Free energy simulations of single and double ion occupancy in gramicidin A

Simultaneous occupancy of the two binding sites in gramicidin A by monovalent cations is a well known property of this channel, but the energetic feasibility of this process in molecular dynamics simulations has not been established so far. Here the authors study the energetics of single and double ion occupancy in gramicidin A by constructing the potential of mean force for single and pair of cations. As representatives of small and large ions, they consider both Na+ and K+ ions in the calculations. Binding constants of ions are estimated from the free energy profiles. Comparisons with the experimental results indicate 3-4 kT discrepancy in the binding energies. They also study the coordination of the ions in their respective binding sites and the dynamic behavior of the channel water during the double ion binding process.     

Stacking and not solely topology of T3 loops controls rigidity and ammonium ion movement within d(G4T3G4)2 G-quadruplex

A solution state NMR study has shown that d(G4T3G4) in the presence of (15)NH4(+) ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K(+) ions [Neidle et al. J. Am. Chem. Soc. 2006, 128, 5480]. In contrast, the presence of K(+) ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets and in this way stabilize a single structure in the presence of (15)NH4(+) ions. The use of heteronuclear NMR enabled us to localize three (15)NH4(+) ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no (15)NH4(+) ion movement within the G-quadruplex was detected at 25 degrees C. At 35 degrees C we were able to observe slow movement of (15)NH4(+) ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of (15)NH4(+) ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.     

金属硫蛋白MT-2a与Cd(Ⅱ)和Cu(Ⅰ)络合的电喷雾质谱表征

采用电喷雾质谱法(ESI-MS)研究金属硫蛋白(MT,存在α和β两种结构域)-2a与金属离子Cd和Cu的络合作用.MT-2a由反相色谱分离纯化制得,并以电喷雾质谱鉴别.通过ESI-MS考察MT-2a与不同量的Cd和Cu的络合,结果表明,Cd能够优先与MT的α结构域络合,形成M2+4S11结构,并且该络合过程存在着明显的协同效应;Cd与MT的β结构域的络合形式为M2+4S9,其呈现出明显的随机松散络合特性;Cu优先与MT的β结构域络合,其络合形式由Cu4逐渐过渡到更高结合态;在Cu含量较高的条件下,Cu与MT呈现出多种络合方式.     

Binding and chemical fractionation of heavy metals in typical peat matter

Laboratory batch studies were conducted to evaluate the binding capacity and the mobility of metal species bound to typical humus peat matter. The identification of phase composition of mineral fractions and functional groups in the organic matter was assessed. The results showed generally high, but different retention capacity and binding strength, suggesting distinct diversity in binding mechanisms, phases and chemical nature of binding sites, depending on the metal species and their input concentrations. In general, the binding capacity of peat for the metal ions studied follows the order: Cr(3+) > Cu(2+) > Zn(2+) > Cd(2+) and results in the decrease of pH in the same order, due to displacement of H(3)O(+) from the peat by metal ions. The highest metal enrichment occurs in fractions F1(EXC), F2(CARB), F4(MRO) and F5(OM) of different binding strength adequate to exchangeable, carbonatic, moderately reducible amorphous Fe-oxide and organic/ sulphidic fractions in soils and sediments. In relation to species distribution in peats, the prevailing part of Cr(3+) is strongly bound in oxidizable organic substrate, while Cu(2+) is highly enriched in the moderately reducible F4(MRO) and the most labile F2(EXC) fractions. Cd(2+) and Zn(2+) are predominantly bound in the labile F1(EXC) and F2(CARB) fractions. Diversity of the predominant binding phases for the studied metals suggests rather weak competition for binding sites between chromium and copper ions; the strongest competition between the sorbed metal ions is anticipated for F1(EXC) and F2(CARB) fractions.     

Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA

The binding sites and consecutive binding constants of alkali metal ions, (M⁺ = Na⁺, K⁺, Rb⁺, and Cs⁺), to thrombin-binding aptamer (TBA) DNA were studied by Fourier-transform ion cyclotron resonance spectrometry. TBA-metal complexes were produced by electrospray ionization (ESI) and the ions of interest were mass-selected for further characterization. The structural motif of TBA in an ESI solution was checked by circular dichroism. The metal-binding constants and sites were determined by the titration method and infrared multiphoton dissociation (IRMPD), respectively. The binding constant of potassium is 5–8 times greater than those of other alkali metal ions, and the potassium binding site is different from other metal binding sites. In the 1:1 TBA-metal complex, potassium is coordinated between the bottom G-quartet and two adjacent TT loops of TBA. In the 1:2 TBA—metal complex, the second potassium ion binds at the TGT loop of TBA, which is in line with the antiparallel G-quadruplex structure of TBA. On the other hand, other alkali metal ions bind at the lateral TGT loop in both 1:1 and 1:2 complexes, presumably due to the formation of ion-pair adducts. IRMPD studies of the binding sites in combination with measurements of the consecutive binding constants help elucidate the binding modes of alkali metal ions on DNA aptamer at the molecular level.     

Real-time NMR studies of electrochemical double-layer capacitors

(11)B NMR spectroscopy has been used to investigate the sorption of BF(4)(-) anions on a highly porous, high surface area carbon, and different binding sites have been identified. By implementing in situ NMR approaches, the migration of ions between the electrodes of the supercapacitors and changes in the nature of ion binding to the surface have been observed in real time.     

通过杯芳烃片段桥联合成杯[4]冠4齐聚物及其络合性能研究

通过杯芳烃片段桥联合成杯[4]冠4齐聚物,并通过两相萃取实验评估其络合性能。络合研究表明,酰胺型杯[4]冠4齐聚物（TCA[4]-III）对软金属银、铅离子和氨基酸具有选择性络合。其对色氨酸和组氨酸的萃取率分别高达87.9% 和 91.5%。     

Comparison of energy interaction parameters for the complexation of Pr(III) with glutathione reduced (GSH) in absence and presence of Zn(II) in aqueous and aquated organic solvents using 4f-4f transition spectra as PROBE

The coordination chemistry of glutathione reduced (GSH) is of great importance as it acts as excellent model system for the binding of metal ions. The GSH complexation with metal ions is involved in the toxicology of different metal ions. Its coordination behaviour for soft metal ions and hard metal ions is found different because of the structure of GSH and its different potential binding sites. In our work we have studied two chemically dissimilar metal ions viz. Pr(III), which prefer hard donor site like carboxylic groups and Zn(II) the soft metal ion which prefer peptide-NH and sulphydryl groups. The absorption difference and comparative absorption spectroscopy involving 4f-4f transitions of the heterobimetallic Complexation of GSH with Pr(III) and Zn(II) has been explored in aqueous and aquated organic solvents. The variation in the energy parameters like Slater-Condon (F(K)), Racah (E(K)) and Lande (xi(4f)), Nephelauxetic parameter (beta) and bonding parameter (b(1/2)) are computed to explain the nature of complexation.     

Characterization of Mercury – Humic Acids Interaction by Potentiometric Titration with a Modified Carbon Paste Mercury Sensor

Stability constant for mercury binding by commercial and natural humic acids (HA) were determined using a new potentiometric mercury(II) sensor based on dithiosalicylic acid modified carbon paste electrode. The sensor present a high selective and sensitive response to mercury(II) ions, and a low detection limit of 1.8×10^?8 M. The potentiometric titrations curves of humic acids against mercury(II) ions were modeled. For 1.00×10^?7 to 3.00×10^?4 M mercury(II) ion concentration levels the results are consistent with the presence of two different binding sites in the humic acid macromolecule. The strongest binding sites (log K₁ ranging from 10.1 to 6.8) are probably due to interaction with carboxylic acid and amine groups in the molecule, whereas weakest binding sites (log K₂ ranging from 8.8 to 4.5) can be associated to phenolic groups.     

尖吻蝮蛇毒抗凝血因子Ⅱ的稀土离子荧光探针研究

尖吻蝮蛇毒抗凝血因子(ACF)分子中有两个钙离子结合位点,钙离子对ACF的内源荧光有增强作用,稀土离子(Nd³⁺,Sm³⁺,Eu³⁺,Gd³⁺和Tb³⁺)能取代ACF分子中的钙离子,并对ACF的内源荧光有不同程度的猝灭作用,其中Tb³⁺接受ACF分子中Trp残基传递的能量后,特征荧光增强.稀土离子与ACF荧光滴定表明,ACF分子中有两个稀土离子结合位点,稀土离子和钙离子在ACF分子中两个结合部位是共同的竞争结合部位.ACF与不同稀土离子之间有相近的表观结合常数K₁或K₂.Tb³⁺与RE³⁺(RE=Nd,Sm,Eu或Gd)间线性自由能关系表明,稀土离子与ACF结合时,没有明显的空间效应.ACF分子中的两个结合位点在结构上都有较大的柔性,这种结构柔性为钙离子在ACF与活化凝血因子X的结合反应中起到的促进作用提供了结构基础.     

Structural and functional consequences of an amide-to-ester substitution in the selectivity filter of a potassium channel

The selectivity filter of K(+) channels comprises four contiguous ion binding sites, S1 through S4. Structural and functional data indicate that the filter contains on average two K(+) ions at any given time and that these ions reside primarily in two configurations, namely to sites S1 and S3 or to sites S2 and S4. Maximum ion flux through the channel is expected to occur when the energy difference between these two binding configurations is zero. In this study, we have used protein semisynthesis to selectively perturb site 1 within the filter of the KcsA channel through use of an amide-to-ester substitution. The modification alters K(+) conduction properties. The structure of the selectivity filter is largely unperturbed by the modification, despite the loss of an ordered water molecule normally located just behind the filter. Introduction of the ester moiety was found to alter the distribution of K(+), Rb(+,) and Cs(+) within the filter, with the most dramatic change found for Rb(+). The redistribution of ions is associated with the appearance of a partially hydrated ion just external to the filter, at a position where no ion is observed in the wild-type channel. The appearance of this new ion-binding site creates a change in the distance between a pair of K(+) ions some fraction of the time, apparently leading to a reduction in the ion conduction rate. Importantly, this finding suggests that the selectivity filter of a potassium channel is optimized both in terms of absolute ion occupancy and in terms of the separation in distance between the conducting ions.     

铝(Ⅲ)与脱铁伴清蛋白结合的紫外差光谱研究

在 pH7.4、 0.1mol· L~(－1)N-2-羟乙基哌嗪- N′-2-乙磺酸（ Hepes）及室温条件下,使用紫外吸收差光谱进行了铝(Ⅲ)对脱铁伴清蛋白的滴定。结果表明铝(Ⅲ)与脱铁伴清蛋白结合后其紫外差光谱在 238nm和 291nm处出现吸收峰。在 238nm处铝(Ⅲ)-脱铁伴清蛋白配合物的摩尔吸光系数是 (1.52± 0.04)× 10~4cm~(－1)· mol~(－1)· L。铝(Ⅲ)可占据脱铁伴清蛋白的两个金属离子结合部位,条件稳定常数是 lgK_N=11.21± 0.12,lgKC=9.53± 0.24。 N-端单铁伴清蛋白的紫外差光谱滴定表明,铝 ?优先占据脱铁伴清蛋白的 N端结合部位。     

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     

Molecular mechanisms of ion-specific effects on proteins

The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG)(120), were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN(-) and I(-) interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl(-) binds far more weakly to the amide nitrogen/α-carbon binding site, while SO(4)(2-) is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na(+) counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.     

Binding and chemical fractionation of heavy metals in typical peat matter

Laboratory batch studies were conducted to evaluate the binding capacity and the mobility of metal species bound to typical humus peat matter. The identification of phase composition of mineral fractions and functional groups in the organic matter was assessed. The results showed generally high, but different retention capacity and binding strength, suggesting distinct diversity in binding mechanisms, phases and chemical nature of binding sites, depending on the metal species and their input concentrations. In general, the binding capacity of peat for the metal ions studied follows the order: Cr³⁺ > Cu²⁺ > Zn²⁺ > Cd²⁺ and results in the decrease of pH in the same order, due to displacement of H₃O⁺ from the peat by metal ions. The highest metal enrichment occurs in fractions F1(EXC), F2(CARB), F4(MRO) and F5(OM) of different binding strength adequate to exchangeable, carbonatic, moderately reducible amorphous Fe-oxide and organic/ sulphidic fractions in soils and sediments. In relation to species distribution in peats, the prevailing part of Cr³⁺ is strongly bound in oxidizable organic substrate, while Cu²⁺ is highly enriched in the moderately reducible F4(MRO) and the most labile F2(EXC) fractions. Cd²⁺ and Zn²⁺ are predominantly bound in the labile F1(EXC) and F2(CARB) fractions. Diversity of the predominant binding phases for the studied metals suggests rather weak competition for binding sites between chromium and copper ions; the strongest competition between the sorbed metal ions is anticipated for F1(EXC) and F2(CARB) fractions.     

稀土离子(Ⅲ)与牛血清白蛋白结合作用的研究

模拟生理条件研究了稀土离子(Ⅲ)与牛血清白蛋白(BSA)的结合性质.荧光光谱结果表明,Tb与BSA形成1∶2配合物,表观络合常数lgK=7.93,并由pH电位法得出相近结果.用平衡透析法确定Pr与BSA结合的高亲合位点数为2,低亲合位点数大于6,两类条件结合常数lgK1=5.157,lgK2=3.435.由NMR法通过²³Na弛豫时间的改变可知稀土与BSA络合后蛋白质体积膨胀,活动性增加,相关时间τ_c减小.     

Importance of receptor flexibility in binding of cyclam compounds to the chemokine receptor CXCR4

We have elucidated the binding sites of four moncyclam and one bicyclam antagonist AMD3100, in the human chemokine receptor CXCR4. Using the predicted structural models of CXCR4, we have further predicted the binding sites of these cyclam compounds. We used the computational method LITiCon to map the differences in receptor structure stabilized by the mono and bicyclam compounds. Accounting for the receptor flexibility lead to a single binding mode for the cyclam compounds, that has not been possible previously using a single receptor structural model and fixed receptor docking algorithms. There are several notable differences in the receptor conformations stabilized by monocyclam antagonist compared to a bicylam antagonist. The loading of the Cu(2+) ions in the cyclam compounds, shrinks the size of the cyclam rings and the residue D262(6.58) plays an important role in bonding to the copper ion in the monocylam compounds while residue E288(7.39) is important for the bicyclam compound.     

Effects of Temperature and Common Ions on Binding of Puerarin to BSA

The effects of temperature and common ions on binding of puerarin to bovine serum albumin (BSA) are investigated. The binding constants (K _a) between puerarin and BSA are 1.13×10⁴ L⋅mol⁻¹ (20 °C) and 1.54×10⁴ L⋅mol⁻¹ (30 °C), and the number of binding sites (n) is (0.95±0.02). However, at a higher temperature (40 °C) the stability of the puerarin–BSA system decreases, which results in a lower binding constant (1.58×10³ L⋅mol⁻¹) and number of binding sites (n=0.73) of the puerarin–BSA system. However, the presence of Cu²⁺ and Fe³⁺ ions increases the binding constants and the number of binding sites in the puerarin–BSA complex.     

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.     

Anions bonded on the supramolecular hydrogel surface as the growth center of biominerals

In this work, a supramolecular hydrogel formed from N,N',N'-tris(3-pyridyl)-trimesic amide was reported to serve as the matrix for the growth of biominerals. The organic hydrogel scaffold contains nitrogen heterocyclic ring and amide groups that can bind anions of the mineral (specially here, carbonate ions and phosphate ions) through hydrogen bonding interactions and act as the biomineralization active sites for growing biominerals. Calcium carbonate nucleated on the site of the hydrogel fiber where carbonate ions bonded and left obvious hydrogel fiber prints on the obtained product. Calcium phosphate grew into curved platelike nanostructures along the hydrogel fibrous network. XRD pattern and FT-IR spectra confirmed the formation of minerals on the hydrogel. The results indicate that the hydrogen bonding interaction can provide strong enough binding force for the growth of the minerals on organic scaffolds. Our finding extends the organic scaffolds into biodegradable small molecule hydrogels and also extends the growth centers of the minerals from conventional carboxylate groups binding Ca(2+) to amide and pyridyl groups binding PO(4)(3-).