Nitrilotris(methylenephosphonates) in aqueous solution and solid state - dilatometric, potentiometric and NMR investigations

Dissociation and alkali complex formation equilibria of nitrilotris(methylenephosphonic acid) (NTMP, H₆L) have been studied by dilatometric, potentiometric and ³¹P NMR-controlled titrations. Dilatometry indicated the formation of alkali complexes ML (M=Li, Na, K, Rb, Cs) at high pH with a stability decreasing from Li to Cs. An efficient combination of potentiometric and NMR methods confirmed two types of alkali metal complexes MHL and ML. Stability constants for the equilibria following M⁺ + HL⁵⁻ ? MHL⁴⁻ and M⁺ + L⁶⁻ ? ML⁵⁻, respectively, were determined: logK_NaHL=1.08(0.07), logK_KHL=0.86(0.08), logK_NaL=2.24(0.03). Systematic errors are introduced by using alkali metal hydroxides as titrants for routine potentiometric determinations of dissociation constants pK_a5^app and pK_a6^app. Correction formulae were derived to convert actual dissociation constants pK_a into apparent dissociation constants pK_a^app (or vice versa). The actual dissociation constants were found: pK_a5(H₂L⁴⁻ ? H⁺ + HL⁵⁻)=7.47(0.03) and pK_a6(HL⁵⁻ ? H⁺ + L⁶⁻)=14.1(0.1). The anisotropy of ³¹P chemical shifts of salts M_nH_6 − nL (M=Li, Na, n=0-5) is more sensitive towards titration (n) than isotropic solution state chemical shifts.     

Measuring Ca binding to short chain fatty acids and gluconate with a Ca electrode: Role of the reference electrode

Many organic anions bind free Ca²⁺, the total concentration of which must be adjusted in experimental solutions. Because published values for the apparent dissociation constant (K_app) describing the Ca²⁺ affinity of short chain fatty acids (SCFAs) and gluconate are highly variable, Ca²⁺ electrodes coupled to either a 3 M KCl or a Na⁺ selective electrode were used to redetermine K_app. All solutions contained 130 mM Na⁺, whereas the concentration of the studied anion was varied from 15 to 120 mM, replacing Cl⁻ that was decreased concomitantly to maintain osmolarity. This induces changes in the liquid junction potential (LJP) at the 3 M KCl reference electrode, leading to a systematic underestimation of K_app if left uncorrected. Because the Na⁺ concentration in all solutions was constant, a Na⁺ electrode was used to directly measure the changes in the LJP at the 3 M KCl reference, which were under 5 mV but twice those predicted by the Henderson equation. Determination of K_app either after correction for these LJP changes or via direct reference to a Na⁺ electrode showed that SCFAs do not bind Ca²⁺ and that the K_app for the binding of Ca²⁺ to gluconate at pH 7.4, ionic strength 0.15 M, and 23 °C was 52.7 mM.     

Kinetic study of dissociation of Eu(III) complex with H8dotp (H8dotp = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylphosphonic acid))

The dissociation kinetics of the europium(III) complex with H₈dotp ligand was studied by means of molecular absorption spectroscopy in UV region at ionic strength 3.0 mol dm⁻³ (Na,H)ClO₄ and in temperature region 25-60 °C. Time-resolved laser-induced fluorescence spectroscopy (TRLIFS) was employed in order to determine the number of water molecules in the first coordination sphere of the europium(III) reaction intermediates and the final products. This technique was also utilized to deduce the composition of reaction intermediates in course of dissociation reaction simultaneously with calculation of rate constants and it demonstrates the elucidation of intimate reaction mechanism. The thermodynamic parameters for the formation of kinetic intermediate (ΔH⁰ = 11 ± 3 kJ mol⁻¹, ΔS⁰ = 41 ± 11 J K⁻¹ mol⁻¹) and the activation parameters (E_a = 69 ± 8 kJ mol⁻¹, ΔH^≠ = 67 ± 8 kJ mol⁻¹, ΔS^≠ = −83 ± 24 J K⁻¹ mol⁻¹) for the rate-determining step describing the complex dissociation were determined. The mechanism of proton-assisted reaction was proposed on the basis of the experimental data.     

Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA

To characterize driving forces and driven processes in formation of a large-interface, wrapped protein-DNA complex analogous to the nucleosome, we have investigated the thermodynamics of binding the 34-base pair (bp) H′ DNA sequence to the Escherichia coli DNA-remodeling protein integration host factor (IHF). Isothermal titration calorimetry and fluorescence resonance energy transfer are applied to determine effects of salt concentration [KCl, KF, K glutamate (KGlu)] and of the excluded solute glycine betaine (GB) on the binding thermodynamics at 20 °C. Both the binding constant K_obs and enthalpy ΔH°_obs depend strongly on [salt] and anion identity. Formation of the wrapped complex is enthalpy driven, especially at low [salt] (e.g., ΔH^o_obs = − 20.2 kcal·mol^− 1 in 0.04 M KCl). ΔH°_obs increases linearly with [salt] with a slope (dΔH°_obs/d[salt]), which is much larger in KCl (38 ± 3 kcal·mol^− 1 M^− 1) than in KF or KGlu (11 ± 2 kcal·mol^− 1 M^− 1). At 0.33 M [salt], K_obs is approximately 30-fold larger in KGlu or KF than in KCl, and the [salt] derivative SK_obs = dlnK_obs/dln[salt] is almost twice as large in magnitude in KCl (− 8.8 ± 0.7) as in KF or KGlu (− 4.7 ± 0.6).A novel analysis of the large effects of anion identity on K_obs, SK_obs and on ΔH°_obs dissects coulombic, Hofmeister, and osmotic contributions to these quantities. This analysis attributes anion-specific differences in K_obs, SK_obs, and ΔH°_obs to (i) displacement of a large number of water molecules of hydration [estimated to be 1.0(± 0.2) × 10³] from the 5340 Å² of IHF and H′ DNA surface buried in complex formation, and (ii) significant local exclusion of F⁻ and Glu⁻ from this hydration water, relative to the situation with Cl⁻, which we propose is randomly distributed. To quantify net water release from anionic surface (22% of the surface buried in complexation, mostly from DNA phosphates), we determined the stabilizing effect of GB on K_obs: dlnK_obs/d[GB]  = 2.7 ± 0.4 at constant KCl activity, indicating the net release of ca. 150 H₂O molecules from anionic surface.     

Kinetic studies on the first dihydrogen aquacomplex, [Ru(H2)(H2O)5]: Formation under H2 pressure and catalytic H/D isotope exchange in water

The ruthenium(II) hexaaqua complex [Ru(H₂O)₆]²⁺ reacts with dihydrogen under pressure to give the η²-dihydrogen ruthenium(II) pentaaqua complex [Ru(H₂)(H₂O)₅]²⁺.The complex was characterized by ¹H, ²H and ¹⁷O NMR: δ_H = −7.65 ppm, J_HD = 31.2 Hz, δ_O = −80.4 ppm (trans to H₂) and δ_O = −177.4 ppm (cis to H₂).The H-H distance in coordinated dihydrogen was estimated to 0.889 Å from J_HD, which is close to the value obtained from DFT calculations (0.940 Å).Kinetic studies were performed by ¹H and ²H NMR as well as by UV-Vis spectroscopy, yielding the complex formation rate and equilibrium constants: k_f = (1.7 ± 0.2) × 10⁻³ kg mol⁻¹ s⁻¹ and K_eq = 4.0 ± 0.5 mol kg⁻¹.The complex formation rate with dihydrogen is close to values reported for other ligands and thus it is assumed that the reaction with dihydrogen follows the same mechanisn (I_d).In deuterated water, one can observe that [Ru(H₂)(H₂O)₅]²⁺ catalyses the hydrogen exchange between the solvent and the dissolved dihydrogen.A hydride is proposed as the intermediate for this exchange.Using isotope labeling, the rate constant for the hydrogen exchange on the η²-dihydrogen ligand was determined as k₁ = (0.24 ± 0.04) × 10⁻³ s⁻¹.The upper and lower limits of the pK_a of the coordinated dihydrogen ligand have been estimated:3 < pK_a < 14.     

The aluminium(III)-sialic acid interaction: A potential role in aluminium-induced cellular membrane degeneration

The coordination between Al(III) and sialic acid (N-acetylneuraminic acid, HL, pK_a = 2.58 ± 0.01) was studied by potentiometric titrations at 25 °C in aqueous 0.2 M KCl, by ¹H NMR, and by electrospray ionization mass spectrometry (ESI-MS). The potentiometric measurements gave the following aluminium complex stoichiometries and stability constants: , log β(AlLH₋₂) = −6.34 ± 0.02, and log β(AlL₂H₋₁) = −1.14 ± 0.04. The ¹H NMR spectra yielded structural information on species . The ESI-MS data confirmed the metal-ligand stoichiometry of the complexes.The metal-ligand speciation at micromolar Al(III) concentrations (i.e., under in vivo conditions) at physiological pH values reveals that considerable amount of Al(III) is complexed. This suggests that the toxic effect of Al(III) towards cellular membranes might be due to its coordination by protein-bound sialic acid.     

Oxidation of thiocyanate by iron(V) in alkaline medium

The oxidation of thiocyanate by iron(V) (Fe(V)) was studied as a function of pH in alkaline solutions by a premix pulse radiolysis technique. The rates decrease with an increase in pH. The rate law for the oxidation of SCN⁻ by Fe(V) was obtained as −d[Fe(V)]/dt = k₁₀{[H⁺]²/([H⁺]² + K₂[H⁺] + K₂K₃)}[Fe(V)][SCN⁻], where k₁₀ = 5.72 ± 0.19 × 10⁶ M⁻¹ s⁻¹, pK₂ = 7.2, and pK₃ = 10.1. The reaction precedes via a two-electron oxidation, which converts Fe(V) to Fe(III). Thiocyanate reacts approximately 10³× faster with iron(V) than does with iron(VI).     

UV-Vis and fluorimetric Al, Zn, Cd and Pb complexation studies of two 3-hydroxyflavones and a 3-hydroxythioflavone

The complexation of Al³⁺, Zn²⁺, Cd²⁺ and Pb²⁺ by the 3-hydroxyflavones: 3-hydroxy-2-(2-methoxyphenyl)-4H-1-benzopyran-4-one (H1) and 3-hydroxy-2-(4-methoxyphenyl)-4H-1-benzopyran-4-one (H2), and by the 3-methoxythioflavone: 3-hydroxy-2-(2-methoxyphenyl)-4H-1-benzopyran-4-thione (H3) have been studied spectrophotometrically and fluorimetrically to determine the corresponding complexation constants, K_sp and K_fl, in 5:95 water:ethanol (v/v) solution for which [HClO₄] was either 10⁻² or 10⁻⁵ mol dm⁻³ and I = 0.10 mol dm⁻³ (NaClO₄) at 298.2 K. Complexation occurs dominantly through the deprotonated ligand for [Al(1)]²⁺ and [Al(2)]²⁺ for which log K_sp = 4.51 and 4.73, respectively, in 10⁻² mol dm⁻³ HClO₄ and 4.21 and 4.61 in 10⁻⁵ mol dm⁻³ HClO₄. For Pb²⁺ complexation by H1, H2 and H3 is characterized by log K_sp = 2.20, 2.57 and 3.22, respectively, in 10⁻² mol dm⁻³ HClO₄ and 4.70, 5.38 and 5.74 in 10⁻⁵ mol dm⁻³ HClO₄. Equilibrium mixtures of [Pb(H1)]²⁺ and [Pb1]⁺, [Pb(H2)]²⁺ and [Pb2]⁺, and [Pb(H3)]²⁺ and [Pb3]⁺ appear to be formed. Complexation of Zn²⁺ and Cd²⁺ by all three ligands was only detected in 10⁻⁵ mol dm⁻³ HClO₄. For Zn²⁺ complexation by H1, H2 and H3 log K_sp = 3.22, 3.74 and 4.46 and for Cd²⁺ the corresponding values are 2.39, 2.40 and 3.72 for Cd²⁺. Only [Al1]²⁺ and [Al2]²⁺ show significant fluorescence and are characterized by log K_fl = 6.30 and 7.49 in 10⁻² mol dm⁻³ HClO₄.     

Kinetic study of base-catalyzed asymmetric nitrogen conversion of cis-folded macrocyclic nickel(II) complex of 1,4,7,11-tetraazacyclotetradecane

In order to examine the effects of coordinated hydroxide ion and free hydroxide ion in configurational conversion of a tetraamine macrocyclic ligand complex, the kinetic of the cis-to-planar interconversion of cis-[Ni(isocyclam)(H₂O)₂]²⁺ (isocyclam = 1,4,7,11-tetraazacyclotetradecane) has been examined spectrophotometrically. All kinetic data have been satisfactorily fitted by the rate law, R = (k₁K_OH[OH⁻]² + k₂[OH⁻])(1 + K_OH[OH⁻])⁻¹(cis-[Ni(isocyclam)(H₂O)₂]²⁺ + [Ni(isocyclam)(OH)]⁺), where k₂ = (3.40 ± 0.12) × 10³ dm³ mol⁻¹ s⁻¹ is almost equal to k_OH determined in buffer solution (lowly basic media), K_OH = 22.7 ± 1.4 dm³ mol⁻¹ at I (ionic strength) = 0.10 mol dm⁻³ (NaClO₄ + NaOH) and 25.0 °C. Rate constants, k₂ and K_OH, are functions of ionic strength, giving a good evidence for an intermolecular pathway. The reaction follows a free-base-catalyzed mechanism where nitrogen inversion, solvation and ring conformational changes are occurred.     

Interaction of dipeptydil peptidase IV with amyloid peptides

The aggregates of amyloid beta peptides (Aβs) are regarded as one of the main pathological hallmarks of Alzheimer’s disease (AD). An imbalance between the rates of synthesis and clearance of Aβs is considered to be a possible cause for the onset of AD. Dipeptidyl peptidases II and IV (DPPII and DPPIV) are serine proteases removing N-terminal dipeptides from polypeptides and proteins with proline or alanine on the penultimate position. Alanine is an N-terminal penultimate residue in Аβs, and we presumed that DPPII and DPPIV could cleave them. The results of present in vitro research demonstrate for the first time the ability of DPPIV to truncate the commercial Aβ40 and Aβ42 peptides, to hinder the fibril formation by them and to participate in the disaggregation of preformed fibrils of these peptides. The increase of absorbance at 334 nm due to complex formation between primary amines with o-phtalaldehyde was used to show cleaving of Aβ40 and Aβ42. The time-dependent increase of the quantity of primary amines during incubation of peptides in the presence of DPPIV suggested their truncation by DPPIV, but not by DPPII. The parameters of the enzymatic breakdown by DPPIV were determined for Aβ40 (K_m = 37.5 μM, k_cat/K_m = 1.7 × 10³ M⁻¹sec⁻¹) and Aβ42 (K_m = 138.4 μM, k_cat/K_m = 1.90 × 10² M⁻¹sec⁻¹). The aggregation-disaggregation of peptides was controlled by visualization on transmission electron microscope and by Thioflavin-T fluorescence on spectrofluorimeter and fluorescent microscope. DPPIV hindered the peptide aggregation/fibrillation during 3-4 days incubation in 20 mM phosphate buffer, pH 7.4, 37 °C by 50–80%. Ovalbumin, BSA and DPPII did not show this effect. In the presence of DPPIV, the preformed fibrils were disaggregated by 30–40%. Conclusion: for the first time it was shown that the Aβ40 and Aβ42 are substrates of DPPIV. DPPIV prohibits the fibrillation of peptides and promotes disaggregation of their preformed aggregates.     

Mixed-valency with cyanides as terminal ligands: Diruthenium(III,II) complexes with the 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine bridge and variable co-ligands (CN vs. bpy or NH3)

New diruthenium complexes (PPN)₄[(NC)₄Ru(μ-bptz)Ru(CN)₄], (PPN)₄1, and [(bpy)₂Ru(μ-bptz)Ru(CN)₄], 2, (PPN⁺ = bis(triphenylphospine)iminium; bptz = 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine; bpy = 2,2′-bipyridine), were synthesised and characterised by spectroscopic and electrochemical techniques. The comproportionation constant K_c = 10^7.0 of the mixed-valent species [(NC)₄Ru(μ-bptz)Ru(CN)₄]³⁻ as obtained by oxidation of 1⁴⁻ in CH₃CN is much lower than the K_c = 10^15.0 previously detected for [(H₃N)₄Ru(bptz)Ru(NH₃)₄]⁵⁺, reflecting the competition between CN⁻ and bptz for the π-electron density of the metals. Comparison with several other bptz-bridged diruthenium(II,III) complexes reveals an approximate correlation between K_c and the diminishing effective π acceptor capacity of the ancillary terminal ligands. In addition to the intense MLCT absorption at λ_max = 624 nm, the main IVCT (intervalence charge transfer) band of 1³⁻ was detected by spectroelectrochemistry at λ_max = 1695 nm (in CH₃CN; ε = 3200 M⁻¹ cm⁻¹). The experimental band width at half-height, Δν_1/2 = 2700 cm⁻¹, is slightly smaller than the theoretical value Δν_1/2 = 3660 cm⁻¹, calculated from the Hush approximation for Class II mixed-valent species. In agreement with comparatively moderate metal-metal coupling, the mixed-valent intermediate 1³⁻ was found to be EPR silent even at 4 K. The unsymmetrical mixed-valent complex [(bpy)₂Ru^II(μ-bptz)Ru^III(CN)₄]⁺, obtained in situ by bromine oxidation of 2 in CH₃CN/H₂O, displays a broad NIR absorption originating from an IVCT transition at λ_max = 1075 nm (ε ≈ 1000 M⁻¹ cm⁻¹, Δν_1/2 ≈ 4000 cm⁻¹). In addition, the lifetime of the excited-state of the mononuclear precursor complex [Ru(bptz)(CN)₄]²⁻ was measured in H₂O by laser flash photolysis; the obtained value of τ = 19.6 ns reveals that bptz induces a metal-to-ligand electronic delocalisation effect intermediate between that induced by bpy and bpz (bpz = 2,2′-bipyrazine) in analogous tetracyanoruthenium complexes.     

Mechanistic studies on monodentate-ligand substitution of five-coordinate trigonal-bipyramidal platinum (II) complexes with tris[2-(diphenylphosphino)ethyl]phosphine

Reaction of the five-coordinate trigonal-bipyramidal platinum(II) complex, [Pt(pt)(pp₃)](BF₄) (pt = 1-propanethiolate, pp₃ = tris[2-(diphenylphosphino)ethyl]phosphine), with I⁻ in chloroform gave the five-coordinate square-pyramidal complex with a dissociated terminal phosphino group and an apically coordinated iodide ion in equilibrium. The thermodynamic parameters for the equilibrium between the trigonal-bipyramidal and square-pyramidal geometries, [Pt(pt)(pp₃)]⁺ + I⁻ ? [PtI(pt) (pp₃)], and the kinetic parameters for the chemical exchange were obtained as follows: , ΔH⁰ = − 10 ± 2.4 kJ mol⁻¹, ΔS⁰ = − 36 ± 10 J K⁻¹ mol⁻¹, , ΔH^‡ = 34 ± 4.7 kJ mol⁻¹, ΔS^‡ = − 50 ± 21 J K⁻¹ mol⁻¹. The square-planar trinuclear platinum(II) complex was formed by bridging reaction of one of the terminal phosphino groups of trigonal-bipyramidal [PtCl(pp₃)]Cl with trans-[PtCl₂(NCC₆H₅)₂] in chloroform. From these facts, ligand substitution reactions of [PtX(pp₃)]⁺ (X = monodentate anion) are expected to proceed via an intermediate with a dissociated phosphino group. The rate constants for the chloro-ligand substitution reactions of [PtCl(pp₃)]⁺ with Br⁻ and I⁻ in chloroform approached the respective limiting values as concentrations of the entering halide ions are increased. These kinetic results confirmed the preassociation mechanism in which the square pyramidal intermediate with a dissociated phosphino group and an apically coordinated halide ion is present in the rapid pre-equilibrium.     

Complexation of curium(III) by adenosine 5′-triphosphate (ATP): A time-resolved laser-induced fluorescence spectroscopy (TRLFS) study

The complex formation of curium(III) with adenosine 5′-triphosphate (ATP) was determined by time-resolved laser-induced fluorescence spectroscopy (TRLFS). The interaction between soluble species of curium(III) with ATP was studied at trace Cm(III) concentrations (3 × 10⁻⁷ M). The concentrations of ATP were varied between 6.0 × 10⁻⁷ and 1.5 × 10⁻⁴ M in the pH range of 1.5-7.0 using 0.154 M NaCl as background electrolyte.Three Cm-ATP species, M_pH_qL_r, could be identified from the fluorescence emission spectra: (i) CmH₂ATP⁺ with a peak maximum at 598.6 nm, (ii) CmHATP with a peak maximum at 600.3 nm, and (iii) CmATP⁻ with a peak maximum at 601.0 nm. The formation constants of these complexes were calculated from TRLFS measurements to be log β₁₂₁ = 16.86 ± 0.09, log β₁₁₁ = 13.23 ± 0.10, and log β₁₀₁ = 8.19 ± 0.16. The hydrated Cm-ATP species showed fluorescence lifetimes between 88 and 96 μs; whereas the CmATP⁻ complex has a significantly longer fluorescence lifetime of 187 ± 7 μs.     

[H,N] NMR studies of the aquation of cis-diamine platinum(II) complexes

Two ¹⁵N-labelled cis-Pt(II) diamine complexes with dimethylamine (¹⁵N-dma) and isopropylamine (¹⁵N-ipa) ligands have been prepared and characterised. [¹H,¹⁵N] HSQC NMR spectroscopy is used to obtain the rate and equilibrium constants for the aquation of cis-[PtCl₂(¹⁵N-dma)₂] at 298 K in 0.1 M NaClO₄ and to determine the pK_a values of cis-[PtCl(H₂O)(¹⁵N-dma)₂]⁺ (6.37) and cis-[Pt(H₂O)₂(¹⁵N-dma)₂]²⁺ (pK_a1 = 5.17, pK_a2 = 6.47). The rate constants for the first and second aquation steps (k₁ = (2.12 ± 0.01) × 10⁻⁵ s⁻¹, k₂ = (8.7 ± 0.7) × 10⁻⁶ s⁻¹) and anation steps (k₋₁ = (6.7 ± 0.8) × 10⁻³ M⁻¹ s⁻¹, k₋₂ = 0.043 ± 0.004 M⁻¹ s⁻¹) are very similar to those reported for cisplatin under similar conditions, and a minor difference is that slow formation of the hydroxo-bridged dimer is observed. Aquation studies of cis-[PtCl₂(¹⁵N-ipa)₂] were precluded by the close proximity of the NH proton signal to the ¹H₂O resonance.     

Introducing transglycosylation activity in Bacillus licheniformis α-amylase by replacement of His235 with Glu

To understand the role of His and Glu in the catalytic activity of Bacillus licheniformis α-amylase (BLA), His235 was replaced with Glu. The mutant enzyme, H235E, was characterized in terms of its mode of action using labeled and unlabeled maltooctaose (Glc8). H235E predominantly produced maltotridecaose (Glc13) from Glc8, exhibiting high substrate transglycosylation activity, with K_m = 0.38 mM and k_cat/K_m = 20.58 mM⁻¹ s⁻¹ for hydrolysis, and K_m2 = 18.38 mM and k_cat2/K_m2 = 2.57 mM⁻¹ s⁻¹ for transglycosylation, while the wild-type BLA exhibited high hydrolysis activity exclusively. Glu235—located on a wide open groove near subsite +1—is likely involved in transglycosylation via formation of an α-1,4-glycosidic linkage and may recognize and stabilize the non-reducing end glucose of the acceptor molecule.     

Quantitative effects of allosteric ligands and mutations on conformational equilibria in Salmonella typhimurium tryptophan synthase

Allosteric communications are important in coordination of the reactions in the tryptophan (Trp) synthase α₂β₂ multienzyme complex. We have measured the conformational equilibria of l-Ser and l-Trp complexes, using absorption and fluorescence spectrophotometry with hydrostatic pressure equilibrium perturbation. The effects of monovalent cations, disodium α-glycerophosphate (Na₂GP), indoleacetylglycine (IAG), and benzimidazole (BZI), as well as of βE109D and βD305A mutations, on K_eq for the conformational equilibria were determined. The l-Ser external aldimine-aminoacrylate equilibrium (K_eq = [external aldimine]/[aminoacrylate]) has the largest value with Na⁺ (0.12), followed by K⁺ (0.04), Li⁺ (7.6 × 10⁻⁴), Rb⁺ (4.3 × 10⁻⁴), NH₄⁺ (2.3 × 10⁻⁴), no cation (2.0 × 10⁻⁴) and Cs⁺ (1.6 × 10⁻⁵). α-Site ligands, Na₂GP and IAG, have modest 3- to 40-fold effects on K_eq in the direction of aminoacrylate, but BZI in the presence of Na⁺ gives a low value of K_eq comparable to that obtained with Cs⁺. There is no additivity of free energy for Na₂GP and BZI, suggesting a common pathway for allosteric communications for both ligands. The values of ΔV_o range from −126 mL/mol for the Na⁺ complex to −204 mL/mol for the Na⁺ complex with BZI. The βD305A mutation changes the K_eq by a factor of at least 10⁵ (26.7 kJ/mol) and nearly abolishes allosteric communications. There are also dramatic decreases in the magnitude of both ΔV_o and ΔS for the l-Ser external aldimine-aminoacrylate equilibrium for βD305A Trp synthase, consistent with a large decrease in solvation accompanying the conformational change in βD305A Trp synthase relative to wild-type Trp synthase. The βE109D mutation has more modest but significant effects on K_eq, which differ with the ligand, ranging from 40-fold for GP to 2200-fold for BZI, even though βGlu-109 is not directly involved in allosteric communications. The effect of GP on the external aldimine-quinonoid intermediate equilibrium of the Trp synthase-l-Trp complex is similar to that of GP on the Trp synthase-l-Ser external aldimine-aminoacrylate equilibrium. These results have allowed a quantitative comparison of the allosteric effects of ligand and mutations in Trp synthase. These allosteric effects are finely tuned to control the synthesis of l-Trp without resulting in substrate or product inhibition.     

Kinetics of the cis-to-planar interconversion of cis-diaqua(1,4,7,11-tetraazacyclotetradecane)nickel(II) ion

In order to examine the effects of coordinated hydroxide ion and free hydroxide ion in configurational conversion of a tetraamine macrocyclic ligand complex, the kinetics of the cis-to-planar interconversion of cis-[Ni(isocyclam)(H₂O)₂]²⁺ (isocyclam, 1,4,7,11-tetraazacyclotetradecane) has been studied spectrophotometrically in basic aqueous solution. The interconversion requires the inversion of one sec-NH center of the folded cis-complex to have the planar species. Kinetic data are satisfactorily fitted by the rate law, R = k_OH[OH⁻][cis-[Ni(isocyclam)(H₂O)₂]²⁺], where k_OH = 3.84 × 10³ dm³ mol⁻¹ s⁻¹ at 25.0 ± 0.1 °C with I = 0.10 mol dm⁻³ (NaClO₄). The large ΔH^≠, 61.7 ± 3.2 kJ mol⁻¹, and the large positive ΔS^≠, 30.2 ± 10.8 J K⁻¹ mol⁻¹, strongly support a free-base-catalyzed mechanism for the reaction.     

Probing the interactions of hemoglobin with antioxidant flavonoids via fluorescence spectroscopy and molecular modeling studies

Steady state and time resolved fluorescence spectroscopy, combined with molecular modeling computations, have been used to explore the interactions of two therapeutically important flavonoids, fisetin (3,7,3′,4′-OH-flavone) and 3-hydroxyflavone (3-HF), with normal human hemoglobin (HbA). Distinctive ‘two color’ fluorescence signatures and fairly high fluorescence anisotropy (r = 0.12-0.28) of fisetin and 3-HF reveal their specific interactions with HbA. Binding constants estimated from the fluorescence studies were ≈ 4.00 × 10⁴ M^− 1 and 9.83 × 10³ M^− 1 for fisetin and 3-HF respectively. Specific interactions with HbA were further confirmed from flavonoid-induced static quenching of the protein tryptophan fluorescence as indicated by: (a) bimolecular quenching constant K_q ? diffusion controlled limit (b) closely matched values of Stern-Volmer quenching constant and binding constant (c) τ_o/τ ≈ 1 (where τ_o and τ are the unquenched and quenched tryptophan fluorescence lifetimes respectively). Molecular docking and electrostatic surface potential calculations reveal contrasting binding modes of fisetin and 3-HF with HbA.     

NMR for direct determination of Km and Vmax of enzyme reactions based on the Lambert W function-analysis of progress curves

¹H NMR spectroscopy was used to follow the cleavage of sucrose by invertase. The parameters of the enzyme's kinetics, K_m and V_max, were directly determined from progress curves at only one concentration of the substrate. For comparison with the classical Michaelis-Menten analysis, the reaction progress was also monitored at various initial concentrations of 3.5 to 41.8 mM. Using the Lambert W function the parameters K_m and V_max were fitted to obtain the experimental progress curve and resulted in K_m = 28 mM and V_max = 13 μM/s. The result is almost identical to an initial rate analysis that, however, costs much more time and experimental effort. The effect of product inhibition was also investigated. Furthermore, we analyzed a much more complex reaction, the conversion of farnesyl diphosphate into (+)-germacrene D by the enzyme germacrene D synthase, yielding K_m = 379 μM and k_cat = 0.04 s^− 1. The reaction involves an amphiphilic substrate forming micelles and a water insoluble product; using proper controls, the conversion can well be analyzed by the progress curve approach using the Lambert W function.     

Dissecting a bimolecular process of MgATP²- binding to the chaperonin GroEL

Although allosteric transitions of GroEL by MgATP²⁻ have been widely studied, the initial bimolecular step of MgATP²⁻ binding to GroEL remains unclear. Here, we studied the equilibrium and kinetics of MgATP²⁻ binding to a variant of GroEL, in which Tyr485 was replaced by tryptophan, via isothermal titration calorimetry (ITC) and stopped-flow fluorescence spectroscopy. In the absence of K⁺ at 4-5 °C, the allosteric transitions and the subsequent ATP hydrolysis by GroEL are halted, and hence, the stopped-flow fluorescence kinetics induced by rapid mixing of MgATP²⁻ and the GroEL variant solely reflected MgATP²⁻ binding, which was well represented by bimolecular noncooperative binding with a binding rate constant, k_on, of 9.14 × 10⁴ M^− 1 s^− 1 and a dissociation rate constant, k_off, of 14.2 s^− 1, yielding a binding constant, K_b (= k_on/k_off), of 6.4 × 10³ M^− 1. We also successfully performed ITC to measure binding isotherms of MgATP²⁻ to GroEL and obtained a K_b of 9.5 × 10³ M^− 1 and a binding stoichiometric number of 6.6. K_b was thus in good agreement with that obtained by stopped-flow fluorescence. In the presence of 10-50 mM KCl, the fluorescence kinetics consisted of three to four phases (the first fluorescence-increasing phase, followed by one or two exponential fluorescence-decreasing phases, and the final slow fluorescence-increasing phase), and comparison of the kinetics in the absence and presence of K⁺ clearly demonstrated that the first fluorescence-increasing phase corresponds to bimolecular MgATP²⁻ binding to GroEL. The temperature dependence of the kinetics indicated that MgATP²⁻ binding to GroEL was activation-controlled with an activation enthalpy as large as 14-16 kcal mol^− 1.