Cation Binding Selectivity Research Articles

Thermodynamics of Cation Binding to the Sarcoendoplasmic Reticulum Calcium ATPase Pump and Impacts on Enzyme Function.

Sarcoendoplasmic reticulum Ca2+-ATPase (SERCA) is a transmembrane pump that plays an important role in transporting calcium into the sarcoplasmic reticulum (SR). While calcium (Ca2+) binds SERCA with micromolar affinity, magnesium (Mg2+) and potassium (K+) also compete with Ca2+ binding. However, the molecular bases for these competing ions' influence on the SERCA function and the selectivity of the pump for Ca2+ are not well-established. We therefore used in silico methods to resolve molecular determinants of cation binding in the canonical site I and II Ca2+ binding sites via (1) triplicate molecular dynamics (MD) simulations of Mg2+, Ca2+, and K+-bound SERCA, (2) mean spherical approximation (MSA) theory to score the affinity and selectivity of cation binding to the MD-resolved structures, and (3) state models of SERCA turnover informed from MSA-derived affinity data. Our key findings are that (a) coordination at sites I and II is optimized for Ca2+ and to a lesser extent for Mg2+ and K+, as determined by MD-derived cation-amino acid oxygen and bound water configurations, (b) the impaired coordination and high desolvation cost for Mg2+ precludes favorable Mg2+ binding relative to Ca2+, while K+ has limited capacity to bind site I, and (c) Mg2+ most likely acts as inhibitor and K+ as intermediate in SERCA's reaction cycle, based on a best-fit state model of SERCA turnover. These findings provide a quantitative basis for SERCA function that leverages molecular-scale thermodynamic data and rationalizes enzyme activity across broad ranges of K+, Ca2+, and Mg2+ concentrations.

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of PV sequence homologues and EF-hand-containing, Ca(2+) binding proteins.

Lanthanide ion complexes of deprotonated p-isopropylcalix[n]arenes in dipolar aprotic solvents

The binding of lanthanide(III) cations with p-isopropylcalix[n]arenes (n = 4, 6, 8) after partial deprotonation has been investigated using UV-Vis absorption spectrophotometry. The ease and degree of deprotonation of the calixarenes closely parallels the behaviour of their t-butyl analogues in the same solvents. The conditional stability constants of the praseodymium, europium, ytterbium and yttrium complexes were determined in DMF and in acetonitrile. The effect of water on the stability of lanthanide complexes in DMF was also treated. The results show that the cation binding selectivity, stoichiometry and stability of the complexes depend on various factors such as the degree of condensation (n) and the consequent number of O-donor atoms as well as the nature of the cation solvation. The stability of the Y(III), Pr(III), Eu(III) and Yb(III) complexes in DMF increased in all cases with increase of the ring size. DFT calculations were used to estimate the influence of the solvent on both the acidity and the conformations of the calixarene anions.

Enhanced cation recognition by a macrocyclic ionophore at the air-solution interface probed by mass spectrometry.

Interfacial environments have the potential to drive unexpected events of supramolecular recognition, leading to advances in the development of novel functional materials and molecular sensing techniques. We present experimental evidence for a noticeable enhancement of the cation binding specificity of a prototype calixarene macrocycle (cesium ionophore II) at the air-solution interface, in comparison to bulk solution and to isolated solvent-less conditions. A rationalization of this intriguing finding is outlined, with the support of quantum calculations, in terms of the 'half-solvation' conditions provided by the interface and of conformational effects posed by the backbone structure and the side chains of the macrocyclic ionophore. The investigation involves the introduction of a mass spectrometry method to determine the relative abundances of interfacial complexes that should be of general application in the field and guide future advances in analytical techniques based on molecular recognition.

Tuning cation-binding selectivity and capacity via side chain-dependent molecular packing in the solid state.

Cavity-containing cation-binding pentameric macrocycles readily assemble, via side chain-dependent molecular packing, into either 1D nanotube bundles with the smallest being 10 nm in diameter or nanoplates of different sizes. The resultant nanostructures are able to selectively remove metal salts from aqueous solutions with varying selectivities and capacities.

Evaluating the cation binding strength and selectivity of calix[4]pyrroles: a computational and ESI-MS/MS study

The cation binding strength of calix[4]pyrroles in the gas phase has been evaluated by computational studies and further substantiated by ESI mass spectrometry experiments. The DFT optimized geometries of [CP + X](+) complexes are found to be stable in a 1,3-alternate conformation through cation-π interactions and interestingly CPs are found to be better cation receptor than calix[4]arenes. The binding energy values of [CP + X](+) complexes computed at B2PLYP/TZVP//M05-2X/TZVP follows the binding order, Li(+) > Na(+) > K(+) > Rb(+) > Cs(+). The diameter of Li(+) matches very well with the cavity size of CP and thus is optimally disposed to interact simultaneously with all four pyrrole rings through multiple cation-π interactions. However, other cations, due to the increase in their size, drift away from the cavity center towards the rim of the cavity exhibiting weak cation-π interactions. Energy decomposition analysis (EDA) reveals that the electrostatic and polarization effects act as the major driving force in these interactions. The important outcome of the current study is that the stability of precursor and product ions is found to be crucial in the experimental evaluation of binding affinity of Li(+) and Na(+) complexes of CP. The ESI-MS/MS experiments on the cation complexes of different substituted CPs revealed that the binding strength of CPs towards cations is also dependant on the substituents at the meso-position.

Molecular clips based on diphenylglycoluril and benzocrown ethers: promising complexing agents for the alkali metal cations

The interaction of new molecular clips containing diphenylglycoluril and benzocrown ethers moieties with alkali metals ions was studied. Stability constants were determined by spectrophotometric titrations with chloride salts in methanol. Complex stability and cation binding selectivity were shown to be dependent on the size of the crown ether moiety. The “sandwich-type” 1:1 (clip to cation) complexes and the “classical” 1:2 complexes were found. Their ratio varies depending on the molecular clips nature and on the cation type. It was found an unexpected selectivity of the molecular clip with benzo-15-crown-5 moieties toward K+ and Rb+ cations. The molecular structure of the clip complex with benzo-15-crown-5 fragments and sodium picrate was determined by X-ray crystallography. The crystal structure and solution-state structure were proven to be similar.

Fluorescent Sodium Ion Indicators Based on the 1,7‐Diaza‐15‐crown‐5 System.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Fluorescent sodium ion indicators based on the 1,7-diaza-15-crown-5 system

A series of novel sodium ion-sensitive fluorescent reagents suitable for biological applications is described. The chelator nitrogen atom substituents affect the selectivity and affinity of cation binding, while the nature of the fluorophore determines the type of fluorescent response to metal ion chelation.

Molecular design of crown ethers. 22. Synthesis of benzocrown ether derivatives and their solvent extraction with univalent/bivalent metal picrates

AbstractThree novel benzocrown ether derivatives have been synthesized and their cation binding behavior with uni‐and bi‐valent metal ions was evaluated by the solvent extraction of aqueous metal picrates. The obtained results indicate that the size‐fit of crown ether and metal cation, and electron effect of the side arm attached to benzocrown ethers affect their cation binding ability and selectivity.

Potassium selective calix[4]semitubes.

A new class of ionophore consisting of two calix[4]arene units linked through the lower rim by two ethylene chains, in combination with propyl ether and phenolic functional groups, has been developed. These calix[4]semitube molecules exhibit remarkable selectivity and fast complexation kinetics for potassium over all Group 1 metal cations. Molecular modelling studies, using structural models derived from crystallographic data, suggest the potassium cation is complexed by a horizontal, side-on route and not through the calix[4]arene annulus. The length of the bridging alkylene chain between the respective calix[4]arenes of the semitube structure dictates the strength and selectivity of alkali metal cation binding.

The synthesis of tetracarbonyl derivatives of thiacalix[4]arene in different conformations and their complexation properties towards alkali metal ions

The three conformations of 5,11,17,23-tetra- tert-butyl-25,26,27,28-tetrakis[(benzoyl)methoxy]-2,8,14,20-tetrathiacalix[4]arene 1 : cone, partial cone and 1,3- alternate, were prepared by the treatment of 5,11,17,23-tetra- tert-butyl-2,8,14,20-tetrathiacalix[4]arene-25,26,27,28-tetraol (TCA) with α-bromo acetophenone in the presence of appropriate alkali carbonate M 2CO 3 (M=Na, K, Cs) as base catalyst in acetonitrile. Structure of the conformers were established by 1H NMR, 1H– 1H COSY, 1D NOE, 2D ROESY and X-ray experiments. The alkali cation binding selectivity of the obtained macrocycles was investigated by the ion-pair extraction method.

The Synthesis and the Cationic Fluorescence Role of Glycols with Aromatic End Groups, Part III

Some novel bis-(substituted-phenoxy) ended glycols were synthesised usinghydroxy aromatics of vanillin, o-vanillin, iso-vanillin and 4-hydroxy coumarin which reacted with bis-dihalides of polyglycols in the presence ofDMSO/alkali carbonate. The novel podands, Ar-(CH2CH2O)m-Ar,(m = 1–4), were identified with IR, 1H-NMR, 13C-NMR and mass spectrometry. The various (formyl-methoxy)phenyl and 4-oxycoumarin derivatives of glycols were studied to estimate the cation binding selectivity of SCN- salts ofLi+, Na+, K+ and Zn2+ cations in acetonitrile using steady statefluorescence spectroscopy. The relevant structures of podands have shown goodselectivity depending on the cation and the glycollength, although the chromophoreend groups have no specific contribution on binding.

Cation Binding Selectivity of Partially Substituted Calix[4]arene Esters

Partially substituted calix[4]arene ethyl ester derivatives were synthesized as important precursors for new series of non-symmetrical ion and molecule receptors by reacting p-t-butyl calix[4]arene and ethyl bromoacetate. Characteristics of PVC-membrane ion-selective electrodes based on the mono- and di-ester derivatives were compared to those of the well-known calix[4]arene tetraester cationophore. Sodium selectivity is only manifested with the tetraester derivative, whereas the diester complexes potassium and caesium, as well as sodium. Energy-minimized structures for the complexes show the ester groups are involved in sodium complexation for the tetraester and diester derivatives, whereas for the monester, the aryl macrocycle is more important. This provides an excellent example of the critical importance of preorganization on host-guest selectivity, which in turn defines the selectivity of chemical sensors based on such receptors. The influence of this selective ion-binding behavior on the characterization of these derivatives using mass spectroscopy is discussed.

Alkali metal mediated resorcarene capsules: an ESI-FTICRMS study on gas-phase structure and cation binding of tetraethyl resorcarene and its per-methylated derivative

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) with additional ab initio calculations were used to examine the alkali metal cation binding selectivity (i.e., molecular recognition) and host properties of tetraethyl resorcarene ( 1) and its per-methylated derivative ( 2). The significance of intramolecular hydrogen bonding for the crown conformation was demonstrated. The presence of intramolecular flip-flop hydrogen bonding in 1 was confirmed both with calculations and in ND 3-exchange experiments. All the alkali metal cations formed host–guest complexes by docking inside the cavity of the host. Complexation with the larger cations, especially Cs +, was favored. All the alkali metal cations also formed dimeric resorcarene capsules with 1. The capsules were directly H-bonded species, with no linking solvent molecules. ND 3-exchange experiments and molecular modeling revealed the significance of direct intermolecular H-bonding for the crown conformation of 1 and stability of the capsule structure.

ChemInform Abstract: Synthesis, Alkali Metal Picrate Extraction, and Alkali Metal Cation Binding Selectivities of Some New Cage‐Annulated Polyoxamacrocyclic Crown Ethers.

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Synthesis, alkali metal picrate extraction, and alkali metal cation binding selectivities of some new cage‐annulated polyoxamacrocyclic crown ethers

AbstractFive new cage‐annulated crown ethers, i.e., 4a, 4b, 6b, 11a, and 11b, have been synthesized and their respective alkali metal picrate extraction profiles along with that of a previously synthesized host molecule, 6a, have been obtained. These results are compared with the corresponding results obtained for electrospray ionization mass spectrometric (ESI‐MS) measurements of relative binding selectivities displayed by the same hosts toward a series of alkali metal chlorides. Among the crown‐5 hosts studied, 6a displays enhanced avidity toward complexation with K+ picrate in liquid‐liquid extraction experiments. Among the three crown‐6 hosts, 4b proved to be the best alkali metal picrate extractant and displayed significant levels of avidity toward complexation with the larger alkali metal cations (i.e., K+, Rb+, and Cs+). The trends in the picrate extraction and the ESI‐MS results obtained herein show several notable similarities and some differences. The similarities generally stem from size‐selective binding properties that are intrinsic to the different cavity sizes of the cage‐annulated macrocycles, whereas the differences reflect the important influence of solvation effects on the binding properties of the macrocycles.

Complexation Thermodynamics of p-tert-Butylcalix[4]arene Derivatives with Light Lanthanoid Nitrates in Acetonitrile

Calorimetric titrations have been performed for the first time in anhydrous acetonitrile at 25°C to give the complex stability constant (K S) and thermodynamic quantities for the complexation of light lanthanoid(III) nitrates (La-Gd) with 5,11,17,23-tetra-tert-butyl-26,28-bis(cyanomethoxy)-25,27-dihydroxy-calix[4]arene (1) and 5,11,17,23-tetra-tert-butyl-26, 28-bis(2-aminoethoxy)-25,27-dihydroxycalix[4]arene (2). X-ray crystallographic structures of 1 and 2 were also determined and compared. Possessing the cyanomethoxy and aminoethyl substituents, 1 and 2 displayed strikingly different cation binding abilities and selectivity profiles with much higher K S values for La3+ and Ce3+, which may be related to the original structures in the solid state. Thus, the binding profile for 2 showed a rapid decrease in K S with decreasing ionic diameter from La3+ to Pr3+ and then became flat up to Gd3+, while 1 gave a very flat profile which is superimposable with that for 2 between Pr3+-Gd3+. Thermodynamically, the complexation is driven absolutely by enthalpy which compensates the entropic loss arising from the structural freezing of the calix[4]arene derivatives upon simultaneous binding of lanthanoid ion by the phenolic oxygen and acetonitrile molecule in the cavity. The general validity and the meaning of the compensative enthalpy-entropy relationship observed are discussed.

Molecular Design of Calixarene 5. Syntheses and Cation Selectivities of Novel Schiff's Base p‐tert‐Butylcalix[4]arenes

AbstractFive novel Schiff's bases p‐tert‐butylcalix[4]arenes have been synthesized in high yields by the reaction of 1,3‐distally disubstituted p‐tert‐butylcalix[4]arene amine (1) with the corresponding aromatic aldehydes, and their cation binding abilities and selectivities with alkali and heavy metal ions have been evaluated by solvent extraction of aqueous metal picrates to show the highest Ag+ extractability for Schiff's base p‐tert‐butylcalix[4]arene (6) and the best Na+/Li+ and Ag+/Ti+ selectivities for Schiff's base p‐tert‐butylcalix[4]arene (4 and 2) over any other calix[4]arene derivatives, respectively.

Conversion of an Engineered Potassium-binding Site into a Calcium-selective Site in Cytochrome c Peroxidase

We have previously shown that the K(+) site found in ascorbate peroxidase can be successfully engineered into the closely homologous peroxidase, cytochrome c peroxidase (CCP) (Bonagura, C. A. , Sundaramoorthy, M., Pappa, H. S., Patterson, W. R., and Poulos, T. L. (1996) Biochemistry 35, 6107-6115; Bonagura, C. A., Sundaramoorthy, M., Bhaskar, B., and Poulos, T. L. (1999) Biochemistry 38, 5538-5545). All other peroxidases bind Ca(2+) rather than K(+). Using the K(+)-binding CCP mutant (CCPK2) as a template protein, together with observations from structural modeling, mutants were designed that should bind Ca(2+) selectively. The crystal structure of the first generation mutant, CCPCA1, showed that a smaller cation, perhaps Na(+), is bound instead of Ca(2+). This is probably because the full eight-ligand coordination sphere did not form owing to a local disordering of one of the essential cation ligands. Based on these observations, a second mutant, CCPCA2, was designed. The crystal structure showed Ca(2+) binding in the CCPCA2 mutant and a well ordered cation-binding loop with the full complement of eight protein to cation ligands. Because cation binding to the engineered loop results in diminished CCP activity and destabilization of the essential Trp(191) radical as measured by EPR spectroscopy, these measurements can be used as sensitive methods for determining cation-binding selectivity. Both activity and EPR titration studies show that CCPCA2 binds Ca(2+) more effectively than K(+), demonstrating that an iterative protein engineering-based approach is important in switching protein cation selectivity.