An NMR Method To Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins

Targeting protein surfaces involved in protein–protein interactions by using supramolecular chemistry is a rapidly growing field. NMR spectroscopy is the method of choice to map ligand‐binding sites with single‐residue resolution by amide chemical shift perturbation and line broadening. However, large aromatic ligands affect NMR signals over a greater distance, and the binding site cannot be determined unambiguously by relying on backbone signals only. We herein employed Lys‐ and Arg‐specific H2(C)N NMR experiments to directly observe the side‐chain atoms in close contact with the ligand, for which the largest changes in the NMR signals are expected. The binding of Lys‐ and Arg‐specific supramolecular tweezers and a calixarene to two model proteins was studied. The H2(C)N spectra track the terminal CH₂ groups of all Lys and Arg residues, revealing significant differences in their binding kinetics and chemical shift perturbation, and can be used to clearly pinpoint the order of ligand binding.     

酒石酸脱除单铽转铁蛋白中铽（III）的荧光动力学研究

0.01 mol/L Hepes, pH7.4,室温条件下,以酒石酸为脱除剂,监测铽（III） 与脱铁蛋白结合的两种配合物C端单铽转铁蛋白和N端单铽转铁蛋白随酒石酸浓度变 化的脱除动力学,根据其动力学行为,我们推测存在两种平行的脱除途径：一次途 径和饱和途径,其中C端单铽转铁蛋白的铽（III）脱除呈现饱和与一次相结合途径 ,N端单铽转铁蛋白为简单的一次途径。NaCl的加入可促进两种单铽（III）的脱除 ,且C端铽转铁蛋白较N端单铽转铁蛋白更易受NaCl的影响。     

Unraveling Complex Small‐Molecule Binding Mechanisms by Using Simple NMR Spectroscopy

Heteronuclear NMR spectroscopy provides a unique way to obtain site‐specific information about protein–ligand interactions. Usually, such studies rely on the availability of isotopically labeled proteins, thereby allowing both editing of the spectra and ligand signals to be filtered out. Herein, we report that the use of the methyl SOFAST correlation experiment enables the determination of site‐specific equilibrium binding constants by using unlabeled proteins. By using the binding of L ‐ and D ‐tryptophan to serum albumin as a test case, we determined very accurate dissociation constants for both the high‐ and low‐affinity sites present at the protein surface. The values of site‐specific dissociation constants were closer to those obtained by isothermal titration calorimetry than those obtained from ligand‐observed methods, such as saturation transfer difference. The possibility of measuring ligand binding to serum albumin at physiological concentrations with unlabeled proteins may open up new perspectives in the field of drug discovery.     

铕(III)离子与人血清脱铁转铁蛋白结合的紫外差光谱研究

在pH7.4,温度为25℃的条件下,用紫外吸收差光谱进行了Eu^3^+对人血清脱铁转铁蛋白的滴定。结果表明Eu^3^+与人血清脱铁转铁蛋白结合后其差光谱在245nm和296nm处出现吸收峰,在245nm处,Eu^3^+-脱铁转铁蛋白配合物的摩尔吸光系数是(2.2±0.1)×10^4cm^-^1.mol^-^1.dm^3,Eu^3^+可占据脱铁转铁蛋白的2个金属离子结合部位,Eu^3^+优先占据脱铁转铁蛋白的C端结合部位,条件平衡常数是logK~C=8.42±0.12,logK~N=6.03±0.42。Eu^3^+与R~E^3^+(R~E=Nd,Sm,Gd和Tb)间的线性自由能关系表明,稀土离子占据脱铁转铁蛋白的C端结合部位时受离子大小的影响。     

Kinetics of Acid‐Catalyzed Dissociation of Nickel (II) N‐Alkyl‐Substituted Diamino Diamide Complexes

The dissociation kinetics of the nickel (II) complexes of 4‐methyl‐4,7‐diazadecanediamide (4‐Me‐L‐2,2,2), 4,7‐dimethyl‐4,7‐diazadecanediamide (4,7‐N, N′‐Me2‐L‐2,2,2), 4‐ethyl‐4,7‐diazadecanediamide (4‐Et‐ L‐2,2,2), and 4‐methyl‐4,8‐diazaundecanediamide (4‐Me‐L‐2,3,2) have been studied at 25.0 °C and μ = 4.0 M (NaClO₄ + HClO₄) by the stopped‐flow method. These reactions are specific‐acid catalyzed; however, the rate constants of these reactions do not depend on the concentrations of acetic, chloro acetic, and dichloroacetic acids. At pH values be low 1.0, both the proton‐assisted and the direct protonation path ways make contributions to the rates. The ratios of the rate constant of dissociation by the direct protonation path way to the rate constant by the proton‐assisted path way for the complexes in aqueous solution were measured and discussed.     

Reactivity comparison of five‐ and six‐membered cyclic carbonates with amines: Basic evaluation for synthesis of poly(hydroxyurethane)

The reaction of six‐ and five‐membered cyclic carbonates, 5‐(2‐propenyl)‐1,3‐dioxan‐2‐one ( 1 ) and 4‐(3‐butenyl)‐1,3‐dioxolan‐2‐one ( 2 ) with hexylamine and benzylamine was carried out in N,N‐dimethylacetamide at 30, 50, and 70 °C. The six‐membered cyclic carbonate 1 proceeded quantitatively with hexylamine at 30 °C for 24 h, while the five‐membered cyclic carbonate 2 converted in 34%. The reaction rate constants at 50 °C are evaluated as follows; 1.42 L/mol · h ( 1 with hexylamine) > 0.29 L/mol · h ( 1 with benzylamine) > 0.04 L/mol · h ( 2 with hexylamine) > 0.01 L/mol · h ( 2 with benzylamine). The activation energies in the reactions of 1 and 2 with hexylamine were estimated to be 10.1 and 24.6 kJ/mol, respectively. The ring‐strain energy was calculated by the semi‐empirical method using the PM3 Hamiltonian. The ring‐strain energy of the six‐membered cyclic carbonate was 2.86 kcal/mol larger than that of five‐membered one. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 162–168, 2001     

脱铁伴清蛋白两结合位点不同酪氨酸氢键的特性

The interaction of gallium（Ⅲ） with the ligands containing phenolic group（s）, such as salicylic acid, 8-hydroxyquinoline, N,N＇-bis（2-hydroxybenzyl）ethylenediamine-N,N＇diacetic acid （HBED）, N,N＇-ethylenebis[2-（o- hydroxyphenyl）glycine （EHPG）, and ovotransferrin, was studied, respectively, by means of fluorescence in 0.01 mol/L Hepes at pH 7.4 and room temperature. Fluorescence intensity showed an increase when gallium（Ⅲ） was bound to 8-hydroxyquinoline and HBED. In contrast, it was decreased with the interaction of gallium（Ⅲ） with salicylic acid and EHPG. At pH 7.4, there was N…H-O type intramolecular hydrogen bond in the former, and the latter existed O…H-O type intramolecular hydrogen bond. Fluorescence titration of apoovotransferrin with gallium（Ⅲ） displayed that the fluorescence intensity was decreased at the N-terminal binding site, while enhanced at the C-terminal binding site. It can account for the O…H-O type intramolecular hydrogen bonds for the phenolic groups of Tyr92 and Tyr191 residues at the N-terminal binding site. And there are N…H-O type intramolecular hydrogen bonds for Tyr431 and Tyr524 residues at the C-terminal binding site. In addition, under the same conditions, the conditional binding constant of gallium（Ⅲ） with EHPG or HBED determined by fluorescence method is lg KGa-EHPG=19.18 or lg KGa-HBED= 19.08.     

Effect of ligand structure on the pathways for iron release from human serum transferrin

Rate constants for the removal of iron from N-terminal monoferric transferrin have been measured for a series of phosphate and phosphonocarboxylic acids in pH 7.4 0.1 M hepes buffer at 25 degrees C. The bidentate ligands pyrophosphate and phosphonoacetic acid (PAA) show a combination of saturation and first-order kinetics with respect to the ligand concentration. Similar results are observed following a single substitution at the 2-position of PAA to give 2-benzyl-PAA and phosphonosuccinic acid. In contrast, disubstitution at the 2-position to form 2,2-dibenzyl-PAA leads to a marked reduction in iron removal via the first-order pathway. Rate constants were also measured for tripolyphosphate and phosphonodiacetic acid, which are elongated versions of PP(i) and PAA. In both cases, this elongation completely eliminates the first-order component for iron release while having relatively little impact on the saturation pathway. The sensitivity of the first-order component to the structure of the ligand strongly indicates that this pathway involves the binding of the ligand to a specific site on the protein and cannot be attributed to changes in the overall ionic strength of the solution as the ligand concentration increases. It is proposed that this structural sensitivity reflects steric restrictions on the ability of the incoming ligand to substitute for the synergistic carbonate anion to form a relatively unstable Fe-ligand-Tf ternary intermediate, which then dissociates to FeL and apoTf.     

Complexation Kinetics of N‐Alkyl‐Substituted Diamino Diamides with Nickel (II) in Aqueous Solution

Equilibrium constants are deter mined for the protonation and metal complexation of the nickel(II) complexes with 4‐methyl‐4,7‐diazadecanediamide (4‐Me‐L‐2,2,2), 4,7‐dimethyl‐4,7‐diazadecanediamide (4,7‐N,N′‐Me₂‐L‐2,2,2), 4‐ethyl‐4,7‐diazadecanediamide (4‐Et‐L‐2,2,2), and 4‐methyl‐4,8‐ diazaundecane diamide (4‐Me‐L‐2,3,2), in 0.10 M KCl at 25.0°C. The formation kinetics of these nickel (II) complexes have been studied under the same conditions with use of the stopped‐flow technique. The possible path ways for the complexation reaction of nickel (II) with these ligands are discussed. The first metal‐nitrogen bond formation is proposed as the rate‐determining step for the reactions of nickel (II) with the unprotonated ligands; proton loss is the rate‐limiting step in the reactions of nickel (II) with the monoprotonated ligands. Similarly, in dissociation reactions of these nickel (II) complexes, the rate‐determining step for the water dissociation pathway is the break age of the second nickel‐nitrogen bond; the rate‐determining step for the proton‐assisted path way is the protonation of the released amino group. The important factors determining the reactivity of these complexes are considered. The kinetic results of the formation and dissociation reactions of these complexes are consistent with dissociative mechanism.     

The Ortho Effect on the Acidic and Alkaline Hydrolysis of Substituted Formanilides

The kinetics of formanilides hydrolysis were determined under first‐order conditions in hydrochloric acid (0.01–8 M, 20–60°C) and in hydroxide solutions (0.01–3 M, 25 and 40°C). Under acidic conditions, second‐order specific acid catalytic constants were used to construct Hammett plots. The ortho effect was analyzed using the Fujita–Nishioka method. In alkaline solutions, hydrolysis displayed both first‐ and second‐order dependence in the hydroxide concentration. The specific base catalytic constants were used to construct Hammett plots. Ortho effects were evaluated for the first‐order dependence on the hydroxide concentration. Formanilide hydrolyzes in acidic solutions by specific acid catalysis, and the kinetic study results were consistent with the A_AC2 mechanism. Ortho substitution led to a decrease in the rates of reaction due to steric inhibition of resonance, retardation due to steric bulk, and through space interactions. The primary hydrolytic pathway in alkaline solutions was consistent with a modified B_AC2 mechanism. The Hammett plots for hydrolysis of meta‐ and para‐substituted formanilides in 0.10 M sodium hydroxide solutions did not show substituent effects; however, ortho substitution led to a decrease in rate constants proportional to the steric bulk of the substituent.     

氯化铝中萃取铁工艺

采用萃取剂N,N,N',N'-四丁基丙二酰胺(TBMA) 、N,N,N',N'-四辛基-3-氧戊二酰胺(TODGA)和甲基异丁基甲酮(MIBK)从氯化铝水溶液中萃取铁,以制备高纯氯化铝。 研究结果表明,当氯化铝溶液中盐酸浓度在4 mol/L左右时,TBMA和MIBK的萃取率在90%以上。 TODGA显示出优异的萃取分离性能。 当氯化铝溶液中Al³⁺浓度为2.0 mol/L,Fe³⁺浓度为0.0036 mol/L(0.2 g/L),HCl浓度为1.2 mol/L时,0.20 mol/L TODGA的环己烷或环己烷有机相对铁的一次萃取率达到99.9%以上,多次萃取后溶液中的铁含量低于0.01 mg/L,能深度去除氯化铝中的铁杂质,在工业化生产中有极大的应用价值。     

Heterogeneous catalysis by new bead‐shaped polymer‐supported multisite phase transfer catalysts

Three different new insoluble bead‐shaped polymer‐supported multisite phase transfer catalysts containing two, four and six active sites have been prepared and characterized by FTIR, TGA, [chloride ion] and SEM analyses. The presence of number of active sites in each catalyst and their corresponding catalytic ability were studied by determining pseudo‐first order rate constants for C‐alkylation of phenylacetonitrile (PAN) and four different substituted PAN as the substrate using a low concentration of NaOH (25% w/w) at 50 °C. The observed rate constants were compared with rate constants of same reactions catalyzed by single‐site catalyst under identical reaction conditions. From comparative study, the efficiency of catalysts were found to be in the order six‐site>four‐site>two‐site>single‐site thus confirming number of active sites in each catalyst. Further, the detailed kinetic profile of C‐alkylation of PAN has been investigated using the superior six‐site catalyst by varying stirring speed, [substrate], [catalyst], [NaOH], and temperature. Based on the observed kinetic and activation parameters, an interfacial mechanism was proposed. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 771–785, 2009     

Characterization of acrylonitrile polymerization by dilatometry and modeling

Solution polymerization of acrylonitrile was investigated in N,N′‐dimethylformamide with various azo‐ and peroxo‐initiators. Investigations were carried out in a concentration range of initiatior from 0.0016 mol/l up to 0.0160 mol/l, constant acrylonitrile concentration of 3.8 mol/l and temperatures from 40°C up to 70°C. The computer combined dilatometric equipment for long time and high conversion investigations was used for estimation of the conversion‐time‐reaction. By means of obtained data a mathematical model was created. The model describes sufficiently precise acrylonitrile polymerization kinetics in N,N′‐dimethylformamide with various initiators in the used range of concentrations and temperatures.     

Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin‐Binding Hemagglutinin

Heparin‐binding hemagglutinin (HBHA) is a 199 amino acid virulence factor at the envelope of Mycobacterium tuberculosis that contributes to latent tuberculosis. The binding of HBHA to respiratory epithelial cells, which leads to extrapulmonary dissemination of the pathogen, is mediated by cell‐surface heparan sulfate (HS). We report the structural characterization of the HBHA/HS complex by NMR spectroscopy. To develop a model for the molecular recognition, the first chemically synthesized uniformly ¹³C‐ and ¹⁵N‐labeled HS octasaccharide and a uniformly ¹³C‐ and ¹⁵N‐labeled form of HBHA were prepared. Residues 180–195 at the C‐terminal region of HBHA show large chemical shift perturbation upon association with the octasaccharide. Molecular dynamics simulations conforming to the multidimensional NMR data revealed key electrostatic and even hydrophobic interactions between the binding partners that may aid in the development of agents targeting the binding event.     

Zero‐Valent Aluminum as Reducer in Sodium Carbonate Solution for Degradation of Imidacloprid

Imidacloprid (IMI ) was reduced by zero‐valent aluminum (ZVAl ) in sodium carbonate solution and tested by high‐performance liquid chromatography (HPLC ). The IMI degradation rate was heavily dependent on Na₂CO₃ concentration and reaction time but only slightly on temperature, reaching 99.4% in 0.5 mol/L Na₂CO₃ solution with 5 g/L ZVAl in 60 min. The degradation of IMI follows first‐order kinetics. We used high‐performance liquid chromatography‐mass spectrometry (HPLC‐MS ) for analyzing the transformation products, and found that IMI disintegrated into IMI urea, IMI guanidine, IMI nitrosamine, and 1‐choloro‐5‐methcyclohea‐1,4‐diene.     

Kinetics of base hydrolysis of novel low spin Fe(II) amino acid Schiff base chelates—hydrophobic structural effects

The reactivity against OH^? ion of some novel Fe(II) complexes of Schiff base ligands derived from salicylaldehyde or o‐hydroxynaphth‐aldehyde and some variety of amino acids has been examined in aqueous and aqua‐ethanol mixtures. The rate law and relevant mechanism were assumed. Base hydrolysis kinetics measurements revealed pseudo‐first‐order doubly stage rates because of the presence of mer‐ and fac‐isomers. The evaluated rate constants and activation parameters are consistent with the stability constants of the investigated complexes. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 595–602, 2002     

Kinetics and mechanism of a catalytic chloride ion effect on the dissociation of model siderophore hydroxamate-iron(III) complexes

Proton-driven ligand dissociation kinetics in the presence of chloride, bromide, and nitrate ions have been investigated for model siderophore complexes of Fe(III) with the mono- and dihydroxamic acid ligands R(1)C(=O)N(OH)R(2) (R(1) = CH(3), R(2) = H; R(1) = CH(3), R(2) = CH(3); R(1) = C(6)H(5), R(2) = H; R(1) = C(6)H(5), R(2) = C(6)H(5)) and CH(3)N(OH)C(=O)[CH(2)](n)C(=O)N(OH)CH(3) (H(2)L(n); n = 2, 4, 6). Significant rate acceleration in the presence of chloride ion is observed for ligand dissociation from the bis(hydroxamate)- and mono(hydroxamate)-bound complexes. Rate acceleration was also observed in the presence of bromide and nitrate ions but to a lesser extent. A mechanism for chloride ion catalysis of ligand dissociation is proposed which involves chloride ion dependent parallel paths with transient Cl(-) coordination to Fe(III). The labilizing effect of Cl(-) results in an increase in microscopic rate constants on the order of 10(2)-10(3). Second-order rate constants for the proton driven dissociation of dinuclear Fe(III) complexes formed with H(2)L(n)() were found to vary with Fe-Fe distance. An analysis of these data permits us to propose a reactive intermediate of the structure (H(2)O)(4)Fe(L(n)())Fe(HL(n))(Cl)(OH(2))(2+) for the chloride ion dependent ligand dissociation path. Environmental and biological implications of chloride ion enhancement of Fe(III)-ligand dissociation reactions are presented.     

Micellar and salt effects on the interaction of [Cu(II)‐Gly‐Gly]+ with ninhydrin

The effect of cationic micelles of cetyltrimethylammonium bromide (CTAB) on the kinetics of interaction of copper dipeptide complex [Cu(II)‐Gly‐Gly]⁺ with ninhydrin has been studied spectrophotometrically at 70°C and pH 5.0. The reaction follows first‐ and fractional‐order kinetics, respectively, in complex and ninhydrin. The reaction is catalyzed by CTAB micelles, and the maximum rate enhancement is about twofold. The results obtained in the micellar medium are treated quantitatively in terms of the kinetic pseudophase and Piszkiewicz models. The rate constants (k_obs or k_Ψ), micellar‐binding constants (k_S for [Cu(II)‐Gly‐Gly]⁺, k_N for ninhydrin), and index of cooperativity (n) have been evaluated. A mechanism is proposed in accordance with the experimental results. The influence of different inorganic (NaCl, NaBr, Na₂SO₄) and organic (NaBenz, NaSal) salts on the reaction rate has also been seen, and it is found that tightly bound/incorporated counterions are the most effective. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 556–564, 2007     

Spectroscopic analysis of the interaction between gallium(III) and apoovotransferrin

Ovotransferrin is a main member of transferrin family and has a dual role in both the transport of iron and antibacterial function. Gallium-67 is widely used as an imaging agent for tumors. It has been reported that Ga(3+) can bind to apoovotransferrin at two sites, one in the N-terminal lobe and another in the C-terminal lobe. However, several details of the interaction between Ga(3+) and apoOTf remain unclear. Here, we report detailed investigations into the interactions of Ga(3+) with apoovotransferrin at the molecular level. First, the characteristics of Ga(3+) binding to apoovotransferrin were analyzed using UV difference spectra. The results show that Ga(3+) prefers to bind to the N-terminal site rather than the C-terminal site under the experimental conditions. Effective stability constants of logK(N)=18.88+/-0.24 and logK(C)=17.65+/-0.12 were determined. Second, conformational changes in apoovotransferrin during Ga(3+) binding were studied using 2-p-toluidinylnaphthalene-6-sulfonate (TNS) as a fluorescence probe. Apoovotransferrin undergoes a large conformational change when Ga(3+) binds to the N-terminal site, and a smaller conformational change when the ion binds to the C-terminal site. UV difference spectra were also used to measure the rate at which EDTA removes Ga(3+) from ovotransferrin carrying one Ga(3+) at the N-terminal site. Ga(3+) removal from the N-terminal binding site follows simple saturation kinetics.     

Exploring Weak Ligand–Protein Interactions by Long‐Lived NMR States: Improved Contrast in Fragment‐Based Drug Screening

Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long‐lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure accurate dissociation constants of fragments that bind weakly to the ATP binding site of the N‐terminal ATPase domain of heat shock protein 90 (Hsp90), a therapeutic target for cancer treatment. The LLS approach allows one to characterize ligands with an exceptionally wide range of affinities, since it can be used for ligand concentrations [L] that are several orders of magnitude smaller than the dissociation constants K_D. This property makes the LLS method particularly attractive for the initial steps of fragment‐based drug screening, where small molecular fragments that bind weakly to a target protein must be identified, which is a difficult task for many other biophysical methods.