Presence Of Different Ligands Research Articles

Ion-exchange equilibrium of cesium/hydrogen ions on zirconium molybdate and zirconium iodomolybdate cation exchangers

The ion-exchange behavior of 134Cs+ onto zirconium molybdate (ZM) and zirconium iodomolybdate (ZIM) under batch conditions was achieved in different media. Acetic acid and EDTA were used as organic ligands; whereas sodium chloride and sodium nitrate were used as inorganic media containing Na+ as competing ion for 134Cs+ adsorption on ZM and ZIM. Based on Davis and Debye–Huckel Equations, the activities and the activity coefficients of the corresponding concentrations were calculated. Different isothermal models were used to express the effect of activity on the amount of 134Cs+ sorbed onto ZM and ZIM. The best-fitted adsorption isotherm models were in the order of BET > Freundlich > Temkin > Sips > Langmuir in case of 134Cs+/ZM, while the order was Temkin > Freundlich > BET > Langmuir > Sips in case of 134Cs+/ZIM. Traditional surface complexation models (SCMs) could not account for the sorption of 134Cs+ onto ZM and ZIM in presence of different ligands or competing ions; the 2-pK basic Stern model and the triple-layer model (TLM) was not satisfactory, due to the high number of adjustable parameters involved in these model variations. Furthermore, a purely diffuse layer model (DLM) generally gave the poorest fit to experimental data when combined with the 1-pK approach and was only slightly better when combined with the 2-pK formalism. Therefore, a new model, surface site competition complexation model (SSCCM) was developed by G. M. Ibrahim and B. El-Gammal, based on 2-pK DLM to test several sets of data, including those containing ligand complexes and competing cations. The theoretical basis, postulates, the model equations, and the calculations were discussed in detail. The new SSCCM succeeded in explanation of the marked sets of sorption data in distinctive ionic strengths giving rise to the different activities, species, and their distributions in existence of both the organic complexing ligands as acetic acid and EDTA and sodium as monovalent competing ion. The SSCCM explained the results of the solubility’s of the inorganic species by calculation of their logarithmic ionic activity products and the corresponding saturation indices. In addition, the surface charges and surface potentials were computed. Since the calculations in the SSCCM are based on the activities, the model could predict the real formation constants, and in turn, it could be precisely used to calculate the different thermodynamic parameters. Negative free energy changes indicate the spontaneous nature of the sorption process, while the positive values for both enthalpy change and entropy change indicates that the sorption process is entropy directed.

Towards Understanding the Interaction of Agonists with the Human α1 Glycine Receptor

The glycine receptor (GlyR) is a member of the Cys-loop receptor family of ligand-gated ion channels that is anion selective. The GlyRs play important roles in mediating inhibitory neurotransmission in the spinal cord and brain stem and excitatory neurotransmission in embryonic neurons. Because of their important physiological roles, GlyRs are considered important targets for drug design. The determinants for efficacy of activation of different agonists are, at present, not well understood. In this study, computational modelling techniques including homology modelling, docking, molecular dynamics simulations, and potential of mean force calculations were used to investigate the determinants that confer the efficacy of these compounds at the molecular level in combination with electrophysiology experiments.Homology models of the GlyR1 were built based on the GluCl channel from C. elegans, and the binding modes of different agonists were investigated using docking and MD simulations. The accuracy of our models was validated by site-directed mutagenesis studies in combination with patch-clamp experiments. Our results suggest that the efficacy of the agonists is closely coupled to the energetics of the C-loop of the receptor. With the presence of different ligands in the binding sites, the C-loop closure energy profiles given by potential of mean force (PMF) calculation reveal interesting differences. The results suggest that the combination of modelling and patch-clamp experiments for partial agonists can be a powerful approach to deciphering the atomistic details of glycine receptor activation.

Functional and fluorescence analyses of tryptophan residues in H+-pyrophosphatase of Clostridium tetani

Homodimeric proton-translocating pyrophosphatase (H+-PPase; EC 3.6.1.1) maintains the cytoplasmic pH homeostasis of many bacteria and higher plants by coupling pyrophosphate (PPi) hydrolysis and proton translocation. H+-PPase accommodates several essential motifs involved in the catalytic mechanism, including the PPi binding motif and Acidic I and II motifs. In this study, 3 intrinsic tryptophan residues, Trp-75, Trp-365, and Trp-602, in H+-PPase from Clostridium tetani were used as internal probes to monitor the local conformational state of the periplasm domain, transmembrane region, and cytoplasmic domain, respectively. Upon binding of the substrate analog Mg-imidodiphosphate (Mg-IDP), local structural changes prevented the modification of tryptophan residues by N-bromosuccinimide (NBS), especially at Trp-602. Following Mg-Pi binding, Trp-75 and Trp-365, but not Trp-602, were slightly protected from structural modifications by NBS. These results reveal the conformation of H+-PPase is distinct in the presence of different ligands. Moreover, analyses of the Stern-Volmer relationship and steady-state fluorescence anisotropy also indicate that the local structure around Trp-602 is more exposed to solvent and varied under different environments. In addition, Trp-602 was identified to be a crucial residue in the H+-PPase that may potentially be involved in stabilizing the structure of the catalytic region by site-directed mutagenesis analysis.

Molecular basis of ligand recognition by OASS from E. histolytica: Insights from structural and molecular dynamics simulation studies

BackgroundO-acetyl serine sulfhydrylase (OASS) is a pyridoxal phosphate (PLP) dependent enzyme catalyzing the last step of the cysteine biosynthetic pathway. Here we analyze and investigate the factors responsible for recognition and different conformational changes accompanying the binding of various ligands to OASS. MethodsX ray crystallography was used to determine the structures of OASS from Entamoeba histolytica in complex with methionine (substrate analog), isoleucine (inhibitor) and an inhibitory tetra-peptide to 2.00Å, 2.03Å and 1.87Å resolutions, respectively. Molecular dynamics simulations were used to investigate the reasons responsible for the extent of domain movement and cleft closure of the enzyme in presence of different ligands. ResultsHere we report for the first time an OASS-methionine structure with an unmutated catalytic lysine at the active site. This is also the first OASS structure with a closed active site lacking external aldimine formation. The OASS-isoleucine structure shows the active site cleft in open state. Molecular dynamics studies indicate that cofactor PLP, N88 and G192 form a triad of energy contributors to close the active site upon ligand binding and orientation of the Schiff base forming nitrogen of the ligand is critical for this interaction. ConclusionsMethionine proves to be a better binder to OASS than isoleucine. The β branching of isoleucine does not allow it to reorient itself in suitable conformation near PLP to cause active site closure. General significanceOur findings have important implications in designing better inhibitors against OASS across all pathogenic microbial species.

Reactions Involving Iron in Mediating Catechol Oxidation in Model Wine

Studies in wine and model systems have established that iron is an essential catalyst that mediates the reaction of polyphenols with oxygen. This investigation examined how this metal exerts its action. When wine is protected from air, iron exists in its reduced ferrous state, Fe(II), which is rapidly oxidized to the ferric state, Fe(III), on exposure to oxygen. This rapid transformation is observed when Fe(II) is added to model wine saturated with aerial oxygen, but the reaction slows to a very slow rate before completion due to the inhibitory action of Fe(III). 4-Methylcatechol was found not to be oxidized by Fe(III) or as Fe(II) was reacting with oxygen. It was apparent, therefore, that the catechol did not react with intermediate oxygen radicals. Consequently, it is proposed that hydroperoxyl radicals are not produced in wine conditions and a revised mechanism for the reaction of Fe(II) with oxygen to produce hydrogen peroxide is proposed. However, sulfite addition, which is known to promote catechol oxidation, resulted in rapid Fe(III) reduction and attainment of an Fe(III)/Fe(II) redox equilibrium. Benzenesulfinic acid, which does not react with oxygen, produced the same effect and it is proposed that nucleophiles, which react rapidly with quinones, allow the oxidation of catechols to proceed. Examination of the Fenton reaction showed that the reaction of Fe(II) with hydrogen peroxide was rapid and resulted in the uptake of oxygen. A comparison of the rates of Fe(II) oxidation and Fe(III) reduction in the presence of different ligands showed a dependence on reduction potentials.

Mechanism and Energetics of Ligand Release in the Aspartate Transporter GltPh

The bacterial aspartate transporter GltPh cotransports three Na(+) ions with the substrate. The mechanism and energetics of ligand binding have previously been studied using molecular dynamics simulations on the crystal structure of GltPh captured in the outward-facing state. Here we use the recent crystal structure of the inward-facing state of GltPh to study the reverse process of unbinding of ligands. Gating behavior is studied in the presence of different ligands. A detailed characterization of the intracellular gate is given, pointing out the differences from the extracellular gate. We then perform free energy simulations to calculate the binding affinities of all the ligands in different combinations, from which the unbinding order is determined as Na2, (gate opens), Asp, Na1, and Na3. The strong coupling between Asp and Na1 is quantified from several free energy calculations. Na3 has the largest affinity to GltPh, and therefore, its unbinding is proposed as the rate-limiting step in the transport cycle. The release time of Na3, estimated from Kramers' rate theory, is shown to be consistent with the experimental turnover rate of the transporter.

Structural and Thermodynamic Insights into Bacterial Outer Membrane Lipid Signaling by the Innate Immune System

Lipopolysaccharide (LPS) from bacterial outer membranes is a potent early indicator of microbial infection and the primary inducer of fatal septic shock syndrome. Its recognition by the immune system is carried out by Toll-like receptor 4 (TLR4) when associated with its co-receptor MD-2, an immunoglobulin-like protein. MD-2 adopts a characteristic “beta-cup” fold with a large hydrophobic cavity, and is able to bind a variety of lipid species. Subtle alterations in the structure of LPS derivatives can profoundly alter the resultant immunological response, hampering the rational design of TLR4 immunomodulators. To unravel the associated structure-activity relationships, we have performed long-timescale, all-atom molecular dynamics simulations and free-energy calculations of the isolated MD-2 co-receptor and the entire signaling-active receptor complex in the presence of a variety of LPS species, as well as an LPS membrane. Unbiased simulations revealed that the MD-2 cavity is highly conformationally flexible, identifying spontaneous switching between active signalling-competent and inactivated states dependent upon the presence of different ligands, leading us to propose a conserved receptor activation mechanism. To gain insights into the thermodynamic determinants of endotoxin recognition, extensive umbrella sampling has been applied to estimate the potential of mean force (PMF) for the binding of LPS molecules to MD-2 co-receptor. Strikingly, stronger binding to signalling-inactivate MD-2 were observed for antagonists, and conversely, stronger binding to active MD-2 for agonists. Comparison of this data to the first ever PMF calculated for extraction of LPS from a model of the bacterial outer membrane has revealed how MD-2 creates a “membrane-like” environment within its protein cavity, providing a mechanism for sensitive LPS recognition by the innate immune system.

ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease

For many targets of pharmaceutical importance conformational changes of the receptor protein are relevant during the ligand binding process. A new docking approach, ReFlexIn (Receptor Flexibility by Interpolation), that combines receptor flexibility with the computationally efficient potential grid representation of receptor molecules has been evaluated on the retroviral HIV-1 (Human Immunodeficiency Virus 1) protease system. An approximate inclusion of receptor flexibility is achieved by using interpolation between grid representations of individual receptor conformations. For the retroviral protease the method was tested on an ensemble of protease structures crystallized in the presence of different ligands and on a set of structures obtained from morphing between the unbound and a ligand-bound protease structure. Docking was performed on ligands known to bind to the protease and several non-binders. For the binders the ReFlexIn method yielded in almost all cases ligand placements in similar or closer agreement with experiment than docking to any of the ensemble members without degrading the discrimination with respect to non-binders. The improved docking performance compared to docking to rigid receptors allows for systematic virtual screening applications at very small additional computational cost.

Ligands Stabilize Specific GPCR Conformations: But How?

Small molecules modulate the activity of G protein-coupled receptors in a number of different ways leading to distinct signaling outcomes, but the mechanisms behind this modulation remain unclear. In this issue of Structure , Zocher et al. have used dynamic single-molecule force spectroscopy to study this question by examining global thermodynamic properties of β 2 AR in the presence of different ligands.

Catalase Activity of Dinuclear MnIII Compounds with Chlorobenzoato Bridges

AbstractThree dinuclear MnIII compounds [{Mn(H2O)(NN)}2(μ‐3‐ClC6H4COO)2(μ‐O)]X2 with NN = 2,2′‐bipyridine (bpy; 1 and 2) or 1,10‐phenanthroline (phen; 3) and X = NO3– (1) or ClO4– (2 and 3) have been synthesized. The X‐ray structures of compounds 1 and 3 were solved and the magnetic properties of the three compounds analyzed. Compounds 1 and 3 showferromagnetic coupling, the J values being 11.8 and 5.7 cm–1,respectively. Compound 2 displays weak antiferromagnetic behavior with a J value of –0.23 cm–1. The catalase activity of these three compounds and that of eight analogous dinuclear MnIII compounds with 2‐ and 4‐chlorobenzoato ligands has been investigated. The presence of different ligands and counteranions allowed the analysis of their effects on the catalytic activity. It was observed that compounds with perchlorate anions show higher activity than compounds with nitrate anions and compounds with 3‐chlorobenzoato ligands are the worst catalysts. Moreover, most of these compounds show higher conversions than other compounds with analogous structures.

Tunable fluorescent pH sensor based on water‐soluble perylene tetracarboxylic acid/Fe3+

A novel fluorescent pH sensor with tunable response range was designed based on highly fluorescent 3,4:9,10-perylene tetracarboxylic ammonium, which could coordinate the paramagnetic Fe(3+) ions to turn off its fluorescence and could also release Fe(3+) to turn on the fluorescence again at higher pH. The fluorescent pH sensor was tunable in the presence of different ligands in aqueous solution.

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

The conformational flexibility of target proteins continues to be a major challenge in accurate modeling of protein-inhibitor interactions. A fundamental issue, yet to be clarified, is whether the observed conformational changes are controlled by the protein or induced by the inhibitor. Although the concept of induced fit has been widely adopted for describing the structural changes that accompany ligand binding, there is growing evidence in support of the dominance of proteins' intrinsic dynamics which has been evolutionarily optimized to accommodate its functional interactions. The wealth of structural data for target proteins in the presence of different ligands now permits us to make a critical assessment of the balance between these two effects in selecting the bound forms. We focused on three widely studied drug targets, HIV-1 reverse transcriptase, p38 MAP kinase, and cyclin-dependent kinase 2. A total of 292 structures determined for these enzymes in the presence of different inhibitors and unbound form permitted us to perform an extensive comparative analysis of the conformational space accessed upon ligand binding, and its relation to the intrinsic dynamics before ligand binding as predicted by elastic network model analysis. Our results show that the ligand selects the conformer that best matches its structural and dynamic properties among the conformers intrinsically accessible to the protein in the unliganded form. The results suggest that simple but robust rules encoded in the protein structure play a dominant role in predefining the mechanisms of ligand binding, which may be advantageously exploited in designing inhibitors.

EGFR ligand switch in late stage prostate cancer contributes to changes in cell signaling and bone remodeling

Bone metastasis occurs frequently in advanced prostate cancer (PCa) patients; however, it is not known why this happens. The epidermal growth factor receptor (EGFR) ligand EGF is available to early stage PCa; whereas, TGF-alpha is available when PCa metastasizes. Since the microenvironment of metastases has been shown to play a role in the survival of the tumor, we examined whether the ligands had effects on cell survival and proliferation in early and late PCa. We used LNCaP cells as a model of early stage, non-metastatic PCa and the isogenic C4-2B cells as a model of late stage, metastatic PCa. We found that the proliferation factor MAPK and the survival factor AKT were differentially activated in the presence of different ligands. TGF-alpha induced growth of C4-2B cells and not of the parental LNCaP cells; however, LNCaP cells expressing a constitutively active AKT did proliferate with TGF-alpha. Therefore, AKT appeared to be the TGF-alpha-responsive factor for survival of the late stage PCa cells. LNCaP cells exposed to EGF produced more osteoprotegerin (OPG), an inhibitor of bone remodeling, than C4-2B cells with TGF-alpha, which had increased expression of RANKL, an activator of bone remodeling. In concordance, TGF-alpha-treated C4-2B conditioned medium was able to differentiate an osteoclast precursor line to a greater extent than EGF-treated C4-2B or TGF-alpha-treated LNCaP conditioned media. The switch in EGFR ligand availability as PCa progresses affects cell survival and contributes to bone remodeling.

NKT lymphocyte polarization determined by microenvironment signaling: A role for CD8 + lymphocytes and β-glycosphingolipids

Natural killer T-cell (NKT) regulatory lymphocytes have been shown to behave differently in various immune settings. The aim of the present study was to determine the effect of microenvironmental signaling on NKT polarization and the process of active CD8 and NKT intrahepatic lymphocyte sequestration. In an in vitro assay, double negative (DN) NKT hybridoma cells were incubated with Hep3B hepatoma cells. This caused a significant increase in the secretion of alpha-fetoprotein (AFP) from Hep3B cells. When NKT cells were exposed to β-glucoslyceramide (β-GC) prior to incubation, Hep3B cells exhibited increased proliferation, increased IFN secretion, and reduced AFP secretion. In vivo, the adoptive transfer of naïve DN NKT cells into athymic nude-nu mice transplanted with human Hep3B hepatocellular carcinoma (HCC) caused accelerated tumor growth. This effect was inhibited by prior ex vivo exposure of DN NKT lymphocytes to β-GC. To assess the effect of the immunological environment on NKT cells, immune mediated hepatitis and colitis were induced simultaneously in mice. Induction of TNBS colitis prior to administration of concanavalin A (Con A) hepatitis resulted in an aggravation of the liver damage caused by Con A hepatitis alone. This effect was associated with reduced intrahepatic CD8 + T cell trapping and an increase in intrahepatic NKT cells. The presence of different ligands altered host microenvironment signaling and influenced the fate and polarization of NKT cells and the sequestration of active intrahepatic lymphocytes. These data support the notion that NKT regulatory lymphocytes have an inherent plasticity that may be important for their regulatory function.

A theoretical study of the principles regulating the specificity for Al(III) against Mg(II) in protein cavities

Several toxic effects arise from Al’s presence in living systems, one of them being the alteration of the natural role of enzymes and non-enzyme proteins. Al(III) is capable of entering protein active sites that in normal conditions should be occupied by other metals. Even if Mg(II) is an ubiquitous metal in biological systems, the interference of aluminium in magnesium metabolism is not clear yet. In this work, a systematic study of the affinity of Al(III) for different protein binding sites is presented, with special attention on structural parameters, the role of the charge and the presence of different ligands in the protein cavity. The specificity of the binding site for Al(III) against Mg(II) has been studied, and also the thermodynamical propensity of a Mg(II)/Al(III) exchange. Quantum mechanical methods that proved to be reliable in previous works have been used, namely, the density functional theory (DFT) and polarizable continuum model (PCM).

The c-Myc Target Gene Rcl (C6orf108) Encodes a Novel Enzyme, Deoxynucleoside 5′-monophosphate N-Glycosidase

RCL is a c-Myc target with tumorigenic potential. Genome annotation predicted that RCL belonged to the N-deoxyribosyltransferase family. However, its putative relationship to this class of enzymes did not lead to its precise biochemical function. The purified native or N-terminal His-tagged recombinant rat RCL protein expressed in Escherichia coli exhibits the same enzyme activity, deoxynucleoside 5'-monophosphate N-glycosidase, never before described. dGMP appears to be the best substrate. RCL opens a new route in the nucleotide catabolic pathways by cleaving the N-glycosidic bond of deoxynucleoside 5'-monophosphates to yield two reaction products, deoxyribose 5-phosphate and purine or pyrimidine base. Biochemical studies show marked differences in the terms of the structure and catalytic mechanism between RCL and of its closest enzyme family neighbor, N-deoxyribosyltransferase. The reaction products of this novel enzyme activity have been implicated in purine or pyrimidine salvage, glycolysis, and angiogenesis, and hence are all highly relevant for tumorigenesis.

Thermodynamic study of the thermal denaturation of a globular protein in the presence of different ligands

By means of difference UV-Vis spectra, the thermal denaturation of catalase has been studied in the presence of different surfactants: sodium perfluorooctanoate, sodium octanoate and sodium dodecanoate. These results indicate that hydrogenated surfactants play two opposite roles in the folding and stability of catalase, they act as a structure stabiliser at a low molar concentrations (enhancing Tm) and as a destabilizer at a higher concentrations (diminishing Tm). Meanwhile sodium perfluorooctanoate enhances Tm in the whole concentration range. An approach for the determination of the heat capacity, enthalpy and entropy has been made, finding that for the three studied surfactants, at all concentrations, the enthalpy term dominates the entropy term.

Co-Transport of Metal Complexes by the Green Mussel Perna viridis

We examined the uptake of ligand-bound metals (Cd and Zn) by the green mussel Perna viridis using defined artificial seawater. Different free ion concentrations (1 pM to 10 microM) in uptake solutions were created by adding different amounts of total metals (Cd 0.1 nM to 0.1 mM; Zn 0.5 nM to 0.05 mM) and ligands (EDTA, NTA, citric acid). Our results showed that Cd and Zn uptake could not be fully explained by the free Cd and Zn concentrations in the presence of different ligands, indicating that metal-ligand complexes were at least partially available for uptake by the mussels. Total Zn concentrations appeared to be a better predictor of metal uptake than the free Zn ion concentrations in the presence of different ligands. Uptake of lipophilic organic metal complexes was substantially greater than the hydrophilic metal complexes, even though the free ion concentration was comparable or lower. Moreover, the radiolabeled ligand compounds were directly accumulated by the mussels. The accumulation of metal complexes may explain the increased metal uptake with increasing ligand and total metal concentration, even though the free ion metal concentration was constant. Overall, our experimental results indicated that free metal ion cannot fully explain metal uptake since metal complex species were also available to the mussels to some extent, apparently through a co-transport process.

Adsorption of heavy metals on vermiculite: Influence of pH and organic ligands

The sorption behaviour of vermiculite has been studied with respect to cadmium, copper, lead, manganese, nickel, and zinc as a function of pH and in the presence of different ligands. The continuous column method was used in order to evaluate the feasibility to use the clay in wastewater purification systems. The total capacity of vermiculite was found to decrease in the following order: Mn > Ni > Zn > Cd > Cu > Pb. The adsorption of metal ions on vermiculite decreases with decreasing pH and increasing ionic strength. In general, the metal uptake on the clay was hindered by the presence of strong complexing agents in solution and it decreases with increasing of the complexation constants of the ligands with exception of cysteine and tiron. It is necessary, hence, to consider all these factors to effectively predict the uptake efficiency of this sorbent. However, it is possible to conclude that the vermiculite has good potentialities for cost-effective treatments of metal-contaminated wastewaters.

Effect of some environmental ligands on the sorption of radionuclidesby peat humin

In a previous paper we studied the interaction of the radionuclides 110mAg, 60Co and 65Zn with peat humin. These nuclides are among the fission or corrosion products in nuclear reactors. The aim of this paper is to study the effect of certain ligands, which are present in the environment, such as humic acid, fulvic acid, EDTA and urea, on the sorption of these radionuclides by humin. The obtained results indicated that urea has no effect on the sorption of Co and Zn by humin, and only a little in case of Ag. However, the presence of the other ligands (humic acid, fulvic acid or EDTA) leads to different decreases in the sorption of the three nuclides by humin. The results are interpreted in the light of the complex formation between ligands and the metal cations and of the strength of binding of these cations to the humin sorbent. The release of Ag+in the presence of different ligands was found to follow the order: humic acid>EDTA>fulvic acid>urea. In the case of both Co2+and Zn2+, the sequence is changed to be: EDTA>humic acid>fulvic acid>urea, with a higher release in the case of Zn2+. The results showed that cobalt is bound more strongly to humin than silver and zinc. The sulphur content of the humic fractions plays a significant role in the competition for silver and zinc.