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.

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.

Properties of the mammalian and yeast metal-ion transporters DCT1 and Smf1p expressed in Xenopus laevis oocytes

2001 ◽  
Vol 204 (6) ◽  
pp. 1053-1061 ◽  
Author(s):  
A. Sacher ◽  
A. Cohen ◽  
N. Nelson
Keyword(s):  
Xenopus Laevis ◽  
Metal Ions ◽  
Metal Ion ◽  
Divalent Cations ◽  
Ion Uptake ◽  
Xenopus Laevis Oocytes ◽  
Ion Transporters ◽  
Divalent Metal Ions ◽  
Transport Pathway ◽  
Metal Ion Uptake

Transition metals are essential for many metabolic processes, and their homeostasis is crucial for life. Metal-ion transporters play a major role in maintaining the correct concentrations of the various metal ions in living cells. Little is known about the transport mechanism of metal ions by eukaryotic cells. Some insight has been gained from studies of the mammalian transporter DCT1 and the yeast transporter Smf1p by following the uptake of various metal ions and from electrophysiological experiments using Xenopus laevis oocytes injected with RNA copies (c-RNA) of the genes for these transporters. Both transporters catalyze the proton-dependent uptake of divalent cations accompanied by a ‘slippage’ phenomenon of different monovalent cations unique to each transporter. Here, we further characterize the transport activity of DCT1 and Smf1p, their substrate specificity and their transport properties. We observed that Zn(2+) is not transported through the membrane of Xenopus laevis oocytes by either transporter, even though it inhibits the transport of the other metal ions and enables protons to ‘slip’ through the DCT1 transporter. A special construct (Smf1p-s) was made to enhance Smf1p activity in oocytes to enable electrophysiological studies of Smf1p-s-expressing cells. 54Mn(2+) uptake by Smf1p-s was measured at various holding potentials. In the absence of Na(+) and at pH 5.5, metal-ion uptake was not affected by changes in negative holding potentials. Elevating the pH of the medium to 6.5 caused metal-ion uptake to be influenced by the holding potential: ion uptake increased when the potential was lowered. Na(+) inhibited metal-ion uptake in accordance with the elevation of the holding potential. A novel clutch mechanism of ion slippage that operates via continuously variable stoichiometry between the driving-force pathway (H(+)) and the transport pathway (divalent metal ions) is proposed. The possible physiological advantages of proton slippage through DCT1 and of Na(+) slippage through Smf1p are discussed.

Molecular simulations of protein disorderThis 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. 269-290 ◽  
Author(s):  
Sarah Rauscher ◽  
Régis Pomès
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Peer Review Process ◽  
Structural Heterogeneity ◽  
Disordered Proteins ◽  
Cellular Biology ◽  
Protein Disorder ◽  
Conformational Ensembles ◽  
Intrinsically Disordered ◽  
Simulation Techniques ◽  
Selection Of

Protein disorder is abundant in proteomes throughout all kingdoms of life and serves many biologically important roles. Disordered states of proteins are challenging to study experimentally due to their structural heterogeneity and tendency to aggregate. Computer simulations, which are not impeded by these properties, have recently emerged as a useful tool to characterize the conformational ensembles of intrinsically disordered proteins. In this review, we provide a survey of computational studies of protein disorder with an emphasis on the interdisciplinary nature of these studies. The application of simulation techniques to the study of disordered states is described in the context of experimental and bioinformatics approaches. Experimental data can be incorporated into simulations, and simulations can provide predictions for experiment. In this way, simulations have been integrated into the existing methodologies for the study of disordered state ensembles. We provide recent examples of simulations of disordered states from the literature and our own work. Throughout the review, we emphasize important predictions and biophysical understanding made possible through the use of simulations. This review is intended as both an overview and a guide for structural biologists and theoretical biophysicists seeking accurate, atomic-level descriptions of disordered state ensembles.

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.

The Effect Of Physiological Metal Ions On The Procoagulant Enzyme-Cofactor Complexes Of The Extrinsic Pathway Of Coagulation

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1096-1096
Author(s):  
Maria Cristina Bravo ◽  
Catherine G McGuinness ◽  
Matthew Gissel ◽  
Thomas Orfeo ◽  
Kenneth G. Mann
Keyword(s):  
Complex Systems ◽  
Metal Ions ◽  
Closed System ◽  
Plasma Levels ◽  
Metal Ion ◽  
Activated Protein C ◽  
Coagulation Cascade ◽  
Divalent Metal Ions ◽  
Zymogen Activation ◽  
Extrinsic Pathway

Abstract Introduction The rapid coagulation response to vascular injury is mediated by the formation of three enzyme cofactor complexes (extrinsic tenase, intrinsic tenase and prothrombinase) on membrane surfaces. A common structural feature of these proteases is their GLA domains, each of which requires the binding of divalent metal ions at multiple sites to achieve the conformation necessary for optimal membrane and cofactor binding. Both Ca2+ and Mg2+ ions have been reported to bind to GLA domain sites. However almost all studies kinetically characterizing these complexes have been done in the presence of Ca2+ (2-5 mM) as the sole metal ion, despite the relatively equivalent availability in plasma of both free Ca2+ (∼1.1 mM) and Mg2+ (∼0.6 mM) (Ca2+/Mg2+). A recent study has systematically examined the effects of various Ca2+ concentrations with and without Mg2+ on the membrane binding of activated protein C (APC) and FVIIa and enzymatic activity of APC and the extrinsic tenase complex which were enhanced in Ca2+/Mg2+ relative to Ca2+ alone (Vadivel, K., et al, 2013 JMB). In the current study we compare the effects of plasma levels of Ca2+ and Mg2+ versus Ca2+alone on the catalytic performances of the extrinsic tenase, intrinsic tenase and prothrombinase complexes individually and collectively. Methods All experiments were conducted in Hepes buffered saline pH 7.4 containing 0.1% PEG and either 2 mM Ca2+ or 1.1 mM Ca2+/0.6 mM Mg2+ (Ca2+/Mg2+). In closed system experiments, enzyme-cofactor complexes were assembled on phospholipid vesicles composed of a 3:1 ratio of synthetic phosphatidylcholine and phosphatidylserine (PCPS), and zymogen activation monitored via sampling into assay mixtures containing the appropriate chromogenic substrate. In open system experiments complexes were preassembled on PCPS coated capillaries, the zymogen delivered in the flowing phase and the extent of zymogen activation monitored in the effluent as described previously (Haynes, LM., et al, 2011 Biophys J). The combined interaction of the procoagulant enzyme cofactor complexes under both metal ion conditions was studied in a synthetic coagulation proteome monitoring thrombin (IIa) generation as previously described (van’t Veer, C., and Mann, KG, 1997 JBC). Results Extrinsic tenase The extrinsic tenase complex had an approximately two-fold higher rate of FXa generation in the presence of Ca2+/Mg2+ (1.78 ±0.05 pM/s) versus Ca2+ alone (0.88 ± 0.02 pM/s) (N=3, p<0.001). Experiments were also conducted in the absence or presence of tissue factor pathway inhibitor (TFPI); in the presence of TFPI and Ca2+/Mg2+ ions the extrinsic tenase complex was three times as catalytically active compared to TFPI and Ca2+ only (N=3, p<0.05). Direct FXa inhibition by TFPI was not significantly different between the Ca2+ and Ca2+/Mg2+ containing buffers. Intrinsic tenase In closed system experiments the intrinsic tenase complex showed impaired FXa generation in the presence of Ca2+/Mg2+ (29.3 ± 3.4 pM/s) compared to Ca2+ alone (51.7 ± 3.0 pM/s) (N=3, p<0.001). Thrombin activation of FVIII was not statistically different between both buffers, however the presence of Ca2+/Mg2+ resulted in a more rapid loss of cofactor activity over Ca2+ alone. Prothrombinase Under flow, IIa generation measured from prothrombinase was not statistically different between both buffers when measured at five different shear rates (100-1000s-1, N≥2). Plasma proteome In the synthetic coagulation proteome (N=4) the presence of Ca2+/Mg2+ led to an average 31% increase in maximum IIa levels compared to Ca2+alone and an average decrease of 1 minute to reach maximum levels. Conclusions In summary, the presence of plasma levels of Ca2+ and Mg2+, compared to Ca2+ alone, enhances the initiation phase of the extrinsic pathway of coagulation by enhancing the rate of FXa generation from the extrinsic tenase complex while also impairing the TFPI inhibition of the extrinsic tenase complex. These procoagulant effects are potentially abrogated by the suppressive effects of Ca2+/Mg2+ on the intrinsic tenase complex, potentially caused by the increased rate of spontaneous inactivation of FVIIIa. These results highlight the importance of complementing the assessments of individual enzyme complex systems with studies of the larger complex systems in which they function to identify the net physiologic impact of metal ions that target various components in the coagulation cascade. Disclosures: Mann: Haematologic Technologies, Inc: Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.

scholarly journals Metal Ion Selectivity of Kojate Complexes: A Theoretical Study

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Sarita Singh ◽  
Jyoti Singh ◽  
Sunita Gulia ◽  
Rita Kakkar
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
Ion Selectivity ◽  
Divalent Metal Ions ◽  
High Energies ◽  
Square Planar ◽  
Metal Ion Selectivity ◽  
Carbonyl Bond ◽  
Complexation Reactions

Density functional calculations have been performed on four-coordinate kojate complexes of selected divalent metal ions in order to determine the affinity of the metal ions for the kojate ion. The complexation reactions are characterized by high energies, showing that they are highly exothermic. It is found that Ni(II) exhibits the highest affinity for the kojate ion, and this is attributed to the largest amount of charge transfer from the ligand to the metal ion. The Ni(II) complex has distorted square planar structure. The HOMOs and LUMOs of the complexes are also discussed. All complexes display a strong band at ~1500 cm−1 corresponding to the stretching frequency of the weakened carbonyl bond. Comparison of the complexation energies for the two steps shows that most of the complexation energy is realized in the first step. The energy released in the second step is about one-third that of the first step.

scholarly journals Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Metal Ion ◽  
Ternary Complex ◽  
Critical Role ◽  
Divalent Metal ◽  
Binary Complex ◽  
Divalent Metal Ions ◽  
Divalent Metal Ion ◽  
Initial Binding

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

scholarly journals Modeling of neotame and fructose thermochemistry: Comparison with mono and divalent metal ions by Computational and experimental approach

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Deepali Sharma ◽  
Suvardhan Kanchi ◽  
Ayyappa Bathinapatla ◽  
Inamuddin ◽  
Abdullah M. Asiri
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Density Functional ◽  
Divalent Metal ◽  
Basis Set ◽  
Hydroxyl Groups ◽  
Specific Cell ◽  
Water Medium ◽  
Artificial Sweetener ◽  
Divalent Metal Ions

AbstractThe metal complexes can demonstrate various interesting biological activities in the human body. However, the role of certain metal ions for specific cell activities is still subject to debate. This study is aimed at comparing the thermochemical properties of neotame (artificial sweetener) and α, β-fructose in gas phase and water medium. The interaction of α and β-fructose, neotame with monovalent and divalent metal ions was studied and comprehended by density functional theory (DFT) using B3LYP functional, 6–311 + G (d, p) and D3 basis set. Metal ion affinities (MIA) values depicted that ionic radius of metal ions played an important role in the interaction of α, β-fructose and neotame. The ∆G parameter was calculated to predict and understand the interaction of metal ions with α and β-fructose, neotame. The results suggested that the presence of hydroxyl groups and oxygen atoms in sugar molecules acted as preferred sites for the binding and interaction of mono and divalent ions. For the first time computational study has been introduced in the present study to review the progress in the application of metal binding with sugar molecules especially with neotame. Moreover, voltammetric behaviour of neotame-Zn2+ was studied using cyclic and differential pulse voltammetry. The obtained results suggest that the peak at −1.13 V is due to the reduction of Zn2+ in 0.1 M phosphate buffer medium at pH 5.5. Whereas, addition of 6-fold higher concentration of neotame to the ZnCl2.2H2O resulted in a new irreversible cathodic peak at −0.83, due to the reduction of neotame-Zn2+ complex. The Fourier transform infrared spectroscopy (FTIR) results indicates that the β-amino group (-NH) and carboxyl carbonyl (-C = O) groups of neotame is participating in the chelation process, which is further supported by DFT studies. The findings of this study identify the efficient chelation factors as major contributors into metal ion affinities, with promising possibilities to determine important biological processes in cell wall and glucose transmembrane transport.

Comparative studies of kinetic and optical properties of rabbit muscle, sturgeon muscle, and yeast pyruvate kinase

1980 ◽  
Vol 58 (3) ◽  
pp. 194-200 ◽  
Author(s):  
Chiu-Yin Kwan ◽  
Jerome L. Gabriel ◽  
Robert C. Davis
Keyword(s):  
Optical Properties ◽  
Metal Ions ◽  
Pyruvate Kinase ◽  
Conformational Changes ◽  
Rabbit Muscle ◽  
Divalent Metal Ions ◽  
Muscle Enzymes ◽  
Muscle Enzyme ◽  
Allosteric Effectors ◽  
Functional Features

The kinetic and optical properties of pyruvate kinase isolated from rabbit muscle, sturgeon muscle, and yeast were compared using various activating divalent metal ions as probes for functional features and using ultraviolet circular dichroism (cd) measurements for conformational features, respectively. All three preparations of pyruvate kinase were similar in many aspects, such as activating efficiencies of the four activating metal ions, Mg(II), Co(II), Mn(II), and Ni(II) and pH-rate profiles, suggesting the presence of a similar metal binding locus of these enzymes as well as a common underlying mechanism of action. L-Phe inhibited the rabbit muscle enzyme and turned the hyperbolic kinetics into a sigmoidal kinetic with respect to phosphoenolpyruvate at alkaline pH, while fructose-1,6-biphosphate activated the sturgeon muscle and yeast enzymes and turned the sigmoidal kinetics into hyperbolic kinetics with respect to phosphoenolpyruvate. The ultraviolet cd spectral changes qualitatively correlated well with kinetic observations of all three native enzymes in the presence and absence of allosteric effectors. Our results suggested that there are at least two conformational states of pyruvate kinase which are inducible by the binding of substrate and (or) allosteric effectors. The conformational changes from one form to another in these enzymes are very similar, especially between the rabbit and sturgeon muscle enzymes.

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