg‐1 Sb, and 0.55 g kg‐1 Cu were measured in the topsoil. Within 40 cm soil depth, however, Pb, Sb, and Cu approached background concentrations of 23 mg kg‐1, 0.4 mg kg‐1, and 9.4 mg kg‐1, respectively. The even horizontal distribution and the steep gradient along soil depth indicate tight metal binding in the topsoil, and a fairly homogeneous transport front. In contrast, water flow through the profile was highly heterogeneous. In the uppermost 20 cm, preferential flow was initiated by heterogeneous infiltration at the soil surface, but had no influence on metal distribution. Below 20 cm, however, preferential flow originated from larger tree roots, and metal concentrations were significantly elevated along these macropores. Spatial distributions of Pb, Sb, and Cu were similar, suggesting that all three metals are strongly retained in the topsoil and transported along preferential water flow paths in the subsoil.

Dynamics of interdomain and intermolecular interactions in mammalian metallothioneins

The structures of mammalian metallothioneins (MTs), as solved by X-ray crystallography and NMR spectroscopy, all show seven divalent metals bound in two separate domains. The marked differences in metal-mobilities found for the two domains has led to the proposal for a dual role for the two MT metal domains. The tight metal binding in the C-terminal α-domain supposedly constitutes the basis for the detoxification of excess heavy metals, while the more labile metals in the N-terminal β-domain function in the homeostasis of the essential elements zinc and copper. In this overview, we compare the two types of dimers found for MTs and their influence on metal-mobilities. In the presence of excess metal, the N-terminal domain is responsible for the formation of metal-bridged dimers while under aerobic conditions, a specific intermolecular disulfide is formed between the C-terminal domains. Both forms of dimers not only involve different domains for their intermolecular protein interactions, they also exhibit radical differences in the reactive properties of their respective cluster bound metal ions. Since the metal exchange within each domain is also influenced by interdomain interactions, the relative orientation of the domains is also most likely important for MT functions. Thus far, the relative orientation of the two domains could only be obtained from the crystal structure. Here, we present evidence for increased mobility in the linker region as the reason for the lack of interdomain constraints in the solution NMR studies of mammalian MTs.

The effect of temperature on tight metal binding by peat and soil derived solid humic acids

The brown biomaterials called humic acids (HA) in peats and soils retain water and bind metal cations and other solutes. Studies of the interactions of purified solid peat and soil-derived HA from different countries with metal cations in water probe HA microstructures and help to characterize the metal binding sites. Labile cations such as Caaq2+, Co aq2+, Cu aq2+, Fe aq3+, Mg aq2+ and Mn aq2+ tightly bind to solid HAs in sequential steps. The isotherms A vs. c are well fitted with the Langmuir model and plots of 1/A vs. 1/c are linear for each step. Here, A is mmol bound metal g–1 HA and c is the equilibrium cation concentration (M). This paper compares the stoichiometric site capacities vi and equilibrium constants Ki for tight binding of Ca aq2+, Co aq2+, Cu aq2+, Fe aq3+, Mg aq2+ and Mn aq2+ at different solid HA sites. Measurements at different temperatures give linearly correlated metal binding enthalpy and entropy changes, indicating that conformational changes and cation/HA hydration/dehydration are important factors in metal binding and release by solid HAs. Key words: Humic acids; metal binding; isotherms; thermodynamics

Overproduction and characterization of a dimeric non-zinc glyoxalase I from Escherichia coli: evidence for optimal activation by nickel ions.

The ubiquitous glyoxalase system converts toxic alpha-keto aldehydes into their corresponding nontoxic 2-hydroxycarboxylic acids, utilizing glutathione (GSH) as a cofactor. The first enzyme in this system, glyoxalase I (GlxI), catalyzes the isomerization of the hemithioacetal formed nonenzymatically between GSH and cytotoxic alpha-keto aldehydes. To study the Escherichia coli GlxI enzyme, the DNA encoding this protein, gloA, was isolated and incorporated into the plasmid pTTQ18. Nucleotide sequencing of the gloA gene predicted a polypeptide of 135 amino acids and Mr of 14 919. The gloA gene has been overexpressed in E. coli and shown to encode for GlxI. An effective two-step purification protocol was developed, yielding 150-200 mg of homogeneous protein per liter of culture. Electrospray mass spectrometry confirmed the monomeric weight of the purified protein, while gel filtration analysis indicated GlxI to be a homodimer of 30 kDa. Zinc, the natural metal ion found in the Homo sapiens and Saccharomyces cerevisiae GlxI, had no effect on the activity of E. coli GlxI. In contrast, the addition of NiCl2 to the growth medium or to purified E. coli apo-GlxI greatly enhanced the enzymatic activity. Inductively coupled plasma and atomic absorption analyses indicated binding of only one nickel ion per dimeric enzyme, suggesting only one functional active site in this homodimeric enzyme. In addition, the apoprotein regained maximal activity with one molar equivalence of nickel chloride, indicative of tight metal binding. The effects of pH on the kinetics of the nickel-activated enzyme were also studied. This is the first example of a non-zinc activated GlxI whose maximal activation is seen with Ni2+.

Tight metal binding by humic acids and its role in biomineralization †

Analytical and thermodynamic data, EPR, FTIR, solution 1H and solid-state 13C cross polarization magic angle spinning NMR and solid-state extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra have been recorded for purified humic acids (HAs) isolated from a German peat (GHA), an Irish peat (IHA), an unpolluted New Hampshire bog soil (NHA) and their tightly bound copper(II), iron(III) and manganese(II) forms. Brief water washing of partly or fully metal-loaded HAs leaves ‘tightly’ bound metal in the isolated freeze-dried solids. Most of this metal is removed by washing with 0.1 M HCl, indicating acidic HA functional groups as principal metal binding sites. The number of nearest-neighbour atoms co-ordinated to tightly bound CuII (four), FeIII (six, probably with distorted geometry) and MnII (six, undistorted) in solid GHA, IHA and NHA were determined by XANES and EXAFS spectroscopy with reference standards. Isotherms measured at 20.0 °C and pH 2.4–3.2 with [M]total = 0.18–25.8 mM for tight, reversible Cu2+(aq), Fe3+(aq), and Mn2+(aq) binding by solid IHA and NHA fit the Langmuir model and give the pH-independent stoichiometric site capacities νi and equilibrium constants Ki for metal binding at specific HA sites i = A, B and C. Tight binding sites A, B and C of IHA are occupied by CuII, sites A and B by FeIII and site A by MnII, while only identical metal binding site A in NHA is tight enough to resist metal removal by brief water washing. A new helical HA molecular model based on the empirical formula C36H30N2O15·xH2O visualizes metal binding and the likely roles of HAs in biomineralization. Site A is suggested to be carboxylate, mixed ligands probably constitute site B, and site C is tentatively assigned as the interior of the HA helix. Binding free energies and EPR evidence suggest that Cu2+(aq), Fe3+(aq) and Mn2+(aq) rapidly transfer between specific HA binding sites. This affects rates of metal release and transfer to minerals.

Metal binding to DNA polymerase I, its large fragment, and two 3‘,5‘-exonuclease mutants of the large fragment.

DNA polymerase I (Pol I) is an enzyme of DNA replication and repair containing three active sites, each requiring divalent metal ions such as Mg2+ or Mn2+ for activity. As determined by EPR and by 1/T1 measurements of water protons, whole Pol I binds Mn2+ at one tight site (KD = 2.5 microM) and approximately 20 weak sites (KD = 600 microM). All bound metal ions retain one or more water ligands as reflected in enhanced paramagnetic effects of Mn2+ on 1/T1 of water protons. The cloned large fragment of Pol I, which lacks the 5',3'-exonuclease domain, retains the tight metal binding site with little or no change in its affinity for Mn2+, but has lost approximately 12 weak sites (n = 8, KD = 1000 microM). The presence of stoichiometric TMP creates a second tight Mn2+ binding site or tightens a weak site 100-fold. dGTP together with TMP creates a third tight Mn2+ binding site or tightens a weak site 166-fold. The D424A (the Asp424 to Ala) 3',5'-exonuclease deficient mutant of the large fragment retains a weakened tight site (KD = 68 microM) and has lost one weak site (n = 7, KD = 3500 microM) in comparison with the wild-type large fragment, and no effect of TMP on metal binding is detected. The D355A, E357A (the Asp355 to Ala, Glu357 to Ala double mutant of the large fragment of Pol I) 3',5'-exonuclease-deficient double mutant has lost the tight metal binding site and four weak metal binding sites. The binding of dGTP to the polymerase active site of the D355A,E357A double mutant creates one tight Mn2+ binding site with a dissociation constant (KD = 3.6 microM), comparable with that found on the wild-type enzyme, which retains one fast exchanging water ligand. Mg2+ competes at this site with a KD of 100 microM. It is concluded that the single tightly bound Mn2+ on Pol I and a weakly bound Mn2+ which is tightened 100-fold by TMP are at the 3',5'-exonuclease active site and are essential for 3',5'-exonuclease activity, but not for polymerase activity. Additional weak Mn2+ binding sites are detected on the 3',5'-exonuclease domain, which may be activating, and on the polymerase domain, which may be inhibitory. The essential divalent metal activator of the polymerase reaction requires the presence of the dNTP substrate for tight metal binding indicating that the bound substrate coordinates the metal.(ABSTRACT TRUNCATED AT 400 WORDS)

Tight divalent metal binding to Escherichia coli F1-adenosinetriphosphatase. Complete substitution of intrinsic magnesium by manganese or cobalt and studies of metal binding sites.

Tight divalent metal binding sites in Escherichia coli F1-adenosinetriphosphatase (F1-ATPase) were studied. Native enzyme contained two Mg per F1, confirming previous results. All of the Mg may be replaced by Co or Mn using a dissociation-repolymerization procedure. The substituted enzymes are homogeneous and contain two Mn per F1 or two Co per F1. They are fully active as ATPases, they rebind to F1-depleted membranes, and they catalyze ATP-driven proton pumping. N,N'-Dicyclohexylcarbodiimide-(DCCD) inactivated F1 retains all the intrinsic tightly bound Mg. Evidence is presented that DCCD affects at least two beta subunits in E. coli F1, and therefore, the tightly bound metals appear not to be bound at the DCCD-reactive glutamate residue on the beta subunit. However, the nature of the tightly bound metal (Mg, Mn, or Co) as well as the presence of added (2 mM) MgSO4, MnSO4, or CoSO4 affected the rate of DCCD inactivation, showing that metal binding changes the beta-subunit conformation. Isolated F1 alpha subunit bound Mg, Mn, or Co stoichiometrically and independently of ATP binding. Isolated F1 beta subunit bound only small amounts of Mg, and no Co or Mn. Therefore, it is possible, although not conclusively shown, that the alpha subunit is the site of tight metal binding in the intact F1.