scholarly journals The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases

Catalysts ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1038
Author(s):  
Mario Prejanò ◽  
Marta Erminia Alberto ◽  
Nino Russo ◽  
Marirosa Toscano ◽  
Tiziana Marino
Keyword(s):  
Metal Ions ◽  
Active Site ◽  
Lewis Acids ◽  
Metal Ion ◽  
Metal Species ◽  
Working Mechanism ◽  
Ion Substitution ◽  
High Concentrations ◽  
Ultra Trace ◽  
Theoretical Results

A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.

Efficient Preconcentration of Cu2+, Zn2+ and Fe3+ with an Agarose-Schiff Base Sorbent

2007 ◽  
Vol 72 (7) ◽  
pp. 908-916 ◽  
Author(s):  
Payman Hashemi ◽  
Hatam Hassanvand ◽  
Hossain Naeimi
Keyword(s):  
Schiff Base ◽  
Metal Ions ◽  
Metal Ion ◽  
Good Accuracy ◽  
Kinetic Studies ◽  
Sample Volume ◽  
Effects Of Ph ◽  
Glass Column ◽  
High Concentrations ◽  
Ph Range

Sorption and preconcentration of Cu2+, Zn2+ and Fe3+ on a salen-type Schiff base, 2,2'- [ethane-1,2-diylbis(nitrilomethylidyne)]bis(2-methylphenol), chemically immobilized on a highly crosslinked agarose support, were studied. Kinetic studies showed higher sorption rates of Cu2+ and Fe3+ in comparison with Zn2+. Half-times (t1/2) of 31, 106 and 58 s were obtained for sorption of Cu2+, Zn2+ and Fe3+ by the sorbent, respectively. Effects of pH, eluent concentration and volume, ionic strength, buffer concentration, sample volume and interferences on the recovery of the metal ions were investigated. A 5-ml portion of 0.4 M HCl solution was sufficient for quantitative elution of the metal ions from 0.5 ml of the sorbent packed in a 6.5 mm i.d. glass column. Quantitative recoveries were obtained in a pH range 5.5-6.5 for all the analytes. The volumes to be concentrated exceeding 500 ml, ionic strengths as high as 0.5 mol l-1, and acetate buffer concentrations up to 0.3 mol l-1 for Zn2+ and 0.4 mol l-1 for Cu2+ and Fe3+ did not have any significant effect on the recoveries. The system tolerated relatively high concentrations of diverse ions. Preconcentration factors up to 100 and detection limits of 0.31, 0.16 and 1.73 μg l-1 were obtained for Cu2+, Zn2+ and Fe3+, respectively, for their determination by a flame AAS instrument. The method was successfully applied to the metal ion determinations in several river water samples with good accuracy.

scholarly journals A trapped human PPM1A–phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity

2018 ◽  
Vol 293 (21) ◽  
pp. 7993-8008 ◽  
Author(s):  
Subrata Debnath ◽  
Dalibor Kosek ◽  
Harichandra D. Tagad ◽  
Stewart R. Durell ◽  
Daniel H. Appella ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Metal Ions ◽  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Protein Phosphatases ◽  
Random Order ◽  
Structural Features

Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg2+ or Mn2+ ions for activity in vitro. The crystal structure of human PPM1A (also known as PP2Cα), the first PPM structure determined, displays two tightly bound Mn2+ ions in the active site and a small subdomain, termed the Flap, located adjacent to the active site. Some recent crystal structures of bacterial or plant PPM phosphatases have disclosed two tightly bound metal ions and an additional third metal ion in the active site. Here, the crystal structure of the catalytic domain of human PPM1A, PPM1Acat, complexed with a cyclic phosphopeptide, c(MpSIpYVA), a cyclized variant of the activation loop of p38 MAPK (a physiological substrate of PPM1A), revealed three metal ions in the active site. The PPM1Acat D146E–c(MpSIpYVA) complex confirmed the presence of the anticipated third metal ion in the active site of metazoan PPM phosphatases. Biophysical and computational methods suggested that complex formation results in a slightly more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetics of PPM1Acat toward a phosphopeptide substrate supported a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. This work illuminates the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases.

scholarly journals Trace Metal Detection in Aqueous Reservoirs Using Stilbene Intercalated Layered Rare-Earth Hydroxide Tablets

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Solomon Omwoma
Keyword(s):  
Trace Metal ◽  
Metal Ions ◽  
Metal Ion ◽  
Aqueous Media ◽  
Mitigation Measures ◽  
Metal Ion Analysis ◽  
Gradual Process ◽  
Metal Detection ◽  
Trace Metal Detection ◽  
High Concentrations

Contamination of aquatic reservoirs with metal ions is a slow gradual process that is not easy to detect. Consequences of the metal ions, especially the ones with high atomic numbers (heavy metals) at high concentrations, are severe and irreversible in aquatic reservoirs. As such, early detection mechanisms, especially at trace concentration, are essential for mitigation measures. In this work, a new, robust, and effective tool for trace metal detection and monitoring in aqueous solutions has been developed. Tablets (1 mm thick and similar to medicinal tablets) were manufactured from a powder comprising stilbene intercalated into gallery spaces of lanthanide-containing layered double hydroxides. The tablets were placed in a water column having different concentrations of Pb2+ and Cu2+ ions, and the water was allowed to flow for 45 minutes at a flow rate of 100 ml/s. Thereafter, the tablets were dried and made to powder, and their phosphorescence was measured. The gradual stilbene phosphorescence turnoff in the tablets from various concentrations of metal ions was correlated with sorption amounts. The tablets were able to detect effectively metal ions (up to Pb2+ 1.0 mmol/L and Cu2+ 5.0 mmol/L) in the aqueous media. As such, the concentrations of Pb2+ and Cu2+ ions at trace levels were determined in the test solutions. This method provides a real-time metal ion analysis and does not involve sampling of water samples for analysis in the laboratory.

scholarly journals Comparison of Inflammatory Effects in THP-1 Monocytes and Macrophages after Exposure to Metal Ions

Materials ◽  
2020 ◽  
Vol 13 (5) ◽  
pp. 1150
Author(s):  
Henrike Loeffler ◽  
Anika Jonitz-Heincke ◽  
Kirsten Peters ◽  
Brigitte Mueller-Hilke ◽  
Tomas Fiedler ◽  
...  
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Cell Types ◽  
Cell Number ◽  
Corrosion Products ◽  
Proinflammatory Mediators ◽  
Csf Proteins ◽  
Monocytes And Macrophages ◽  
High Concentrations ◽  
Negative Controls

Monocytes and macrophages are the first barrier of the innate immune system, which interact with abrasion and corrosion products, leading to the release of proinflammatory mediators and free reactive molecules. The aim of this study was to understand inflammation-relevant changes in monocytes and macrophages after exposure to corrosion products. To do this, the THP-1 cell line was used to analyze the effects of metal ions simultaneously in monocytes and differentiated macrophages. Cells were stimulated with several concentrations of metal salts (CoCl2, NiCl2, CrCl3 × 6H2O) to analyze viability, gene expression, protein release and ROS production. Untreated cells served as negative controls. While exposure to Cr(3+) did not influence cell viability in both cell types, the highest concentration (500 µM) of Co(2+) and Ni(2+) showed cytotoxic effects mirrored by significantly reduced metabolism, cell number and a concomitant increase of ROS. The release of IL-1β, IL-8, MCP-1 and M-CSF proteins was mainly affected in macrophages after metal ion exposure (100 µM), indicating a higher impact on pro-inflammatory activity. Our results prove that monocytes and macrophages react very sensitively to corrosion products. High concentrations of bivalent ions lead to cell death, while lower concentrations trigger the release of inflammatory mediators, mainly in macrophages.

scholarly journals Kinetic characterization of enzyme forms involved in metal ion activation and inhibition of myo-inositol monophosphatase

1995 ◽  
Vol 307 (2) ◽  
pp. 585-593 ◽  
Author(s):  
F Strasser ◽  
P D Pelton ◽  
A J Ganzhorn
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Catalytic Mechanism ◽  
Inositol Monophosphatase ◽  
Inositol 1 ◽  
Enzyme Substrate ◽  
Nitrophenyl Phosphate ◽  
Preferential Binding ◽  
Sugar Phosphates ◽  
High Concentrations

Activation and inhibition of recombinant bovine myo-inositol monophosphatase by metal ions was studied with two substrates, D,L-inositol 1-phosphate and 4-nitrophenyl phosphate. Mg2+ and Co2+ are essential activators of both reactions. At high concentrations, they inhibit hydrolysis of inositol 1-phosphate, but not 4-nitrophenyl phosphate. Mg2+ is highly selective for inositol 1-phosphate (kcat. = 26 s-1) compared with the aromatic substrate (kcat. = 1 s-1), and follows sigmoid activation kinetics in both cases. Co2+ catalyses the two reactions at similar rates (kcat. = 4 s-1), but shows sigmoid activation only with the natural substrate. Li+ and Ca2+ are uncompetitive inhibitors with respect to inositol 1-phosphate, but non-competitive with respect to 4-nitrophenyl phosphate. Both metal ions are competitive inhibitors with respect to Mg2+ with 4-nitrophenyl phosphate as the substrate. With inositol 1-phosphate, Ca2+ is competitive and Li+ non-competitive with respect to Mg2+. Multiple inhibition studies indicate that Li+ and Pi can bind simultaneously, whereas no such complex was detected with Ca2+ and Pi. Several sugar phosphates were also characterized as substrates of myo-inositol monophosphatase. D-Ribose 5-phosphate is slowly hydrolysed (kcat. = 3 s-1), but inhibition by Li+ is very efficient (Ki = 0.15 mM), non-competitive with respect to the substrate and competitive with respect to Mg2+. Depending on the nature of the substrate, Li+ inhibits by preferential binding to free enzyme (E), the enzyme-substrate (E.S) or the enzyme-phosphate (E.Pi) complex. Ca2+, on the other hand, inhibits by binding to E and E.S, in competition with Mg2+. The results are discussed in terms of a catalytic mechanism involving two metal ions.

scholarly journals An unusual metal ion configuration in a viral DNA-packaging nuclease active site

2014 ◽  
Vol 70 (a1) ◽  
pp. C489-C489
Author(s):  
Haiyan Zhao ◽  
Theodore Christensen ◽  
Zihan Lin ◽  
Annie Lynn ◽  
Liang Tang
Keyword(s):  
Nucleic Acid ◽  
Metal Ions ◽  
Active Site ◽  
Short Distance ◽  
Metal Ion ◽  
Catalytic Mechanism ◽  
Dna Packaging ◽  
Viral Dna ◽  
Viral Dna Packaging ◽  
Ion Cluster

Nucleic acid metabolism is fundamental to many biological processes. A large class of enzymes such as RNase H, reverse transcriptase, retroviral integrase, topoisomerase, DNA and RNA polymerase, transposase, Holliday-junction resolvase, RNAi slicer Argonaute, and viral DNA-packaging terminase, utilize a common two-metal-ion catalytic mechanism for cleavage or synthesis of nucleic acid chains. Here we report an unusual metal-ion cluster in the active site of the nuclease domain of a viral DNA-packaging terminase unveiled by X-ray structures up to 1.38 Angstrom resolution. Two Mg2+ ions are situated in a coupled octahedral coordination system with liganding oxygen atoms from aspartic acid residues as well as water molecules. The two Mg2+ ions are located within a strikingly short distance of ~2.5 Å, which is unusual given the 1.6 Å atomic radius of Mg2+ and is shorter than previously observed metal-metal distances in metallocluster-containing enzymes or other biological systems. This provides the structural basis for distinguishing Mg2+ from other metal ions such as Ca2+ which are well known to support binding of the nucleic acid substrate but not support catalysis. Such an ultra-short distance between two metal-ions may be essential for generation of a highly positive niche, leading to nucleophilic attack at the phosphodiester bond of DNA. These results have defined the precise chemical configuration of the active site in nucleases using two-metal-ion catalytic mechanism. Moreover, assembly of this two-metal-ion cluster in the viral DNA-packaging terminase is mediated by an adjacent Lys residue, likely serving as a regulatory mechanism for activation of the nuclease activity of the terminase during packaging of viral genome.

scholarly journals Cyclophospholipids Increase Protocellular Stability to Metal Ions

2019 ◽  
Author(s):  
Ö. Duhan Toparlak ◽  
Megha Karki ◽  
Veronica Egas Ortuno ◽  
Ramanarayanan Krishnamurthy ◽  
Sheref Mansy
Keyword(s):  
Fatty Acids ◽  
Life Cycle ◽  
Metal Ions ◽  
Metal Ion ◽  
Narrow Range ◽  
Ion Concentration ◽  
Darwinian Evolution ◽  
Early Earth ◽  
Biological Polymers ◽  
High Concentrations

<p>Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and life as we know it is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here we show that prebiotically plausible monoacyl cyclophospholipids form robust vesicles that survive a broad range of pH and high concentrations of Mg2+, Ca2+, and Na+. Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+. These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.</p>

scholarly journals Active site metals mediate an oligomeric equilibrium in Plasmodium M17 aminopeptidases.

2020 ◽  
pp. jbc.RA120.016313
Author(s):  
Tess R Malcolm ◽  
Matthew J Belousoff ◽  
Hariprasad Venugopal ◽  
Natalie A Borg ◽  
Nyssa Drinkwater ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Metal Ions ◽  
Active Site ◽  
Metal Ion ◽  
Drug Targets ◽  
Dynamic Equilibrium ◽  
Metal Ion Binding ◽  
X Ray Crystallography ◽  
Solution Studies ◽  
Catalytically Active

M17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases from Plasmodium falciparum (PfA-M17) and Plasmodium vivax (Pv-M17) function as catalytically active hexamers to generate free amino acids from human hemoglobin and are drug targets for the design of novel anti-malarial agents. However, the molecular basis for oligomeric assembly is not fully understood. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found that PfA-M17 and Pv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species, that can be controlled by manipulating the identity and concentration of metals available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of Pv-M17 by cryo-electron microscopy and X-ray crystallography together with solution studies revealed that PfA-M17 and Pv-M17 bind metal ions and substrates in a conserved fashion, although Pv-M17 forms the active hexamer more readily and processes substrates faster than PfA-M17. On the basis of these studies, we propose a dynamic equilibrium between monomer  dimer  tetramer  hexamer, which becomes directional towards the large oligomeric states with the addition of metal ions. This sophisticated metal-dependent dynamic equilibrium may apply to other M17 aminopeptidases and underpin the moonlighting capabilities of this enzyme family.

Nanopore analysis of the interaction of metal ions with prion proteins and peptidesThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 347-358 ◽  
Author(s):  
Radu I. Stefureac ◽  
Claudia Avis Madampage ◽  
Olga Andrievskaia ◽  
Jeremy S. Lee
Keyword(s):  
Metal Ions ◽  
Conformational Changes ◽  
Metal Ion ◽  
Prion Proteins ◽  
Peer Review Process ◽  
Cellular Biology ◽  
Divalent Metal Ions ◽  
High Concentrations ◽  
Individual Peptide ◽  
Selection Of

Nanopore analysis can be used to study conformational changes in individual peptide or protein molecules. Under an applied voltage there is a change in the event parameters of blockade current or time when a molecule bumps into or translocates through the pore. If a molecule undergoes a conformational change upon binding a ligand or metal ion the event parameters will be altered. The objective of this research was to demonstrate that the conformation of the prion protein (PrP) and prion peptides can be modulated by binding divalent metal ions. Peptides from the octarepeat region (Octa2, (PHGGGWGQ)2 and Octa 4, (PHGGGWGQ)4), residues 106–126 (PrP106–126), and the full-length Bovine recombinant prion (BrecPrP) were studied with an α-hemolysin pore. Octa2 readily translocated the pore but significant bumping events occurred on addition of Cu(II) and to a lesser extent Zn(II), demonstrating that complex formation was occurring with concomitant conformational changes. The binding of Cu(II) to Octa4 was more pronounced and at high concentrations only a small proportion of the complex could translocate. Addition of Zn(II) also caused significant changes to the event parameters but Mg(II) and Mn(II) were inert. Addition of Cu(II) to PrP106–126 caused the formation of a very tight complex, which could not translocate the pore. Small changes were observed with Zn(II), but not with Mg(II) or Mn(II). Analysis of BrecPrP showed that about 37% were translocation events, but on addition of Cu(II) or Zn(II) these disappeared and only bumping events were recorded. Suprisingly, addition of Mn(II) caused an increase in translocation events to about 64%. Thus, conformational changes to prions upon binding metal ions are readily observed by nanopore analysis.

scholarly journals Cyclophospholipids Increase Protocellular Stability to Metal Ions

2019 ◽  
Author(s):  
Ö. Duhan Toparlak ◽  
Megha Karki ◽  
Veronica Egas Ortuno ◽  
Ramanarayanan Krishnamurthy ◽  
Sheref Mansy
Keyword(s):  
Fatty Acids ◽  
Life Cycle ◽  
Metal Ions ◽  
Metal Ion ◽  
Narrow Range ◽  
Ion Concentration ◽  
Darwinian Evolution ◽  
Early Earth ◽  
Biological Polymers ◽  
High Concentrations

<p>Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and life as we know it is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here we show that prebiotically plausible monoacyl cyclophospholipids form robust vesicles that survive a broad range of pH and high concentrations of Mg2+, Ca2+, and Na+. Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+. These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.</p>

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