Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A2

The empirical energy parameters for a calcium ion and its ligands in proteins were determined within a pairwise additive framework. The interaction energies of Ca²⁺-water, Ca²⁺-peptide group and Ca²⁺-carboxyl group systems were calculated using the ab initio molecular orbital method with basis sets of double zeta quality including polarization or diffuse functions. The resulting potential energy surfaces served as references for the determination of the nonbonded parameters in the empirical energy function. The nonadditive corrections for the Ca²⁺-ligand pair potentials are incorporated implicitly in the nonbonded paremeters by treating three-body (1:2 complex) or seven-body (1:6 complex) systems in reference calculations. Ligand polarizations induced by Ca²⁺ are estimated from the partial atomic charges of two-body (1:1 complex) systems. The charge sets were determined by scaling so as to reproduce the reference potential energy surfaces. The newly determined parameter set was used in a stochastic boundary molecular dynamics simulation of phospholipase A₂. The solvated structure of the Ca²⁺-binding site obtained from an X-ray crystallographic study is well reproduced by the parameter set.     

Investigation of structure of Fe3+ magnetic center in polyparaphenylene

In the temperature range between 4.2 and 300 K, the EPR spectrum of the impurity Fe³⁺ ion in the organic polyparaphenylene has been investigated. An effect developed as an unusual temperature change of Fe³⁺ EPR spectrum has been revealed. The EPR spectrum of powder sample consists of two resonance lines. Line 1 with the effective g‐value equal to g₁ = 4.21 ± 0.05 is of the maximum intensity at T = 4.2 K. With temperature increase, the intensity of line 1 decreases until vanishing. Line 2 is observed over the whole temperature range. For T = 300 K, the g‐value of line 2 is g₂ = 2.00 ± 0.09. To study the structure of magnetic ion molecular environment and define nonequivalent positions of the magnetic ion in polyparaphenylene, a calculation was done of the energy of Fe³⁺ magnetic ion for various possible molecular environments. It is shown that in polyparaphenylene for the Fe³⁺ magnetic ion there are two different stationary molecular environments. The obtained model of magnetic ion molecular environment was used to explain the temperature dependence of the EPR spectrum. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

New Calcium‐Selective Smart Contrast Agents for Magnetic Resonance Imaging

Calcium plays a vital role in the human body and especially in the central nervous system. Precise maintenance of Ca²⁺ levels is very crucial for normal cell physiology and health. The deregulation of calcium homeostasis can lead to neuronal cell death and brain damage. To study this functional role played by Ca²⁺ in the brain noninvasively by using magnetic resonance imaging, we have synthesized a new set of Ca²⁺‐sensitive smart contrast agents (CAs). The agents were found to be highly selective to Ca²⁺ in the presence of other competitive anions and cations in buffer and in physiological fluids. The structure of CAs comprises Gd³⁺‐DO3A (DO3A=1,4,7‐tris(carboxymethyl)‐1,4,7,10‐tetraazacyclododecane) coupled to a Ca²⁺ chelator o‐amino phenol‐N,N,O‐triacetate (APTRA). The agents are designed to sense Ca²⁺ present in extracellular fluid of the brain where its concentration is relatively high, that is, 1.2–0.8 mM . The determined dissociation constant of the CAs to Ca²⁺ falls in the range required to sense and report changes in extracellular Ca²⁺ levels followed by an increase in neural activity. In buffer, with the addition of Ca²⁺ the increase in relaxivity ranged from 100–157 %, the highest ever known for any T₁‐based Ca²⁺‐sensitive smart CA. The CAs were analyzed extensively by the measurement of luminescence lifetime measurement on Tb³⁺ analogues, nuclear magnetic relaxation dispersion (NMRD), and ¹⁷O NMR transverse relaxation and shift experiments. The results obtained confirmed that the large relaxivity enhancement observed upon Ca²⁺ addition is due to the increase of the hydration state of the complexes together with the slowing down of the molecular rotation and the retention of a significant contribution of the water molecules of the second sphere of hydration.     

Molecular modeling of polymers: 18. Molecular dynamics simulation of poly(acrylic acid) copolymer analogs. Capture of calcium ions as a function of monomer structure,sequence and flexibility

The behavior of four derivative copolymers of poly(acrylic acid) were modeled in dilute aqueous polymer solutions with calcium counterions. Molecular dynamics simulations of negatively charged copolymer models in the presence of different Ca²⁺ ion concentrations at 300 K, using an effective molecular dielectric constant of 3.5, were performed. Analyses of the dependence of the total potential energy, the counterion binding energy and the time average chain segment length of each of the copolymer models on Ca²⁺ ion concentration was performed. One of the copolymer models was predicted to have the greatest propensity to capture the calcium counterions. Unusually strong binding interactions between the copolymer and Ca²⁺ counterions were identified for this copolymer. Structure-binding analysis led to the identification of a specific Ca²⁺ binding site sequence and geometry as being responsible for the strong counterion binding. The events that take place during the calcium capturing process at this binding-site are discussed in terms of intramolecular dynamics and intermolecular electrostatic interactions. The existence of this specific Ca²⁺ binding sequence is a clear example of how property optimization studies in the laboratory mimic breakthrough outcomes realized in natural evolution.     

Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca2+‐ATPase

Calcium ATPase is a member of the P‐type ATPase, and it pumps calcium ions from the cytoplasm into the reticulum against a concentration gradient. Several X‐ray structures of different conformations have been solved in recent years, providing basis for elucidating the active transport mechanism of Ca²⁺ ions. In this work, molecular dynamics (MD) simulations were performed at atomic level to investigate the dynamical process of calcium ions moving from the outer mouth of the protein to their binding sites. Five initial locations of Ca²⁺ ions were considered, and the simulations lasted for 2 or 6 ns, respectively. Specific pathways leading to the binding sites and large structural rearrangements around binding sites caused by uptake of calcium ions were identified. A cooperative binding mechanism was observed from our simulation. Firstly, the first Ca²⁺ ion binds to site I , and then, the second Ca²⁺ ion approaches. The interactions between the second Ca²⁺ and the residues around site I disturb the binding state of site I and weaken its binding ability for the first bound Ca²⁺. Because of the electrostatic repulsion of the second Ca²⁺ and the electrostatic attraction of site II , the first bound Ca²⁺ shifts from site I to site II . Concertedly, the second Ca²⁺ binds to site I , forming a binding state with two Ca²⁺ ions, one at site I and the other at site II . Both of Glu908 and Asp800 coordinate with the two Ca²⁺ ions simultaneously during the concerted binding process, which is believed to be the hinge to achieve the concerted binding. In our simulations, four amino acid residues that serve as the channel to link the outer mouth and the binding sites during the binding process were recognized, namely Tyr837, Tyr763, Asn911, and Ser767. The analyses regarding the activity of the proteins via mutations of some key residues also supported our cooperative mechanism. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Chirality Transfer in Propeller‐Shaped Cyclen?Calcium(II) Complexes: Metal‐Coordinating and Ion‐Pairing Anion Procedures

A series of quadruple‐stranded Na⁺ and Ca²⁺ complexes with octadentate cyclen ligands was synthesized to produce complexes that contained four different side‐arm combinations (one triazole? coumarin group and three pyridine groups ( 1 ), four pyridine groups ( 2 ), one triazole? coumarin group and three quinoline groups ( 3 ), and four quinoline groups ( 4 )). X‐ray crystallographic analysis revealed that no significant changes occurred in the stereostructure of these complexes upon replacing one pyridine group with a triazole? coumarin moiety, or by replacing Na⁺ ions with Ca²⁺ ions, although the coordination number of the complexes in the solid state decreased when pyridine groups were replaced by quinoline groups. In solution, all of the side arms were arranged in a propeller‐like pattern to yield an enantiomer pair of Δ and Λ forms in each metal complex. The addition of a tert‐butoxycarbonyl (Boc)‐protected amino acid anion, that is, a coordinative chiral carboxylate anion, to the cyclen? Ca²⁺ complex induced circular dichroism (CD) signals in the aromatic region by forming a 1:1 mixture of diastereomeric ternary complexes with opposite complex chirality, whilst the corresponding Na⁺ complexes rarely showed any response. In complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺, this chirality‐transfer process was efficiently followed by considering the induction of the CD signals at two different wavelengths, that is, the coumarin‐chromophore region and the aza‐aromatic region. The sign and intensity of the CD signal were significantly dependent on both the nature of the aza‐aromatic moiety and the enantiomeric purity of the external anion. These Ca²⁺ complexes worked as effective probes for the determination of the enantiomeric excess of the chiral anion. The cyclen? Ca²⁺ complexes also interacted with the non‐coordinative Δ‐TRISPHAT anion through an ion‐pairing mechanism to achieve chirality transfer from the anion to the metal complex; both complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺ clearly showed induced CD signals in the coumarin‐chromophore region, owing to ion‐paring interactions with the Δ‐TRISPHAT anion. Thus, the proper combination of an octadentate cyclen ligand and a metal center demonstrated effective chirality transfer.     

Effect of Na+ and Ca2+ Ions on a Lipid Langmuir Monolayer: An Atomistic Description by Molecular Dynamics Simulations

Studying the effect of alkali and alkaline‐earth metal cations on Langmuir monolayers is relevant from biophysical and nanotechnological points of view. In this work, the effect of Na⁺ and Ca²⁺ on a model of an anionic Langmuir lipid monolayer of dimyristoylphosphatidate (DMPA^?) is studied by molecular dynamics simulations. The influence of the type of cation on lipid structure, lipid–lipid interactions, and lipid ordering is analyzed in terms of electrostatic interactions. It is found that for a lipid monolayer in its solid phase, the effect of the cations on the properties of the lipid monolayer can be neglected. The influence of the cations is enhanced for the lipid monolayer in its gas phase, where sodium ions show a high degree of dehydration compared with calcium ions. This loss of hydration shell is partly compensated by the formation of lipid–ion–lipid bridges. This difference is ascribed to the higher charge‐to‐radius ratio q/r for Ca²⁺, which makes ion dehydration less favorable compared to Na⁺. Owing to the different dehydration behavior of sodium and calcium ions, diminished lipid–lipid coordination, lipid–ion coordination, and lipid ordering are observed for Ca²⁺ compared to Na⁺. Furthermore, for both gas and solid phases of the lipid Langmuir monolayers, lipid conformation and ion dehydration across the lipid/water interface are studied.     

Investigation of the stereodynamics of tris‐(α‐diimine)–transition metal complexes by enantioselective dynamic MEKC

Enantiomerization of octahedral tris(α‐diimine)–transition metal complexes was investigated by enantioselective dynamic MEKC. Varying both the transition metal ion (Fe²⁺, Fe³⁺, and Ni²⁺) and the bidentate diimine ligand (1,10‐phenanthroline and 2,2′‐bipyridyl), the enantiomer separations were performed either in a 100 mM sodium tetraborate buffer (pH 9.3) or in a 100 mM sodium tetraborate/sodium dihydrogenphosphate buffer (pH 8.0) both containing sodium cholate as chiral surfactant. The unified equation of dynamic chromatography was employed to determine apparent reaction rate constants from the electropherograms showing distinct plateau formation. Apparent activation parameters ΔH^? and ΔS^? were calculated from temperature‐dependent measurements between 10.0 and 35.0°C in 2.5 K steps. It was found that the nature of the central metal ion and the ligand strongly influence the enantiomerization barrier. Surprisingly, complexes containing the 2,2′‐bipyridyl ligand show highly negative activation entropies between ?103 and ?116 J (K mol)^?1 while the activation entropy of tris(1,10‐phenanthroline) complexes is positive indicating a different mechanism of interconversion. Furthermore, it was found that the Ni²⁺ complexes are stereostable under the conditions investigated here making them a lucent target as enantioselective catalysts.     

Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca2+‐regulated Photoproteins of Different Organisms

Upon binding their metal ion cofactors, Ca²⁺‐regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study, we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca²⁺‐regulated photoproteins—aequorin from Aequorea victoria, clytin from Clytia gregaria, mitrocomin from Mitrocoma cellularia and obelins from Obelia longissima and Obelia geniculata—demonstrate the same bioluminescent kinetics pattern. Based on these findings, for the first time we propose a unanimous kinetic model describing the bioluminescence mechanism of Ca²⁺‐regulated photoproteins.     

Control of the Spin Dynamics of Single‐Molecule Magnets by using a Quasi One‐Dimensional Arrangement

Magnetic dipole interactions are dominate in quasi one‐dimensional (1D) molecular magnetic materials, in which TbNcPc units (Tb³⁺=terbium(III) ion, Nc^2?=naphthalocyaninato, Pc^2?=phthalocyaninato) adopt a structure similar to TbPc₂ single‐molecule magnets (SMMs). The magnetic properties of the [TbNcPc]^0/+ (neutral 1 and cationic 2 ) with 1D structures are significantly different from those of a magnetically diluted sample ( 3 ). In particular, the magnetic relaxation time (τ) of 2 in the low‐temperature region is five orders of magnitude slower than that of 3 . Furthermore, the coercivity (H_C) of 2 remained up to about 20 K. The single‐ion anisotropy of Tb³⁺ ions in a 1D structure and the magnetic dipole interactions acting among molecules determines the direction of the magnetic properties. These results show that the spin dynamics can be improved by manipulating the arrangement of SMMs in the solid state.     

Hydrated germanium (II): Irregular structural and dynamical properties revealed by a quantum mechanical charge field molecular dynamics study

Structural and dynamical properties of Ge (II) in aqueous solution have been investigated using the novel ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism. The first and second hydration shells were treated by ab initio quantum mechanics at restricted Hartree–Fock (RHF) level using the cc‐pVDZ‐PP basis set for Ge (II) and Dunning double‐ζ plus polarization basis sets for O and H. Besides ligand exchange processes and mean ligand residence times to observe dynamics, tilt‐ and theta‐angle distributions along with an advanced structural parameter, namely radial and angular distribution functions (RAD) for different regions were also evaluated. The combined radial and angular distribution depicted through surface plot and contour map is presented to provide a detailed insight into the density distribution of water molecules around the Ge²⁺ ion. A strongly distorted hydration structure with two trigonal pyramidal substructures within the first hydration shell is observed, which demonstrates the lone‐pair influence and provides a new basis for the interpretation of the catalytic and pharmacological properties of germanium coordination compounds. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

QSPR Modeling of Potentiometric Mg2+/Ca2+ Selectivity for PVC‐plasticized Sensor Membranes

The development of novel ionophores for ion‐selective sensors is a time‐consuming and tedious process requiring synthesis of candidate substances, preparation of plasticized polymeric membranes, and their thorough characterization with traditional protocols to assess sensitivity, selectivity and detection limits for target ions. The vast amount of literature data accumulated on various ion‐selective sensors allows for significant facilitation of the development through in silico experiments. In this report, we performed the feasibility study on the prediction of potentiometric Mg²⁺/Ca²⁺ selectivity for various amide ligands using quantitative structure‐property relationship (QSPR) modeling. The approach proved to be promising for ionophore screening purposes with achieved precision in prediction of the selectivity coefficient logK(Mg²⁺/Ca²⁺) of 0.5 in the range from ?1.7 to +2.3. The study also shows a route for prediction of new potential ionophores with high selectivity values.     

Direct ab initio dynamics study of the reaction of C2(A3Πu) with CH4

The reaction of C₂(A³Π_u) with CH₄ has been investigated over a wide temperature range 200–3,000 K by direct ab initio dynamics method at the BMC‐CCSD//BB1K/6‐311+G(2d,2p) level of theory. The optimized geometries and frequencies of the stationary points are calculated at the BB1K/6‐311+G(2d,2p) level, and then the energy profiles of the reactions are refined using the BMC‐CCSD method. The activation barrier height for H‐abstraction reaction was calculated to be 4.44 kcal/mol in temperature range (337–605 K), and the electron transfer behavior was also analyzed by quasi‐restricted molecular orbital method in detail. The canonical variational transition‐state theory (CVT) with the small curvature tunneling (SCT) correction method is used to calculate the rate constants over a wide temperature range 200–3,000 K. The theoretical results shows that variational effect is to some extent large in lower temperature range, and small curvature and tunneling effect play important roles to the H‐atom abstraction only at lower temperatures. The CVT/SCT rate constants are in good agreement with the available experimental results. Our theoretical study is expected to provide a direct insight into the reaction mechanism and may be useful for estimating the kinetics of the title reaction over a wide temperature range where no experimental data are available so far. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration

The enzyme, cutinase from Saccharomonospora viridis AHK190 (Cut190), can hydrolyze the inner block of polyethylene terephthalate (PET). Cut190 has a unique feature that both its activity and thermal stability are increased upon Ca²⁺ binding. In consideration of the glass transition temperature of PET, which is between 60 and 65 °C, the increased activity and thermal stability are of great interest to apply for PET bio-recycling. Our previous mutational analysis showed that the S226P/R228S mutant (Cut190*) has a higher activity and thermal stability than those of the wild type. In this study, we analyzed the folding thermodynamics of the inactive mutant of Cut190*, Cut190*S176A, using circular dichroism and differential scanning calorimetry. The results show that the denaturation temperature increases from 54 to 71 °C due to the addition of 250 mM Ca²⁺, in a Ca²⁺ concentration-dependent manner. The increased thermal stability is mainly due to the increased enthalpy change, partially compensated by the increased entropy change. Based on the crystal structure of Cut190*S176A bound to Ca²⁺, molecular dynamics simulations were carried out to analyze the effects of Ca²⁺ on the structural dynamics, showing that the Ca²⁺-bound structure fluctuated less than the Ca²⁺-free structure. Structural analysis indicates that Ca²⁺ binding increases the intramolecular interactions of the enzyme, while decreasing its fluctuation, which are in good correlation with the experimental results of the folding thermodynamics.

     

Indirect ultraviolet detection of alkaline earth metal ions using an imidazolium ionic liquid as an ultraviolet absorption reagent in ion chromatography

A convenient and versatile method was developed for the separation and detection of alkaline earth metal ions by ion chromatography with indirect UV detection. The chromatographic separation of Mg²⁺, Ca²⁺, and Sr²⁺ was performed on a carboxylic acid base cation exchange column using imidazolium ionic liquid/acid as the mobile phase, in which the imidazolium ionic liquid acted as an UV‐absorption reagent. The effects of imidazolium ionic liquids, detection wavelength, acids in the mobile phase, and column temperature on the retention of Mg²⁺, Ca²⁺, and Sr²⁺ were investigated. The main factors influencing the separation and detection were the background UV absorption reagent and the concentration of hydrogen ion in ion chromatography with indirect UV detection. The successful separation and detection of Mg²⁺, Ca²⁺, and Sr²⁺ within 14 min were achieved using the selected chromatographic conditions, and the detection limits (S /N = 3) were 0.06, 0.12, and 0.23 mg/L, respectively. A new separation and detection method of alkaline earth metal ions by ion chromatography with indirect UV detection was developed, and the application range of ionic liquids was expanded.     

ESI‐MS studies of the non‐covalent interactions between biologically important metal ions and N‐sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non‐covalent interaction of two biologically active ligands, N‐1 ‐ (p‐toluenesulfonyl)cytosine, 1‐TsC, 1 and N‐1 ‐ methanesulfonylcytosine, 1‐MsC, 2 and their Cu(II) complexes Cu(1‐TsC‐N3)₂Cl₂, 3 and Cu(1‐MsC‐N3)₂Cl₂ and 4 with biologically important cations: Na⁺, K⁺, Ca²⁺, Mg²⁺ and Zn²⁺. The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1–4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.     

Combining fragment homology modeling with molecular dynamics aims at prediction of Ca2+ binding sites in CaBPs

The family of calcium-binding proteins (CaBPs) consists of dozens of members and contributes to all aspects of the cell’s function, from homeostasis to learning and memory. However, the Ca²⁺-binding mechanism is still unclear for most of CaBPs. To identify the Ca²⁺-binding sites of CaBPs, this study presented a computational approach which combined the fragment homology modeling with molecular dynamics simulation. For validation, we performed a two-step strategy as follows: first, the approach is used to identify the Ca²⁺-binding sites of CaBPs, which have the EF-hand Ca²⁺-binding site and the detailed binding mechanism. To accomplish this, eighteen crystal structures of CaBPs with 49 Ca²⁺-binding sites are selected to be analyzed including calmodulin. The computational method identified 43 from 49 Ca²⁺-binding sites. Second, we performed the approach to large-conductance Ca²⁺-activated K⁺ (BK) channels which don’t have clear Ca²⁺-binding mechanism. The simulated results are consistent with the experimental data. The computational approach may shed some light on the identification of Ca²⁺-binding sites in CaBPs.     

Preparation,Crystal Structures,and Thermal Studies of Alkaline Earth Nitrocarboxylates

The preparation, crystal structures, and thermal properties of [Ca(pyr)₂(4‐nba)₂]_n ( 1 ) (pyr = pyrazole; 4‐nba = 4‐nitrobenzoate) {[Ca(H₂O)₂(3‐npth)] · H₂O}_n ( 2 ) (3‐npth = 3‐nitrophthalate), [Mg(H₂O)₅(3‐npth)] · 2H₂O ( 3 ), and [Mg(H₂O)₄(2‐nba)₂] ( 4 ) (2‐nba = 2‐nitrobenzoate) are reported. The anhydrous Ca^II compound 1 and the diaqua Ca^II‐3‐nitrophthalate monohydrate 2 are one‐dimensional coordination polymers containing a hexacoordinate Ca^II ion located on a center of inversion in 1 and a heptacoordinated Ca^II ion in 2 . In 1 , the 4‐nitrobenzoate moiety acts as a μ₂‐bridging bidentate ligand, whereas the 3‐nitrophthalate anion exhibits a μ₃‐bridging pentadentate coordination mode in 2 . The hexacoordinate Mg^II‐containing compounds 3 and 4 do not contain a [Mg(H₂O)₆]²⁺ unit and the central Mg^II ion is coordinated to at least one monodentate carboxylate unit namely the monodentate 3‐npth molecule in 3 and two trans monodentate 2‐nba molecules in 4 . Hydrogen bonding between the lattice water molecules results in the formation of a water dimer in 3 . A comparative study of 17 alkaline earth nitrocarboxylates is described.     

An All‐solid‐state Polymeric Membrane Ca2+‐selective Electrode Based on Hydrophobic Alkyl‐chain‐functionalized Graphene Oxide

An all‐solid‐state polymeric membrane Ca²⁺‐selective electrode based on hydrophobic octadecylamine‐functionalized graphene oxide has been developed. The hydrophobic composite in the ion‐selective membrane not only acts as a transduction element to improve the potential stability for the all‐solid‐state Ca²⁺‐selective electrode, but also is used to immobilize Ca²⁺ ionophore with lipophilic side chains through hydrophobic interactions. The developed all‐solid‐state Ca²⁺‐selective electrode shows a stable potential response in the linear range of 3.0×10⁻⁷–1.0×10⁻³ M with a slope of 24.7±0.3 mV/dec, and the detection limit is (1.6±0.2 )×10⁻⁷ M (n =3). Additionally, due to the hydrophobicity and electrical conductivity of the composite, the proposed all‐solid‐state ion‐selective electrode exhibits an improved stability with the absence of water layer between the ion‐selective membrane and the underlying glassy carbon electrode. This work provides a simple, efficient and low‐cost methodology for developing stable and robust all‐solid‐state ion‐selective electrode with ionophore immobilization.