Metal Complexation for the Rational Design of Gemcitabine Formulations in Cancer Therapy

Nanoformulation of chemotherapies represents a promising strategy to enhance outcomes in cancer therapy. Gemcitabine is a chemotherapeutic agent approved by the Food and Drug Administration for the treatment of various solid tumors. Nevertheless, its therapeutic effectiveness is constrained by its poor metabolic stability and pharmacokinetic profile. Nanoformulations of gemcitabine in lipid and polymer nanocarriers usually lead to poor loading capability and an inability to effectively control its release profile due to the physicochemical characteristics of the drug and matrices. Here, we propose metal-gemcitabine complexation with biorelevant metal cations as a strategy to alter the properties of gemcitabine in a noncovalent manner, paving the way for the development of novel nanoformulations. A speciation study on gemcitabine and Mn2+, Zn2+, and Ca2+ was performed with the aim of investigating the extent of the interaction between the drug and the proposed metal cations, and selecting the best conditions of temperature, pH, and drug-to-metal molar ratio that optimize such interactions. Also, a series of density functional theory calculations and spin-polarized ab initio molecular dynamics simulations were carried out to achieve insights on the atomistic modalities of these interactions. Mn2+-gemcitabine species demonstrated the ability to maintain gemcitabine's biological activity in vitro. The scientific relevance of this study lies in its potential to propose metal-gemcitabine as a valuable strategy for developing nanoformulations with optimized quality target product profiles. The work is also clinically relevant because it will lead to improved treatment outcomes, including enhanced efficacy and pharmacokinetics, decreased toxicity, and new clinical possibilities for this potent therapeutic molecule.

One Scaffold, Two Conformations: The Ring-Flip of the Messenger InsP8 Occurs under Cytosolic Conditions

Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are central eukaryotic messengers. These very highly phosphorylated molecules can exist in two distinct conformations, a canonical one with five phosphoryl groups in equatorial positions, and a “flipped” conformation with five axial substituents. Using 13C-labeled InsPs/PP-InsPs, the behavior of these molecules was investigated by 2D-NMR under solution conditions reminiscent of a cytosolic environment. Remarkably, the most highly phosphorylated messenger 1,5(PP)2-InsP4 (also termed InsP8) readily adopts both conformations at physiological conditions. Environmental factors—such as pH, metal cation composition, and temperature—strongly influence the conformational equilibrium. Thermodynamic data revealed that the transition of InsP8 from the equatorial to the axial conformation is, in fact, an exothermic process. The speciation of InsPs and PP-InsPs also affects their interaction with protein binding partners; addition of Mg2+ decreased the binding constant Kd of InsP8 to an SPX protein domain. The results illustrate that PP-InsP speciation reacts very sensitively to solution conditions, suggesting it might act as an environment-responsive molecular switch.

Nucleotide Interaction with Nanocrystalline Ceria Surface

The adsorption of nucleotides on the surface of nanocrystalline cerium dioxide (pHpzc = 6.3) in NaCl solutions was investigated using multi-batch adsorption experiments over a wide range of pH. The obtained results were interpreted as a formation of outer and inner sphere surface complexes with the participation of phosphate moieties. The Basic Stern surface complexation model was applied to obtain quantitative equilibrium reaction constants.

Characterisation of kinetics, substrate inhibition and product activation by AMP of bifunctional ADP-dependent glucokinase/phosphofructokinase from Methanococcus maripaludis

Methanogenic archaea have received attention due to their potential use in biotechnological applications such as methane production, so their metabolism and regulation are topics of special interest. When growing in a nutrient-rich medium, these organisms exhibit gluconeogenic metabolism; however, under starvation conditions, they turn to glycolytic metabolism. To date, no regulatory mechanism has been described for this gluconeogenic/glycolytic metabolic switch. Here, we report that adenosine monophosphate (AMP) activates both enzymatic activities of the bifunctional adenosine diphosphate (ADP)-dependent phosphofructokinase/glucokinase from Methanococcus maripaludis (MmPFK/GK). To understand this phenomenon, we performed a comprehensive kinetic characterisation, including determination of the kinetics, substrate inhibition and AMP activation mechanism of this enzyme. We determined that MmPFK/GK has an ordered-sequential mechanism, in which MgADP is the first substrate to bind and AMP is the last product released. The enzyme also displays substrate inhibition by both sugar substrates; we determined that this inhibition occurs through the formation of catalytically nonproductive enzyme complexes caused by sugar binding. For both activities, the AMP activation mechanism occurs primarily through incremental changes in the affinity for the sugar substrate, with this effect being higher in the GK than in the PFK activity. Interestingly, due to the increase in the sugar substrate affinity caused by AMP, an enhancement in the sugar substrate inhibition effect was also observed for both activities, which can be explained by an increase in sugar binding leading to the formation of dead-end complexes. These results shed light on the regulatory mechanisms of methanogenic archaeal sugar metabolism, a phenomenon that has been largely unexplored.

Assessment of the Equilibrium Constants of Mixed Complexes of Rare Earth Elements with Acidic (Chelating) and Organophosphorus Ligands

A survey of the experimental equilibrium constants in solution for the mixed complexes of 4f ions with acidic (chelating) and O-donor organophosphorus ligands published in the period between 1954 and 2022 is presented. These data are widely used in both analytical and solvent extraction chemistry. Important data evaluation criteria involved the specification of the essential reactions, process conditions and the correctness of techniques and calculations used, as well as appropriate equilibrium analysis of experimental data. Higher-quality data have been evaluated, compiled and presented herein, providing a synoptic view of the unifying theme in this area of research, i.e., synergism.

Insights into the product release mechanism of dengue virus NS3 helicase

The non-structural protein 3 helicase (NS3h) is a multifunctional protein that is critical in RNA replication and other stages in the flavivirus life cycle. NS3h uses energy from ATP hydrolysis to translocate along single stranded nucleic acid and to unwind double stranded RNA. Here we present a detailed mechanistic analysis of the product release stage in the catalytic cycle of the dengue virus (DENV) NS3h. This study is based on a combined experimental and computational approach of product-inhibition studies and free energy calculations. Our results support a model in which the catalytic cycle of ATP hydrolysis proceeds through an ordered sequential mechanism that includes a ternary complex intermediate (NS3h-Pi-ADP), which evolves releasing the first product, phosphate (Pi), and subsequently ADP. Our results indicate that in the product release stage of the DENV NS3h a novel open-loop conformation plays an important role that may be conserved in NS3 proteins of other flaviviruses as well.

Thenoyltrifluoroacetone: Preferable Molecule for Solvent Extraction of Metals—Ancient Twists to New Approaches

A review of the investigations devoted to the solvent extraction processes of metal ions with a chelating ligand thenoyltrifluoroacetone (HTTA) is presented herein. It seems that this molecule has been preferred in the field for more than half a century, and that it is used very often as an extractant for almost all metals. The main objective of the present review is also to provide an overview of the synergistic solvent extraction of lanthanoids, particularly with the use of a β-diketone−neutral mixture. Based on the previous published results in the open literature, the extraction efficiency has been examined in detail and discussed further mainly in terms of the corresponding equilibrium constants among other outlined, so-important parameters. Major conclusions on the role of ligating groups of extractants towards the mechanism, an improved extraction enhancement, and selectivity are additionally provided. The fact that ionic liquids (ILs) appear to be replacing volatile diluents in the field of the liquid–liquid extraction of metals, again with the participation of this β-diketone, is not surprising. As is well known, a very efficient and simple way to determine the stoichiometry of the extracted species in the organic phase is by the simple use of the slope analysis method; however, it is sometimes difficult to perform, either because it somehow requests good solubility of the ligand or because obtained slopes are quite often far from integer values in ILs.

Physico-analytical studies on some heterocyclic azo dyes and their metal complexes with some transition metals

In this investigation, the azo dyes; 2-(3′-phenyl-5′-pyrazolyl azo) schaffer acid (la) and 2-(3′-phenyl-5′-pyrazolyl azo) resorcinol (Ib); were prepared through diazotizing 3-phenyl-5-aminopyrazole (PAP) and coupling the resulting diazonium salt with Schäffer acid and resorcinol respectively. The prepared azo dyes are characterized using both IR spectra and the elemental analysis (C, H, N and S). The prepared azo dyes are used as chromogenic reagents for the spectrophotometric determination of copper (II), nickel (II), cobalt (II) and zinc (II) ions. The conditional acid dissociation constants of these azo dyes (la and Ib) and the stability constants of its metal ion complexes have been determined by spectro-analytical methods. The effect of pH, time, organic solvent and the foreign ions on the spectrophotometric determination of these ions and their complexes with the azo dyes under study were studied. The stoichiometric ratio (M:L) of the formed complexes was also determined. The molar absorptivity, the Sandell's sensitivity values, the obeyance of Beers law and the stability constants of the formed complexes have been also determined and discussed.

ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling

The metazoan innate immune second messenger 2′3′-cGAMP is present both inside and outside cells. However, only extracellular cGAMP can be negatively regulated by the extracellular hydrolase ENPP1. Here, we determine whether ENPP1’s regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating stimulator of interferon genes (STING) signaling. We identified ENPP1H362A, a point mutation that cannot degrade the 2′-5′ linkage in cGAMP while maintaining otherwise normal function. The selectivity of this histidine is conserved down to bacterial nucleotide pyrophosphatase/phosphodiesterase (NPP), allowing structural analysis and suggesting an unexplored ancient history of 2′-5′ cyclic dinucleotides. Enpp1H362A mice demonstrated that extracellular cGAMP is not responsible for the devastating phenotype in ENPP1-null humans and mice but is responsible for antiviral immunity and systemic inflammation. Our data define extracellular cGAMP as a pivotal STING activator, identify an evolutionarily critical role for ENPP1 in regulating inflammation, and suggest a therapeutic strategy for viral and inflammatory conditions by manipulating ENPP1 activity.

Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization

The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca²⁺ than Mg²⁺, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg²⁺). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.

Modulation of P2X4 pore closure by magnesium, potassium, and ATP

The P2X4 receptor plays a prominent role in cellular responses to extracellular ATP. Through classical all-atom molecular dynamics (MD) simulations totaling 24 μs we have investigated how metal-complexed ATP stabilizes the channel's open state and prevents its closing. We have identified two metal-binding sites, Mg2+ and potassium K+, one at the intersection of the three subunits in the ectodomain (MBS1) and the second one near the ATP-binding site (MBS2), similar to those characterized in Gulf Coast P2X. Our data indicate that when Mg2+ and K+ ions are complexed with ATP, the channel is locked into an open state. Interestingly, irrespective of the number of bound ATP molecules, Mg2+ ions bound to the MBS2 impeded the collapse of the open-state protein to a closed state by stabilizing the ATP-protein interactions. However, when Mg2+ in the MBS2 was replaced with K+ ions, as might be expected when in equilibrium with an extracellular solution, the interactions between the subunits were weakened and the pore collapsed. This collapse was apparent when fewer than two ATPs were bound to MBS2 in the presence of K+. Therefore, the different capacities of common cations to stabilize the channel may underlie a mechanism governing P2X4 channel gating in physiological systems. This study therefore provides structural insights into the differential modulation of ATP activation of P2X4 by Mg2+ and K+.

Functional characterization of Legionella pneumophila Cu+ transport ATPase. The activation by Cu+ and ATP

Cu⁺-ATPases are integral membrane proteins belonging to the IB subfamily of the P-type ATPases that couple Cu⁺ transport to the hydrolysis of ATP. As some structural and functional particularities arise for Cu⁺-ATPases, several authors suggest that some of the reaction steps of the Albers-Post model postulated for other P-ATPases may be different. In this work we describe a functional characterization of Legionella pneumophila Cu⁺-ATPase (LpCopA), the first P_IB-ATPase whose structure was determined by X-ray crystallography. Cu⁺-ATPase activity of the enzyme presents a maximum at ∼37 °C and pH 6.6-6.8. Phospholipids enhance LpCopA Cu⁺-ATPase activity in a non-essential mode where optimal activity is achieved at an asolectin molar fraction of 0.15 and an amphiphile-protein ratio of ~30,000. As described for other P-ATPases, Mg²⁺ acts as an essential activator. Furthermore, Cu⁺-ATPase activity dependence on [Cu⁺] and [ATP] can both be described by a sum of two hyperbolic functions. Based on that, and the [Cu⁺] and [ATP] dependencies of the best fitting parameters of the hyperbolae pointed above, we propose a minimal reaction scheme for the catalytic mechanism that shares the basic reaction steps of the Albers-Post model for P-type ATPases. The reaction scheme postulated contemplates two different binding affinities for a single ATP (apparent affinities of 0.66 and 550 μM at [Cu⁺] → ∞) and binding of at least 2 Cu⁺ with different affinities as well (apparent affinities of 1.4 and 102.5 μM at [ATP] → ∞).

Calcium in Signaling: Its Specificity and Vulnerabilities toward Biogenic and Abiogenic Metal Ions

Divalent calcium ion (Ca²⁺) plays an indispensable role as a second messenger in a myriad of signal transduction processes. Of utmost importance for the faultless functioning of calcium-modulated signaling proteins is their binding selectivity of the native metal cation over rival biogenic/abiogenic metal ion contenders in the intra/extracellular fluids. In this Perspective, we summarize recent findings on the competition between the cognate Ca²⁺ and other biogenic or abiogenic divalent cations for binding to Ca²⁺-signaling proteins or organic cofactors. We describe the competition between the two most abundant intracellular biogenic metal ions (Mg²⁺ and Ca²⁺) for Ca²⁺-binding sites in signaling proteins, followed by the rivalry between native Ca²⁺ and "therapeutic" Li⁺ as well as "toxic" Pb²⁺. We delineate the key factors governing the rivalry between the native and non-native cations in proteins and highlight key implications for the biological performance of the respective proteins/organic cofactors.

Nucleotide Interaction with a Chitosan Layer on a Silica Surface: Establishing the Mechanism at the Molecular Level

The growing interest in gene therapy is coupled with the strong need for the development of safe and efficient gene transfection vectors. A composite based on chitosan and fumed silica has been found to be a prospective gene delivery carrier. This study presents an investigation of the nature of the bonds between a series of nucleotides with a chitosan layer deposited on a fumed silica surface. Experimentally measured surface complex formation constants (logK) of the nucleotides were found to be in the range of 2.69-4.02, which is higher than that for the orthophosphate (2.39). Theoretically calculated nucleotide complexation energies for chitosan deposited on the surface range from 11.5 to 23.0 kcal·mol^-1, in agreement with experimental data. The adsorption of nucleotides was interpreted using their calculated speciation in an aqueous solution. Based on the structures of all optimized complexes determined from quantum-chemical PM6 calculations, electrostatic interactions between the surface-located NH₃⁺ groups and -PO₃H^--/-PO₃^2- fragments of the nucleotides were identified to play the decisive role in the adsorption mechanism. The saccharide fragment of monophosphates also plays an important role in the binding of the nucleotides to chitosan through the creation of hydrogen bonds.

Detailed evaluation of pyruvate dehydrogenase complex inhibition in simulated exercise conditions

The mammalian pyruvate dehydrogenase complex (PDC) is a mitochondrial multienzyme complex that connects glycolysis to the tricarboxylic acid cycle by catalyzing pyruvate oxidation to produce acetyl-CoA, NADH, and CO₂. This reaction is required to aerobically utilize glucose, a preferred metabolic fuel, and is composed of three core enzymes: pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase (E2), and dihydrolipoyl dehydrogenase (E3). The pyruvate-dehydrogenase-specific kinase (PDK) and pyruvate-dehydrogenase-specific phosphatase (PDP) are considered the main control mechanism of mammalian PDC activity. However, PDK and PDP activity are allosterically regulated by several effectors fully overlapping PDC substrates and products. This collection of positive and negative feedback mechanisms confounds simple predictions of relative PDC flux, especially when all effectors are dynamically modulated during metabolic states that exist in physiologically realistic conditions, such as exercise. Here, we provide, to our knowledge, the first globally fitted, pH-dependent kinetic model of the PDC accounting for the PDC core reaction because it is regulated by PDK, PDP, metal binding equilibria, and numerous allosteric effectors. The model was used to compute PDH regulatory complex flux as a function of previously determined metabolic conditions used to simulate exercise and demonstrates increased flux with exercise. Our model reveals that PDC flux in physiological conditions is primarily inhibited by product inhibition (∼60%), mostly NADH inhibition (∼30-50%), rather than phosphorylation cycle inhibition (∼40%), but the degree to which depends on the metabolic state and PDC tissue source.

Monitoring inorganic pyrophosphatase activity with the fluorescent dizinc(ii) complex of a macrocycle bearing one dansylamidoethyl antenna

The dizinc(ii) complexes of L were used for the recognition of anions by fluorescence spectroscopy (L is a heteroditopic hexaazamacrocycle with two diethylenetriamine coordination heads with 2-methylpyridyl and dansylamido ethyl arms, and m-xylyl spacers). The protonation of L and stability constants of its zinc(ii) complexes were determined in aqueous solution, at 298.2 ± 0.1 K and I = 0.10 ± 0.01 M in KNO₃. At a 2 : 1 Zn²⁺/L ratio, the dinuclear complexes clearly dominate. The ligand alone does not display fluorescence changes upon increasing the pH value, but in the presence of Zn²⁺ the emission reaches a maximum at pH ≅ 7.5, at which 95% of the ligand is in the dinuclear complex form. The emission appears concomitantly with the [Zn₂H_-1L]³⁺ species formation, which supports that the latter complex corresponds to the metal-promoted deprotonation of dansylamide NH. The [Zn₂H_-1L]³⁺ complexes were used for the recognition of phosphate and polyphosphate anions in aqueous solution buffered at pH 7.5 with 2 mM PIPPS, at 298.2 K. The binding of anions causes a decrease of the emission. The association constant determination revealed that HPPi^3- is the strongest bound anion (log K_app = 5.57), followed by HATP^3- (two times weaker), and the remaining anions show lower binding constants, with HPO₄^2- having the weakest uptake by the receptor. The observed selectivity of the [Zn₂H_-1L]³⁺ receptor for PPi in relation to HPO₄^2-, and the fact that the formation of the [Zn₂H_-1L]³⁺ complex is not disturbed by the presence of Mg²⁺, allowed monitoring of the PPi hydrolysis by using inorganic pyrophosphatase in real-time.

Understanding the Solution Behavior of Epinephrine in the Presence of Toxic Cations: A Thermodynamic Investigation in Different Experimental Conditions

The interactions of epinephrine ((R)-(-)-3,4-dihydroxy-α-(methylaminomethyl)benzyl alcohol; Eph-) with different toxic cations (methylmercury(II): CH3Hg+; dimethyltin(IV): (CH3)2Sn2+; dioxouranium(VI): UO22+) were studied in NaClaq at different ionic strengths and at T = 298.15 K (T = 310.15 K for (CH3)2Sn2+). The enthalpy changes for the protonation of epinephrine and its complex formation with UO22+ were also determined using isoperibolic titration calorimetry: HHL = -39 ± 1 kJ mol-1, HH2L = -67 ± 1 kJ mol-1 (overall reaction), HML = -26 ± 4 kJ mol-1, and HM2L2(OH)2 = 39 ± 2 kJ mol-1. The results were that UO22+ complexation by Eph- was an entropy-driven process. The dependence on the ionic strength of protonation and the complex formation constants was modeled using the extended Debye-Hückel, specific ion interaction theory (SIT), and Pitzer approaches. The sequestering ability of adrenaline toward the investigated cations was evaluated using the calculation of pL0.5 parameters. The sequestering ability trend resulted in the following: UO22+ >> (CH3)2Sn2+ > CH3Hg+. For example, at I = 0.15 mol dm-3 and pH = 7.4 (pH = 9.5 for CH3Hg+), pL0.5 = 7.68, 5.64, and 2.40 for UO22+, (CH3)2Sn2+, and CH3Hg+, respectively. Here, the pH is with respect to ionic strength in terms of sequestration.

Why Cellular Di/Triphosphates Preferably Bind Mg2+ and Not Ca2

Di/triphosphates perform a multitude of essential tasks, being important components of many vital organic cofactors such as adenosine/guanosine di/triphosphate (ADP/GDP, ATP/GTP), flavin adenine dinucleotide, and nicotinamide adenine dinucleotide and its phosphate derivative. They are generally bound to cations inside cells, in particular Mg²⁺ in the case of ATP/GTP. Yet how their metal-binding modes depend on the number, charge, and solvent exposure of the polyphosphate group and how Mg²⁺and Ca²⁺ dications that coexist in cellular fluids compete for di/triphosphates in biological systems remain elusive. Using density functional theory calculations combined with a polarizable continuum model, we have determined the relative free energies and stabilities of the different binding modes of di- and triphosphate groups to Mg²⁺ and Ca²⁺. We show that the thermodynamic outcome of the competition between Mg²⁺ and Ca²⁺ for cellular di/triphosphates depends mainly on the oligomericity/charge and metal-binding mode of the phosphate ligand as well as the solvent exposure of the binding site. Increasing the charge and thus denticity of the phosphate ligand from bi- to tridentate in a buried binding pocket enhances the affinity of the host system for the stronger charge acceptor, Mg²⁺. The cellular di/triphosphates's intrinsic properties and the protein matrix allowing them to bind a dication bi/tridentately, along with the higher cytosolic concentration of Mg²⁺ compared to Ca²⁺, enables Mg²⁺ to outcompete Ca²⁺ in binding to these highly charged anions. This suggests an explanation for why nature has chosen Mg²⁺ but not Ca²⁺ to perform most of the essential tasks associated with biological triphosphates.

Where to find equilibrium constants?

A crucial part of any equilibrium modelling calculation is the selection of equilibrium constants that quantify the strength of interactions between metals and ligands. For researchers new to the field of solution chemistry, locating suitable equilibrium constants that lead to reliable model results can be problematic. Numerous large compilations of equilibrium constant values have been published each having their own limitations, coverage and availability. This work surveys eleven major compilations of equilibrium constants including those from authoritative groups such as IUPAC, NIST, and NEA. For each compilation surveyed, details are given related to the historical background and underlying project, scope of the database with respect to range of included metals and ligands, and the present-day availability of publications or computer databases resulting from the project. The various methods employed by different data compilers in their critical assessment for each compilation are also discussed.

How does the mood stabilizer lithium bind ATP, the energy currency of the cell: Insights from solid-state NMR

BACKGROUND

Lithium, in the form of a salt, is a mood stabilizer and a leading drug for the treatment of bipolar disorder. It has a very narrow therapeutic range and a variety of side effects. Lithium can replace magnesium and other cations in enzymes and small molecules, among them ATP, thereby affecting and inhibiting many biochemical pathways. The form of binding of lithium ions to ATP is not known.

METHODS

Here we extract the binding environment of lithium in solid ATP using a multi-nuclear multi-dimensional solid-state NMR approach.

RESULTS

We determine that the coordination sphere of lithium includes, at a distance of 3.0(±0.4) Å, three phosphates; the two phosphates closest to the ribose ring from one ATP molecule, and the middle phosphate from another ATP molecule. A water molecule most probably completes the fourth coordination. Despite the use of excess lithium in the preparations, sodium ions still remain bound to the sample, at distances of 4.3-5.5 Å from Li, and coordinate the first phosphate and two terminal phosphates.

CONCLUSIONS

Solid-state NMR enables to unravel the exact coordination of lithium in ATP showing binding to three phosphates from two molecules, none of which are the terminal gamma phosphate.

GENERAL SIGNIFICANCE

The methods we use are applicable to study lithium bound to a variety of ATP-bound enzymes, or to other cellular targets of lithium, consequently suggesting a molecular basis for its mode of action.

Surface Complexation Modeling of Biomolecule Adsorptions onto Titania

The adsorption of nucleic acid components on the surface of nanocrystalline titaniumdioxide (anatase, pH_pzc = 6.5) in NaCl solutions was investigated using potentiometric titrationsand multibatch adsorption experiments over a wide range of pH and ionic strengths. The BasicStern surface complexation model was applied to experimental data to obtain quantitativeequilibrium reaction constants. Adsorption results suggest that there is a considerable difference inthe binding of nucleobases, nucleosides, and nucleotides with an anatase surface.

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism

The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.

Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite

The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.

Activity and fidelity of human DNA polymerase α depend on primer structure

DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Polα catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer. Unexpectedly, in the ternary complex with a DNA:DNA duplex and dCTP, the "fingers" subdomain of Polα is in the open conformation. Polα induces conformational changes in the DNA and hybrid duplexes to produce the universal double helix form. Pre-steady-state kinetic studies indicated for both duplex types that chemical catalysis rather than product release is the rate-limiting step. Moreover, human Polα extended DNA primers with higher efficiency but lower processivity than it did with RNA and chimeric primers. Polα has a substantial propensity to make errors during DNA synthesis, and we observed that its fidelity depends on the type of sugar at the primer 3'-end. A detailed structural comparison of Polα with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication.

Study of Al3+ interaction with AMP, ADP and ATP in aqueous solution

The interaction of Al³⁺ and nucleotide ligands, namely adenosine-5'-monophosphate, (AMP), adenosine-5'-diphosphate, (ADP), adenosine-5'-triphosphate, (ATP), has been studied in aqueous solution at T = 298.15 K and I = 0.15 mol L^-1 in NaCl (only for Al³⁺-ATP system at I = 0.1 mol L^-1). Formation constants and speciation models for the species formed are discussed on the basis of potentiometric results. The speciation models found for the three systems include ML and ML₂ species in all the cases, and for Al³⁺-ADP and ATP systems, MLH, MLOH and ML₂OH species as well. The formation constant value for ML species shows the trend, AMP < ADP < ATP. ¹H NMR spectroscopy was also employed for the study of Al³⁺-ATP system. The ¹H NMR results are in agreement with the speciation model obtained from analysis of potentiometric titration data, confirming the stabilities of the main species. Enthalpy change values were obtained by titration calorimetry; for the main Al³⁺-ATP species (at T = 298.15 K and I = 0.1 mol L^-1 in NaCl), they resulted always higher than zero, as typical for hard-hard interactions. The dependence of formation constants on ionic strength over the range I = 0.1 to 1 mol L^-1 in NaCl is also reported for Al³⁺-ATP system. The sequestering ability of the nucleotides under study towards Al³⁺ was also evaluated by the empirical parameter pL_0.5.

Molar absorption coefficients and stability constants of Zincon metal complexes for determination of metal ions and bioinorganic applications

Zincon (ZI) is one of the most common chromophoric chelating probes for the determination of Zn²⁺ and Cu²⁺ ions. It is also known to bind other metal ions. However, literature data on its binding properties and molar absorption coefficients are rather poor, varying among publications or determined only in certain conditions. There are no systematic studies on Zn²⁺ and Cu²⁺ affinities towards ZI performed under various conditions. However, this widely commercially available and inexpensive agent is frequently the first choice probe for the measurement of metal binding and release as well as determination of affinity constants of other ligands/macromolecules of interest. Here, we establish the spectral properties and the stability of ZI and its complexes with Zn²⁺, Cu²⁺, Cd²⁺, Hg²⁺, Co²⁺, Ni²⁺ and Pb²⁺ at multiple pH values from 6 to 9.9. The obtained results show that in water solution the MZI complex is predominant, but in the case of Co²⁺ and Ni²⁺, M(ZI)₂ complexes are also formed. The molar absorption coefficient at 618 nm for ZnZI and 599nm for CuZI complexes at pH7.4 in buffered (I=0.1M) water solutions are 24,200 and 26,100M^-1cm^-1, respectively. Dissociation constants of those complexes are 2.09×10^-6 and 4.68×10^-17M. We also characterized the metal-assisted Zincon decomposition. Our results provide new and reassessed optical and stability data that are applicable to a wide range of chemical and bioinorganic applications including metal ion detection, and quantification and affinity studies of ligands of interest.

SYNOPSIS

Accurate values of molar absorption coefficients of Zincon complex with Zn²⁺, Cd²⁺, Hg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Pb²⁺ for rapid metal ion quantification are provided. Zincon stability constants with Zn²⁺ and Cu²⁺ in a wide pH range were determined.

Mitochondrial ATP-Mg/phosphate carriers transport divalent inorganic cations in complex with ATP

The ATP-Mg/phosphate carriers (APCs) modulate the intramitochondrial adenine nucleotide pool size. In this study the concentration-dependent effects of Mg²⁺ and other divalent cations (Me²⁺) on the transport of [³H]ATP in liposomes reconstituted with purified human and Arabidopsis APCs (hAPCs and AtAPCs, respectively, including some lacking their N-terminal domains) have been investigated. The transport of Me²⁺ mediated by these proteins was also measured. In the presence of a low external concentration of [³H]ATP (12 μM) and increasing concentrations of Me²⁺, Mg²⁺ stimulated the activity (measured as initial transport rate of [³H]ATP) of hAPCs and decreased that of AtAPCs; Fe²⁺ and Zn²⁺ stimulated markedly hAPCs and moderately AtAPCs; Ca²⁺ and Mn²⁺ markedly AtAPCs and moderately hAPCs; and Cu²⁺ decreased the activity of both hAPCs and AtAPCs. All the Me²⁺-dependent effects correlated well with the amount of ATP-Me complex present. The transport of [¹⁴C]AMP, which has a much lower ability of complexation than ATP, was not affected by the presence of the Me²⁺ tested, except Cu²⁺. Furthermore, the transport of [³H]ATP catalyzed by the ATP/ADP carrier, which is known to transport only free ATP and ADP, was inhibited by all the Me²⁺ tested in an inverse relationship with the formation of the ATP-Me complex. Finally, direct measurements of Mg²⁺, Mn²⁺, Fe²⁺, Zn²⁺ and Cu²⁺ showed that they are cotransported with ATP by both hAPCs and AtAPCs. It is likely that in vivo APCs transport free ATP and ATP-Mg complex to different degrees, and probably trace amounts of other Me²⁺ in complex with ATP.

Molecular mechanism of bacterial Hsp90 pH-dependent ATPase activity

Hsp90 is a dimeric molecular chaperone that undergoes an essential and highly regulated open-to-closed-to-open conformational cycle upon ATP binding and hydrolysis. Although it has been established that a large energy barrier to closure is responsible for Hsp90's low ATP hydrolysis rate, the specific molecular contacts that create this energy barrier are not known. Here we discover that bacterial Hsp90 (HtpG) has a pH-dependent ATPase activity that is unique among other Hsp90 homologs. The underlying mechanism is a conformation-specific electrostatic interaction between a single histidine, H255, and bound ATP. H255 stabilizes ATP only while HtpG adopts a catalytically inactive open configuration, resulting in a striking anti-correlation between nucleotide binding affinity and chaperone activity over a wide range of pH. Linkage analysis reveals that the H255-ATP salt bridge contributes 1.5 kcal/mol to the energy barrier of closure. This energetic contribution is structurally asymmetric, whereby only one H255-ATP salt-bridge per dimer of HtpG controls ATPase activation. We find that a similar electrostatic mechanism regulates the ATPase of the endoplasmic reticulum Hsp90, and that pH-dependent activity can be engineered into eukaryotic cytosolic Hsp90. These results reveal site-specific energetic information about an evolutionarily conserved conformational landscape that controls Hsp90 ATPase activity.

A putative adenosine kinase family protein possesses adenosine diphosphatase activity

Adenosine kinase is a potential target for development of new types of drugs. The COG1839 family has been defined as "adenosine-specific kinase" family based on structural analysis and the adenosine-binding ability of a family member, PAE2307. However, there has been no experimental evidence with regard to the enzymatic function of this protein family. Here we measured the enzymatic activity of TTHA1091, a COG1839 family protein from Thermus thermophilus HB8. The phosphorylation of adenosine by TTHA1091 was undetectable when ATP or ADP were used as phosphate donor. However, the degradation of ADP to AMP was detected, indicating that this protein possessed adenosine diphosphatase (ADPase) activity. The (ADPase) activity was inhibited by divalent cations and was specific to ADP and CDP. Thus, this study provides the first experimental evidence for the enzymatic function of the "adenosine-specific kinase" family and suggests a need to reexamine its functional annotation.

Alkali Metal Ion Complexes with Phosphates, Nucleotides, Amino Acids, and Related Ligands of Biological Relevance. Their Properties in Solution

Alkali metal ions play very important roles in all biological systems, some of them are essential for life. Their concentration depends on several physiological factors and is very variable. For example, sodium concentrations in human fluids vary from quite low (e.g., 8.2 mmol dm(-3) in mature maternal milk) to high values (0.14 mol dm(-3) in blood plasma). While many data on the concentration of Na(+) and K(+) in various fluids are available, the information on other alkali metal cations is scarce. Since many vital functions depend on the network of interactions occurring in various biofluids, this chapter reviews their complex formation with phosphates, nucleotides, amino acids, and related ligands of biological relevance. Literature data on this topic are quite rare if compared to other cations. Generally, the stability of alkali metal ion complexes of organic and inorganic ligands is rather low (usually log K < 2) and depends on the charge of the ligand, owing to the ionic nature of the interactions. At the same time, the size of the cation is an important factor that influences the stability: very often, but not always (e.g., for sulfate), it follows the trend Li(+) > Na(+) > K(+) > Rb(+) > Cs(+). For example, for citrate it is: log K ML = 0.88, 0.80, 0.48, 0.38, and 0.13 at 25 °C and infinite dilution. Some considerations are made on the main aspects related to the difficulties in the determination of weak complexes. The importance of the alkali metal ion complexes was also studied in the light of modelling natural fluids and in the use of these cations as probes for different processes. Some empirical relationships are proposed for the dependence of the stability constants of Na(+) complexes on the ligand charge, as well as for correlations among log K values of NaL, KL or LiL species (L = generic ligand).

Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction

DNA polymerases (pols) are sophisticated protein machines operating in the replication, repair and recombination of genetic material in the complex environment of the cell. DNA pol reactions require at least two divalent metal ions for the phosphodiester bond formation. We explore two understudied roles of metals in pol transactions with emphasis on polα, a crucial enzyme in the initiation of DNA synthesis. We present evidence that the combination of many factors, including the structure of the template/primer, the identity of the metal, the metal turnover in the pol active site, and the influence of the concentration of nucleoside triphosphates, affect DNA pol synthesis. On the poly-dT70 template, the increase of Mg(2+) concentration within the range typically used for pol reactions led to the severe loss of the ability of pol to extend DNA primers and led to a decline in DNA product sizes when extending RNA primers, simulating the effect of "counting" of the number of nucleotides in nascent primers by polα. We suggest that a high Mg(2+) concentration promotes the dynamic formation of unconventional DNA structure(s), thus limiting the apparent processivity of the enzyme. Next, we found that Zn(2+) supported robust polα reactions when the concentration of nucleotides was above the concentration of ions; however, there was only one nucleotide incorporation by the Klenow fragment of DNA pol I. Zn(2+) drastically inhibited polα, but had no effect on Klenow, when Mg(2+) was also present. It is possible that Zn(2+) perturbs metal-mediated transactions in pol active site, for example affecting the step of pyrophosphate removal at the end of each pol cycle necessary for continuation of polymerization.

The biological inorganic chemistry of zinc ions

The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the “mobile” zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn²⁺ without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn²⁺ differs from s-block cations such as Ca²⁺ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol.

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Zinc ions not bound to proteins have critical roles in cell biology.

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Zinc has a unique coordination chemistry, poorly appreciated in the biosciences.

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Its coordination chemistry is significantly different from that of calcium ions.

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Specific conditions apply for buffering cellular zinc ions.

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Investigations with zinc need to consider solution chemistry and metal buffering.

Attachment of ribonucleotides on α-alumina as a function of pH, ionic strength, and surface loading

The interactions between nucleic acids and mineral surfaces have been the focus of many studies in environmental sciences, in biomedicine, as well as in origin of life studies for the prebiotic formation of biopolymers. However, few studies have focused on a wide range of environmental conditions and the likely modes of attachment. Here we investigated the adsorption of ribonucleotides onto α-alumina surfaces over a wide range of pH, ionic strength, and ligand-to-solid ratio, by both an experimental and a theoretical approach. The adsorption of ribonucleotides is strongly affected by pH, with a maximum adsorption at pH values around 5. Alumina adsorbs high amounts of nucleotides >2 μmol/m(2). We used the extended triple-layer model (ETLM) to predict the speciation of the surface complexes formed as well as the stoichiometry and equilibrium constants. We propose the formation of two surface species: a monodentate inner-sphere complex, dominant at pH <7, and a bidentate outer-sphere complex, dominant at higher pH. Both complexes would involve interactions between the negatively charged phosphate group and the positively charged surface of alumina. Our results provide a better understanding of how nucleic acids attach to mineral surfaces under varying environmental conditions. Moreover, the predicted configuration of nucleotide surface species, bound via the phosphate group, could have implications for the abiotic formation of nucleic acids in the context of the origin of life.

Cooperative substrate binding by a diguanylate cyclase

XAC0610, from Xanthomonas citri subsp. citri, is a large multi-domain protein containing one GAF (cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA) domain, four PAS (Per-Arnt-Sim) domains and one GGDEF domain. This protein has a demonstrable in vivo and in vitro diguanylate cyclase (DGC) activity that leads to the production of cyclic di-GMP (c-di-GMP), a ubiquitous bacterial signaling molecule. Analysis of a XacΔ0610 knockout strain revealed that XAC0610 plays a role in the regulation of Xac motility and resistance to H2O2. Site-directed mutagenesis of a conserved DGC lysine residue (Lys759 in XAC0610) resulted in a severe reduction in XAC0610 DGC activity. Furthermore, experimental and in silico analyses suggest that XAC0610 is not subject to allosteric product inhibition, a common regulatory mechanism for DGC activity control. Instead, steady-state kinetics of XAC0610 DGC activity revealed a positive cooperative effect of the GTP substrate with a dissociation constant for the binding of the first GTP molecule (K1) approximately 5× greater than the dissociation constant for the binding of the second GTP molecule (K2). We present a general kinetics scheme that should be used when analyzing DGC kinetics data and propose that cooperative GTP binding could be a common, though up to now overlooked, feature of these enzymes that may in some cases offer a physiologically relevant mechanism for regulation of DGC activity in vivo.