Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study

Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.     

内含式化合物X@Al12P12的结构与稳定性研究

采用B3LYP／6—31G*方法,对内含式化合物X@Al12P12(X=Li^0/ ,Na^0/ ,K^0/2 ,Be^0/2 ,Mg^0/2 ,Ca^0/2 ,H和He)的不同对称性构型进行计算,讨论其最稳定构型的几何参数、布居分析、偶极矩、电离势、包含能、频率、HOMO—LUMO能隙和自旋密度．发现X@Al12P12化合物中,客体X=Na^0/ ,K^0/ ,Mg和He几乎处在笼的中心,Be和Ca^0/2 处在中心附近0．033nm的半径内,Li^0/ ,Be^2 ,Mg^2 和H很大程度上偏离笼的中心位置．大部分金属内含式化合物的C3对称性构型稳定．Li^0/ 。,Be^0/2 ,Mg^2 ,Ca^2 和H与其它离子相比更易嵌入笼内形成稳定的内含式化合物．     

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure of glycine and zwitterionic glycine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. Here, the effect of metal ions and water on the structure of glycine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water on structures of Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (m = 0, 2, 5) complexes have been determined theoretically by employing the hybrid B3LYP exchange-correlation functional and using extended basis sets. Selected calculations were carried out also by means of CBS-QB3 model chemistry. The interaction enthalpies, entropies, and Gibbs energies of eight complexes Gly.Mn+ (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) were determined at the B3LYP density functional level of theory. The computed Gibbs energies DeltaG degrees are negative and span a rather broad energy interval (from -90 to -1100 kJ mol(-1)), meaning that the ions studied form strong complexes. The largest interaction Gibbs energy (-1076 kJ mol(-1)) was computed for the NiGly2+ complex. Calculations of the molecular structure and relative stability of the Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+; m = 0, 2, and 5) systems indicate that in the complexes with monovalent metal cations the most stable species are the NO coordinated metal cations in non-zwitterionic glycine. Divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ prefer coordination via the OO bifurcated bonds of the zwitterionic glycine. Stepwise addition of two and five water molecules leads to considerable changes in the relative stability of the hydrated species. Addition of two water molecules at the metal ion in both Gly.Mn+ and GlyZwitt.Mn+ complexes reduces the relative stability of metallic complexes of glycine. For Mn+ = Li+ or Na+, the addition of five water molecules does not change the relative order of stability. In the Gly.K+ complex, the solvation shell of water molecules around K+ ion has, because of the larger size of the potassium cation, a different structure with a reduced number of hydrogen-bonded contacts. This results in a net preference (by 10.3 kJ mol(-1)) of the GlyZwitt.K+H2O5 system. Addition of five water molecules to the glycine complexes containing divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ results in a net preference for non-zwitterionic glycine species. The computed relative Gibbs energies are quite high (-10 to -38 kJ mol(-1)), and the NO coordination is preferred in the Gly.Mn+(H2O)5 (Mn+ = Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) complexes over the OO coordination.     

Factors governing the metal coordination number in isolated group IA and IIA metal hydrates

Many of the group IA and IIA metal ions, such as Na+, K+, Mg2+, and Ca2+, play crucial roles in biological functions. Previous theoretical studies generally focus on the number of water molecules bound to a particular (as opposed to all) alkali or alkaline earth cations and could not establish a single preferred CN for the heavier alkali and alkaline earth ion-water complexes. Crystal structures of hydrated Na+, K+, and Rb+ also cannot establish the preferred number of inner-shell water molecules bound to these cations. Consequently, it is unclear if the gas-phase CNs of group IA metal hydrates increase with increasing ion size, as observed for the group IIA series from the Cambridge Structural Database, and if the same factors govern the gas-phase CNs of both group IA and IIA ion-water complexes. Thus, in this work, we determine the number of water molecules directly bound to the series of alkali (Li+, Na+, K+, and Rb+) and alkaline earth (Be2+, Mg2+, Ca2+, Sr2+, and Ba2+) metal ions in the gas phase by computing the free energy for forming an isolated metal-aqua complex as a function of the number of water molecules at 298 K. The preferred gas-phase CNs of group IA hydrates appear insensitive to the ion size; they are all 4, except for Rb+, where a CN of 6 seems as likely. In contrast, the preferred gas-phase CNs of the group IIA dications increase with increasing ion size; they are 4 for Be2+, 6 for Mg2+ and Ca2+, and 7 for Sr2+ and Ba2+. An entropic penalty disfavors a gas-phase CN greater than 4 for group IA hydrates, but it does not dictate the gas-phase CNs of group IIA hydrates. Instead, interactions between the metal ion and first-shell water molecules and between first-shell and second-shell water molecules govern the preferred gas-phase CNs of the group IIA metal hydrates.     

微量热法研究碱土金属离子与18-冠-6结合的热力学常数

通过微量热法研究了18-冠-6与碱土金属离子结合过程. 根据反应后的平衡关系, 求出反应平衡常数、焓、熵和吉布斯自由能变化. 金属离子由原来溶剂化的游离态变为与18-冠-6以静电力结合, 体系的能量降低, 放出了热量;同时由原来的自由运动变为被限制在冠醚孔穴内, 自由度减小, 熵值减少. 冠醚内的氧原子能够紧紧地围绕着半径为138 pm的Ba2+, 而离子半径较小的其它离子, 围绕得不够紧密, 与氧原子之间的作用力变小. 从Be2+、Mg2+、Ca2+、Sr2+到Ba2+, 与冠醚结合的放热增加, 平衡常数也逐渐增大.     

A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1

Structural and thermodynamic aspects of alkaline earth metal dication (Mg(2+), Ca(2+), Sr(2+), Ba(2+)) binding to E. coli ribonuclease H1 (RNase H1) have been investigated using both experimental and theoretical methods. The various metal-binding modes of the enzyme were explored using classical molecular dynamics simulations, and relative binding free energies were subsequently evaluated by free energy simulations. The trends in the free energies of model systems based on the simulation structures were subsequently verified using a combination of density functional theory and continuum dielectric methods. The calculations provide a physical basis for the experimental results and suggest plausible role(s) for the metal cation and the catalytically important acidic residues in protein function. Magnesium ion indirectly activates water attack of the phosphorus atom by freeing one of the active site carboxylate residues, D70, to act as a general base through its four first-shell water molecules, which prevent D70 from binding directly to Mg(2+). Calcium ion, on the other hand, inhibits enzyme activity by preventing D70 from acting as a general base through bidentate interactions with both carboxylate oxygen atoms of D70. These additional interactions to D70, in addition to the D10 and E48 monodentate interactions found for Mg(2+), enable Ca(2+) to bind tighter than the other divalent ions. However, a bare Mg(2+) ion with two or less water molecules in the first shell could bind directly to the three active-site carboxylates, in particular D70, thus inhibiting enzymatic activity. The present analyses and results could be generalized to other members of the RNase H family that possess the same structural fold and show similar metal-binding site and Mg(2+)-dependent activity.     

The interaction of dolomite surfaces with metal impurities: a computer simulation study

This study investigates the behaviour of selected, morphologically important surfaces of dolomite (CaMg(CO3)2), using computational modelling techniques. Interatomic potential methods have been used to examine impurity substitution at cationic sites in these surfaces. Environmentally prevalent cations were studied to this end, namely Ni2+, Co2+, Zn2+, Fe2+, Mn2+ and Cd2+, all of which are also found as end-member carbonate minerals. Solid-solution substitution was investigated and showed that Cd and Mn will substitute from their end-member carbonate phase at either dolomite cation site. Mn is found to preferentially substitute at Mg sites, in agreement with experimental findings. For Ni2+, Co2+ and Zn2+, the magnitude of substitution energies is approximately equal for all surfaces, with the exception of the (1014) surface. However, for the larger cations, a far greater disparity in substitution energies is observed. At a stepped surface, analogous substitutions were performed and it was found that substitution energies for all impurity cations were reduced, indicating that uptake is more viable during growth. The predominant surface, the (1014), was solvated with a monolayer of water in order to investigate the influence of hydration on substitution energetics. The addition of water changes the relative preference for substitution of the different cations. Under aqueous conditions, the substitution energy is determined by three competing factors, the relative importance of which cannot be predicted without this type of computational investigation.     

磷酸二甲酯阴离子(DMP~-)与一价、二价金属离子 相互作用的理论研究

在B3LYP、HF和MP2水平上运用全电子从头算(AE)和相对论有效实势(RECP)及6-311+G**和LanL2DZ基组计算Ⅰa、Ⅰb、Ⅱa和Ⅱb族金属离子与磷酸二甲酯阴离子(DMP-)的相互作用。 RECP用于除Li+、Be2+外所有的金属离子。 对Na+、K+、Cu+、Mg2+、Ca2+、Zn2+用AE和RECP 2种方法处理。 结果表明:RECP能可靠地用于重金属离子络合物; 二价金属离子络合物(DMP-—M2+)比一价金属离子络合物 (DMP-—M+)稳定;二价金属离子(M2+)可能比一价金属离子(M+)更易使多核苷酸折叠。     

Favorable pendant-amino metal chelation in VX nerve agent model systems

We have performed DFT computational studies [B3LYP, 6-31+G] to obtain metal ion coordination isomers of VX-Me [MeP(O)(OMe)(SCH2CH2NMe2)], a model of two of the most lethal nerve agents: VX [MeP(O)(OEt)(SCH2CH2N(iPr)2)] and Russian-VX [MeP(O)(OCH2CHMe2)(SCH2CH2N(Et)2)]. Our calculations involved geometry optimizations of the neutral VX-Me model as well as complexes with H+, Li+, Na+, K+, Be2+, Mg2+, and Ca2+ that yielded 2-8 different stable chelation modes for each ion that involved mainly mono- and bidentate binding. Importantly, our studies revealed that the [O(P),N] bidentate binding mode, long thought to be the active mode in differentiating the hydrolytic path of VX from other nerve agents, was the most stable for all ions studied here. Binding energy depended mainly on ionic size as well as charge, with binding energies ranging from 364 kcal mol(-1) for Be2+ to 33 kcal mol(-1) for K+. Furthermore, calculated NMR shifts for VX-Me correlate to experimental values of VX.     

D－葡萄糖、D－果糖与Ca~（2＋）、Mg~（2＋）、Cu~（2＋）、Zn~（2＋）、Cd~（2＋）反应的热力学函数

Ｄ－葡萄糖、Ｄ－果糖与Ｃａ~（２＋）、Ｍｇ~（２＋）、Ｃｕ~（２＋）、Ｚｎ~（２＋）、Ｃｄ~（２＋）反应的热力学函数张保林（南京大学配位化学研究所，配位化学国家重点实验室，南京，２１０００８）王文清，陶祖贻（北京大学技术物理系，北京）（兰州大学现代物理系?..     

Fluorescence sensing and binding behavior of aminobenzenesulfonamidoquinolino-beta-cyclodextrin to Zn2+

A water-soluble fluorescent zinc sensor which binds strongly to Zn2+ (log K = 12.4) was successfully synthesized under physiological conditions. This sensor exhibits a good fluorescence response to Zn2+ over a wide pH range in water. Under the same conditions, several metal ions commonly present in a physiological environment, such as Na+, K+, Ca2+, Mg2+, Mn2+, Fe2+, and Co2+, showed little interference to the fluorescence response to Zn2+. [structure: see text]     

香豆素/Betti碱主体合成及其对铷、钡离子的选择性响应(英文)

合成了一个新型香豆素/Betti碱主体化合物1,并对其进行了结构表征。在乙腈/水溶液中进行主体1和碱金属、碱土金属相关离子(Li+,Na+,K+,Rb+,Cs+,Be2+,Mg2+,Ca2+,Sr2+,Ba2+)的相互作用研究时,发现仅Rb+,Ba2+离子对主体1有敏感的紫外光谱及荧光光谱响应,而其它的碱金属、碱土金属离子无敏感性光响应。紫外光谱显示,Rb+,Ba2+离子使主体1产生明显的红移(ε=4.66×102L·(mol·cm)-1,Δ=91nm),肉眼可观察到明显的由浅黄向橙红色的颜色变化,并使主体1的荧光光谱发生一定程度的猝灭。     

毛细管区带电泳分析水中阳离子

选用一种新的缓冲液体系，采用毛细管区带电泳法，同时分离水中铵奶离子及碱金属、碱土金属和过渡金属等１２种分属不同类型的阳离子，并对电泳分离用金属阳离子弱络合剂、电解质ＰＨ值作了研究。方法用于环境水样分析，获得了满意效果。     

The energetics of shooting ions into the dodecahedrane cage

The activation barriers and energy profiles along the inclusion coordinate for the penetration of H+, He, Li+, Be+, Be2+, and Mg2+ into dodecahedrane 1 vary considerably with the nature of the projectile. Using Hartree-Fock and MP2 derived structures and energies, the overall process of creating endohedral X n+@1 complexes is examined in detail.     

Theoretical Studies on the Interactions of Cations with Diazine

1 INTRODUCTION Interaction between cations and π electron systems is a kind of common and important non-covalent inter- action[1～21]. It could be observed in many systems, such as gas ion-molecule complexes and biological macromolecular proteins. Especially, in biological macromolecular systems, this interaction is signi- ficant for revealing the structures and functions of proteins or disclosing the atomic essence of protein- ligand effect. Interaction between benzene and metal ions h…     

Principal component analysis of the absorption and resonance Raman spectra of the metallochromic indicator antipyrylazo III

Metallochromic indicators, whose spectral properties are changed in the presence of metal cations, are used mainly in biological studies to monitor Ca2+ and Mg2+ ions. Antipyrylazo III is such indicator, employed for mid-range Ca2+ concentrations (10-1000 microM). The stoichiometry of the interactions of antipyrylazo III with Ca2+, Mg2+, Ba2+, Sr2+ and Zn2+ ions and the relevant binding constants were studied by principal component analysis (PCA) of the absorption spectral changes. The resonance Raman spectra of the above systems were measured as well, and the resolved Raman spectra of the various species were calculated and assigned. The vibrational spectra are more featured, more characteristic of the binding ions and exhibit stronger relative spectral changes upon binding the cations. The basis sets of Raman spectra could thus be used as an analytical tool for these divalent metallic cations.     

内含式复合物X@(HAlNH)12 (X=Be,Mg, Ca,Zn, Al+, Ga+)的结构和稳定性

在研究闭式多面体(HAlNH)12簇合物几何构型及稳定性的基础上, 用DFT的B3LYP方法在6-31G(d)的水平上, 对其内含式复合物X@(HAlNH)12 (X= Be, Mg, Ca, Zn, Al+, Ga+)进行了构型优化和能量计算, 并讨论了稳定结构的几何构型、自然键轨道(NBO)、振动频率、能量参数及NMR数据与结构的关系. 用Gaussian 03的QST3方法确定了客体X通过笼面6-元环的迁移过渡态(TS)结构, 并用IRC方法对所得TS结构进行了验证. 最后得到内含式复合物X@(HAlNH)12结构在热力学和动力学上的稳定性信息, 其中复合物Ga+@(HAlNH)12的结构相对最稳定.     

Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.     

碱(土)金属离子与2-(3′-羟基-2′-吡啶基)苯并噁唑阳离子-π复合物及其分子内质子转移过程的理论研究

采用密度泛函B3LYP方法,在6-311++G(d,p)基组水平上对碱(土)金属离子(Li+,Na+,K+,Be2+,Mg2+和Ca2+)与2-(3’-羟基-2’-吡啶基)苯并噁唑(HPyBO)的36种阳离子-π复合物的初始构型进行了几何全优化,并计算了其相互作用能.结果表明,碱(土)金属离子与HPyBO复合物有较强的阳离子-π相互作用,部分复合物甚至达到了化学键的强度.相对能量的变化表明碱(土)金属离子的作用能改变HPyBO分子内质子转移过程的能垒,甚至可以导致优势构型反转.当考虑水的溶剂效应后,各质子转移异构体的相对能量及质子转移的能垒均有一定程度的改变.另外,应用分子中的原子(AIM)方法对复合物分子内氢键的键临界点性质进行了分析.     

An application of electrospray ionization tandem mass spectrometry to probe the interaction of Ca2+/Mg2+/Zn2+ and Cl- with gramicidin A

The peptide, gramicidin A (GrA), has been demonstrated to interact with divalent salts (CaCl2, MgCl2, and ZnCl2) using electrospray ionization mass spectrometry (ESI-MS). The ESI-MS analysis revealed different complexes formed due to the interaction of Val-GrA and Ile-GrA with divalent salts: [Val or Ile-GrA-H+M]+, [Val or Ile-GrA+MCl]+ and [Val or Ile-GrA+M]2+, where M is Ca or Mg or Zn. All these complexes have been subjected to collisionally activated dissociation (CAD). CAD of singly and doubly charged GrA and metal complexes exhibited the losses of water molecules, indicating the ligand preference of GrA. MS/MS and MS3 of [Val or Ile-GrA+MCl]+ resulted in the elimination of chloride ion and water, respectively. The tandem mass spectrometry data of the complex [Val-GrA+MCl]+ suggest that chloride interaction is stronger in the presence of Ca than of Mg and Zn. This study reveals that GrA could interact with Ca, Mg, and Zn in metal ion form as well as in ion pair (MCl) form. The interactions of GrA with Ca support the proposal of a physical basis for the messenger role of Ca (Urry et al., J. Biol. Chem. 1982, 257: 6659-6661).