Molecular dynamics characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization

Aicardi–Goutières syndrome, a rare genetic disorder characterized by calcification of basal ganglia, results in psychomotor delays and epilepsy states from the early months of children life. This disease is caused by mutations in seven different genes encoding proteins implicated in the metabolism of nucleic acids, including SAMHD1. Twenty SAMHD1 gene variants have been discovered and in this work, a structural characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant is reported by classical molecular dynamics simulation. Four simulations have been carried out and compared. Two concerning the wild-type SAMHD1 form in presence and absence of cofactors, in order to explain the role of cofactors in the SAMHD1 assembly/disassembly process and, two concerning the Arg145Gln mutant, also in presence and absence of cofactors, in order to have an accurate comparison with the corresponding native forms. Results show the importance of native residue Arg145 in maintaining the tetramer, interacting with GTP cofactor inside allosteric sites. Replacement of arginine in glutamine gives rise to a loosening of GTP–protein interactions, when cofactors are present in allosteric sites, whilst in absence of cofactors, the occurrence of intra and inter-chain interactions is observed in the mutant, not seen in the native enzyme, making energetically unfavourable the tetramerization process.     

Metal and cofactor insertion

Cells require metal ions as cofactors for the assembly of metalloproteins. Principally one has to distinguish between metal ions that are directly incorporated into their cognate sites on proteins and those metal ions that have to become part of prosthetic groups, cofactors or complexes prior to insertion of theses moieties into target proteins. Molybdenum is only active as part of the molybdenum cofactor, iron can be part of diverse Fe-S clusters or of the heme group, while copper ions are directly delivered to their targets. We will focus in greater detail on molybdenum metabolism because molybdenum metabolism is a good example for demonstrating the role and the network of metals in metabolism: each of the three steps in the pathway of molybdenum cofactor formation depends on a different metal (iron, copper, molybdenum) and also the enzymes finally harbouring the molybdenum cofactor need additional metal-containing groups to function (iron sulfur-clusters, heme-iron).     

Indium(III)-induced fluorescent excimer formation and extinction in calix[4]arene-fluoroionophores

New fluorogenic or/and chromogenic calix[4]arenes 1-3 with two facing amide groups linked to fluorescent pyrene units are synthesized. Orientations of the pyrene units are remote from each other in 1 and face-to-face pi-stacked in 2, which produces different photophysical properties. In the excited state, the two pyrene units of 2 form a strong intramolecular excimer displaying an emission at 472 nm with a relatively weak monomer emission at 395 nm. In contrast, 1 exhibits only a monomer emission at 398 nm because intramolecular hydrogen bonding between the phenolic OH oxygens and the amide hydrogens prevents pi-stacking of the two pyrene groups. Fluorescence changes upon addition of various metal ions show that 1 has a remarkably high selectivity for In(3+) over the other metal ions tested. Compound 1 forms 2:1 (metal:ligand), as well as 1:1 complexes, with In(3+), with fluorescence varying uniquely with the complex stoichiometry. Compound 3, which possess two pyrene units and two chromogenic azo groups, shows almost the same binding behavior toward metal ions as does 1, together with additional bathochromic shifts of the absorption maximum. Compared with 1, compound 3 emits a considerably weaker fluorescence, which is attributed to electron transfer from the pyrene units to the nitro groups of the phenylazo moieties.     

Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme

Background: RNA and DNA are polymers that lack the diversity of chemical functionalities that make proteins so suited to biological catalysis. All naturally occurring ribozymes (RNA catalysts) that catalyze the formation, transfer and hydrolysis of phosphodiesters require metal-ion cofactors for their catalytic activity. We wished to investigate whether, and to what extent, DNA molecules could catalyze the cleavage (by either hydrolysis or transesterification) of a ribonucleotide phosphodiester in the absence of divalent or higher-valent metal ions or, indeed, any other cofactors.Results: We performed in vitro selection and amplification experiments on a library of random-sequence DNA that incorporated a single ribonucleotide, a suitable site for cleavage. Following 12 cycles of selection and amplification, a ‘first generation’ of DNA enzymes (DNAzymes) cleaved their internal ribonucleotide phosphodiesters at rates ∼ 10⁷-fold faster than the spontaneous rate of cleavage of the dinucleotide ApA in the absence of divalent cations. Re-selection from a partially randomized DNA pool yielded ‘second generation’ DNAzymes that self-cleaved at rates of ∼ 0.01 min⁻¹ (a 10⁸-fold rate enhancement over the cleavage rate of ApA). The properties of these selected catalysts were different in key respects from those of metal-utilizing ribozymes and DNAzymes. The catalyzed cleavage took place in the presence of different chelators and ribonuclease inhibitors. Trace-metal analysis of the reaction buffer (containing very high purity reagents) by inductively coupled plasma-optical emission spectrophotometry indicated that divalent or higher-valent metal ions do not mediate catalysis by the DNAzymes.Conclusions: Our results indicate that, although ribozymes are sometimes regarded generically to be metalloenzymes, the nucleic acid components of ribozymes may play a substantial role in the overall catalysis. Given that metal cofactors increase the rate of catalysis by ribozymes only ∼ 10²−10³-fold above that of the DNAzyme described in this paper, it is conceivable that substrate positioning, transition-state stabilization or general acid/base catalysis by the nucleic acid components of ribozymes and DNAzymes may contribute significantly to their overall catalytic performance.     

Bifunctional fluorescent calix[4]arene chemosensor for both a cation and an anion

[reaction: see text] A new fluorogenic cone calix[4]triazacrown-5 (1) bearing two pyrene amide groups and its structural analogue 2 have been prepared. Excited at 343 nm, 1 and 2 reveal excimer emissions at 448 and 472 nm, respectively. When heavy metal ions such as Pb(2+) and Co(2+) are bound to 1, the fluorescence intensities of both monomer and excimer are quenched whereas H bonding-assisted F(-) binding to 1 gives rise to a quenched monomer emission with little excimer emission change.     

Effect of alkali metal ions on photochromic behavior of bisviologen-incorporated oligo-oxyethylene units

Two bisviologen derivatives, 1,11-bis(N-propyl-4,4'-bipyridinium)-3,6,9-trioxaundecane tetrakis-(hexafluorophosphate) (1) and 1,8-bis(N-propyl-4,4'-bipyridinium)-3,6-dioxaoctane tetrakis-(hexafluorophosphate) (2), each incorporating trioxaundecane and dioxaoctane groups between two viologen units, respectively, were prepared so that their photochromic behavior in the absence and the presence of alkali metal ions in a thin polymer film could be investigated. Photoirradiation of the films containing 1 and 2 caused color changes from pale yellow to blue, associated with the photoinduced reduction of the viologen units from the dication to the radical cation. The addition of alkali metal ions, especially, K+ and Na+, caused change in the spectra of the photoreduced viologen radical cation for 1 and 2, respectively, because of the increase in the fractional amplitude for the dimer component of the radical cation rather than the monomer one. This may be related to the guest-induced conformational change of 1 and 2, in which the alkali metal ion is surrounded by the oligo-oxyethylene unit of 1 and 2. The regulation in photochromic properties of viologen derivatives can be achieved by addition of alkali metal ions.     

Role of cofactors in folding of the blue-copper protein azurin

Many proteins in living cells coordinate cofactors, such as metal ions, to attain their activity. Since the cofactors in such cases often can interact with their corresponding unfolded polypeptides in vitro, it is important to unravel how cofactors modulate protein folding. In this review, I will discuss the role of cofactors in folding of the blue-copper protein Pseudomonas aeruginosa azurin. In the case of both copper (Cu(II) and Cu(I)) and zinc (Zn(II)), the metal can bind to unfolded azurin. The residues involved in copper (Cu(II) and Cu(I)) coordination in the unfolded state have been identified as Cys112, His117, and Met121. The affinities of Cu(II), Cu(I), and Zn(II) are all higher for the folded than for the unfolded azurin polypeptide, resulting in metal stabilization of the native state as compared to the stability of apo-azurin. Cu(II), Zn(II), and several apo forms of azurin all fold in two-state kinetic reactions with roughly identical polypeptide-folding speeds. This suggests that the native-state beta-barrel topology, not cofactor interactions or thermodynamic stability, determines azurin's folding barrier. Nonetheless, copper binds much more rapidly (i.e., 4 orders of magnitude) to unfolded azurin than to folded azurin. Therefore, the fastest route to functional azurin is through copper binding before polypeptide folding; this sequence of events may be the relevant biological pathway.     

Crystal structure of the oxygen-evolving complex of photosystem II

The oxygen in our atmosphere is derived from and maintained by the water-splitting process of photosynthesis. The enzyme that facilitates this reaction and therefore underpins virtually all life on our planet is known as photosystem II (PSII). It is a multisubunit enzyme embedded in the lipid environment of the thylakoid membranes of plants, algae, and cyanobacteria. Powered by light, PSII catalyzes the chemically and thermodynamically demanding reaction of water splitting. In so doing, it releases molecular oxygen into the atmosphere and provides the reducing equivalents required for the conversion of carbon dioxide into the organic molecules of life. Recently, a fully refined structure of an isolated 700 kDa cyanobacterial dimeric PSII complex was elucidated by X-ray crystallography, which gave organizational and structural details of the 19 subunits (16 intrinsic and 3 extrinsic) that make up each monomer and provided information about the position and protein environments of the many different cofactors it binds. The water-splitting site was revealed as a cluster of four Mn ions and a Ca ion surrounded by amino acid side chains, of which six or seven form direct ligands to the metals. The metal cluster was originally modeled as a cubane-like structure composed of three Mn ions and the Ca (2+) linked by oxo bonds and the fourth Mn attached to the cubane via one of its O atoms. New data from X-ray diffraction and X-ray spectroscopy suggest some alternative arrangements. Nevertheless, all of the models are sufficiently similar to provide a basis for discussing the chemistry by which PSII splits water and makes oxygen.     

Fluorescence ratiometry of monomer/excimer emissions in a space-through PET system

[Reaction: see text]. Fluorogenic calix[4]arenes (1 and 2) bearing a pendent ethyleneamine on their triazacrown rings, respectively, were synthesized in the cone conformation. Compared with 4, free 1 and 2 display a relatively weak emission, reflecting that a PET process from the pendent amine group (-CH2CH2NH2) to the fluorogenic pyrenes is mainly operated. Addition of various metal ions or anions to the solution of 1 or 2 reduces the PET because the pendent alkylamine takes part in the complexation, causing their fluorescence spectra to be changed. When Pb2+, a quenching metal ion, is added to 1 or 2, their pyrene monomer emission is enhanced with their excimer emission quenched, which is due to conformational changes of the facing carbonyl groups as well as to the participation of the ethyleneamine into the three-dimensional Pb2+ ion encapsulation. In contrast, upon addition of alkali metal ions to the 1 and 2, both monomer and excimer emissions are observed to increase, which is attributable to the CHEF effect and the retained conformations. For anion sensing, both 1 and 2 show a high selectivity for F- ions over other anions tested. When the F- ion is bound to 1 or 2 by hydrogen bonding between the amide NH of the triazacrown ring and F-, both their monomer and excimer emissions are weakened due to PET from the bound F- to the pyrene units.     

Fluorescence Switches Triggered by Metal Ions

Molecular switches 1 with a modular architecture whose functional principle is based on conformational changes around two acetylene axes were developed. By systematic screening of various metal ions, it was found that especially Pb²⁺ ions effectively trigger the switching event. The reporting of this event takes place by the change of the ratio between excimer and monomer fluorescence emission of two pyrene moieties.     

Copper and Nickel Removal from Aqueous Solutions Using New Chelating Poly[Acrylamide/N‐vinyl pyrrolidone/3‐(2‐hydroxyethyl carbamoyl)acrylic acid] Hydrogels

New poly[Acrylamide/N‐vinyl pyrrolidone/3‐(2‐hydroxyethyl carbamoyl)acrylic acid], poly [AAm/NVP/HECA], chelating hydrogels with different composition of HECA monomer have been prepared via free radical solution polymerization using N,N‐methylene bisacrylamide as a crosslinker. The hydrogels obtained were loaded with metal ions and characterized by FT‐IR spectroscopy, Scanning Electron Microscope (SEM) and Thermogravimatric analysis (TGA). The removal of Cu²⁺ and Ni²⁺ from aqueous solutions by the hydrogel was examined by a batch equilibrium method. The influence of treatment time, pH, initial concentration of the metal ions and HECA content in the feed compositions on the amount of adsorbed metal ions was studied. Swelling of the hydrogel was also carried out in distilled water and metal ion solutions. The removal of the metal ions followed the following order: Ni²⁺>Cu²⁺. The amount of metal ions removed increased with increasing HECA content in the feed composition, treatment time, pH of the medium and initial concentration of metal ions. The desorption of metal ions were carried out using 1 N HCl and 0.5 N H₂SO₄. The poly[AAm/NVP/HECA] hydrogels could be used many times without significantly decreasing their adsorption capacity.     

Comparison of energy interaction parameters for the complexation of Pr(III) with glutathione reduced (GSH) in absence and presence of Zn(II) in aqueous and aquated organic solvents using 4f-4f transition spectra as PROBE

The coordination chemistry of glutathione reduced (GSH) is of great importance as it acts as excellent model system for the binding of metal ions. The GSH complexation with metal ions is involved in the toxicology of different metal ions. Its coordination behaviour for soft metal ions and hard metal ions is found different because of the structure of GSH and its different potential binding sites. In our work we have studied two chemically dissimilar metal ions viz. Pr(III), which prefer hard donor site like carboxylic groups and Zn(II) the soft metal ion which prefer peptide-NH and sulphydryl groups. The absorption difference and comparative absorption spectroscopy involving 4f-4f transitions of the heterobimetallic Complexation of GSH with Pr(III) and Zn(II) has been explored in aqueous and aquated organic solvents. The variation in the energy parameters like Slater-Condon (F(K)), Racah (E(K)) and Lande (xi(4f)), Nephelauxetic parameter (beta) and bonding parameter (b(1/2)) are computed to explain the nature of complexation.     

Luminescent properties of water-soluble conjugated metallopolymers and their application to fluorescent nitric oxide detection

Water-soluble pi-conjugated polymers (CPs) incorporating 5,5'-(2,2'-dipyridyl) (CP1) or 6,6'-(2,2'-dipyridyl) (CP2) units within the pi-conjugated backbone were prepared as scaffolds for macromolecular metal complexation. The response of CP emission to a range of metal ions was investigated in water, 10 mM aqueous sodium dodecyl sulfate, and acetonitrile/water (95:5). Cupric ions are the most efficient quenchers of CP emission, with K(SV) = 1.1 x 10(5) and 5.2 x 10(4) M(-1) in water for CP1a (40% bipyridyl monomer units) and CP1b (20% bipyridyl monomer units), respectively. Quenching is approximately twice as effective in acetonitrile/water (95:5) (K(SV) = 3.1 x 10(5) M(-1) for CP1a and 1.1 x 10(5) M(-1) for CP1b). Partial restoration of emission was observed upon exposure of Cu(II)-CP solutions to excess NO(g) in acetonitrile/water (95:5) or 10 mM SDS(aq).     

Synthesis,redox properties,and EPR spectroscopy of manganese(III) complexes of the ligand N,N-bis(2-hydroxybenzyl)-N'-2-hydroxybenzylidene-1,2-diaminoethane: formation of mononuclear,dinuclear, and even higher nuclearity complexes

The synthesis and characterization of the title trisphenolate ligand are described. From its reaction with manganese(III) three complexes were isolated. The crystal structures revealed one pentacoordinate monomer and two similar dimers with different solvents of crystallization. In the dimers the metal ions are hexacoordinate and connected through bridging of two phenolates. A combination of electrochemistry and EPR spectroscopy showed that, in acetonitrile, the isolated batches were all identical and mainly monomeric, indicating that the mononuclear complex is in equilibrium with the dimer and perhaps also with complexes of higher nuclearity, as suggested by the detection of both the trimer and the tetramer by electrospray ionization mass spectrometry (ESI-MS). The successful use of the monomer batch as an epoxidation catalyst indicated that a high-valent manganese-oxo species can be formed, although it is probably short-lived. This is also suggested by EPR studies of the species formed by electrochemical oxidation of the complex. Upon one-electron oxidation, a manganese(IV) species was formed, which was at least partly converted to another species containing a phenoxy radical.     

Removal of Pb2+ and Cd2+ ions from aqueous solutions using guanidine modified hydrogels

In this study, experimental measurements have been made on the batch adsorption of cadmium and lead ions from aqueous solutions using poly(guanidine modified 2‐acrylamido‐2‐methylpropan sulfonic acid/acrylic acid/N‐vinylpyrrolidone/2‐Hydroxyethyl methacrylate), P(AMPSG/AAc/NVP/HEMA) hydrogels. The guanidyl end group bearing AMPSG monomer was synthesized from the reaction of AMPS and guanidine. The hydrogels were prepared by UV‐curing technique. The morphology of the dry H10‐hydrogel sample was examined by SEM. The influence of the uptake conditions, such as pH, functional monomer per cent, contact time, initial feed concentration, and foreign metal ions on the metal ion binding capacity of hydrogel, was also tested. The selectivity of the hydrogel toward the different metal ions tested was Hg(II) > Pb(II) > Au(III) > Cd(II). The adsorption isotherm models were applied to the experimental data, and it was seen that the Langmuir isotherm model was the best fit for the adsorption of Cd(II) and Pb(II) ions on P(AMPSG/AAc/NVP/HEMA) hydrogel. It was found that adsorbed lead and cadmium ions on P(AMPSG/AAc/NVP/HEMA) hydrogel can be effectively desorbed by acid leaching and the regenerated P(AMPSG/AAc/NVP/HEMA) hydrogel can be reused almost five times less without any loss of adsorption capacity. Copyright © 2009 John Wiley & Sons, Ltd.     

Chiral separation of racemic mandelic acids by use of an ionic liquid-mediated imprinted monolith with a metal ion as self-assembly pivot

A new chiral stationary phase based on molecularly imprinted polymers (MIP) was prepared in ionic liquid by use of the metal pivot concept. Imprinted monoliths were synthesized by use of a mixture of R-mandelic acid (template), 4-vinylpyridine, ethylene glycol dimethacrylate, and several metal ions as pivot between the template and functional monomer. A ternary mixture of dimethyl sulfoxide–dimethylformamide–[BMIM]BF₄ containing metal ions was used as the porogenic system. Separation of the enantiomers of rac-mandelic acid was successfully achieved on the MIP thus obtained, with resolution of 1.87, whereas no enantiomer separation was observed on the imprinted monolithic column in the absence of metal ions. The effects of polymerization conditions, including the nature of the metal ion and the ratios of template to metal ions and template to functional monomer, on the chiral separation of mandelic acid were investigated. The results reveal that use of metal ions as a pivot, in combination with ionic liquid, is an effective method for preparation of a highly efficient MIP stationary phase for chiral separation.

Synthesis,characterization, and polychelatogenic properties of poly(acrylic acid-co-acrylamide)

The radical copolymerization of acrylic acid with acrylamide was carried out at different monomer ratios in solution (DMF) at 60°C. The corresponding homopolymers were also synthesized to compare their metal ion binding abilities. All the copolymers were characterized by elemental analysis. The metal ion binding properties of these water-soluble polymers with Cu(II), Co(II), Ni(II), Cd(II), Zn(II), Pb(II), Hg(II), Fe(III), and Cr(III) ions were investigated in aqueous solution using the Liquid-Phase Polymer-Based Retention (LPR) technique. Poly(acrylic acid-co-acrylamide) showed a higher retention compared to the homopolymers for all the metal ions except of Hg(II), which was not retained. Besides, the retention of Cd(II) is higher than that an addition of the retention of both homopolymers. It may be attributed to a synergic effect. Maximum capacity for Cu(II) at pH 5.0 was determined to be 1 mmol g⁻¹ (63.5 mg g⁻¹). © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 2461–2467, 1997     

Synthesis and fluorescence studies of novel bis(azacrown ether) type chemosensors containing an acridinone unit

Three new bis(azacrown ether)s containing an acridinone fluorescent signalling unit were prepared by reacting 9-chloro-4,5-bis(chloromethyl)acridine with monoazacrown ethers with different cavity sizes followed by a hydrolysis step. Their fluorescent characteristics and the complexation properties of the one containing two monoaza-18-crown-6 ether receptors towards selected metal ions were studied. The operation of the latter ligand is based on the photoinduced electron transfer (PET) process, thus it shows fluorescence enhancement in the presence of metal ions. Since the sensor molecule contains two receptor moieties, it is able to form two types of complex with 1:1 and 1:2 ligand to metal ion ratios, which have different emission spectra. The reason for this spectral difference may be that the 1:1 complex is a sandwich type one in which the acridinone unit can undergo structural changes.     

A biologically stable,self-catalytic DNAzyme machine encapsulated by metal-phenolic nanoshells for multiple microRNA imaging

DNAzyme machines play critical roles in the fields of cell imaging, disease diagnosis, and cancer therapy. However, the applications of DNAzyme machines are limited by the nucleases-induced degradation, non-specific binding of proteins, and insufficient provision of cofactors. Herein, protected DNAzyme machines with different cofactor designs (referred to as ProDs) were nanoengineered by the construction of multifunctional metal-phenolic nanoshells to deactivate the interferential proteins, including nucleases and non-specific binding proteins. Moreover, the nanoshells not only facilitate the cellular internalization of ProDs but provide specific metal ions acting as cofactors of the designed DNAzymes. Cellular imaging results demonstrated that ProDs could effectively and simultaneously monitor multiple tumor-related microRNAs in living cells. This facile and rapid strategy that encapsulates DNAzyme machines into the protective metal-phenolic nanoshells is anticipated to extend to a wide range of functional nucleic acids-based biomedical applications.