Probing the role of the divalent metal ion in uteroferrin using metal ion replacement and a comparison to isostructural biomimetics

Purple acid phosphatases (PAPs) are a group of heterovalent binuclear metalloenzymes that catalyze the hydrolysis of phosphomonoesters at acidic to neutral pH. While the metal ions are essential for catalysis, their precise roles are not fully understood. Here, the Fe(III)Ni(II) derivative of pig PAP (uteroferrin) was generated and its properties were compared with those of the native Fe(III)Fe(II) enzyme. The k _cat of the Fe(III)Ni(II) derivative (approximately 60 s⁻¹) is approximately 20% of that of native uteroferrin, and the Ni(II) uptake is considerably faster than the reconstitution of full enzymatic activity, suggesting a slow conformational change is required to attain optimal reactivity. An analysis of the pH dependence of the catalytic properties of Fe(III)Ni(II) uteroferrin indicates that the μ-hydroxide is the likely nucleophile. Thus, the Ni(II) derivative employs a mechanism similar to that proposed for the Ga(III)Zn(II) derivative of uteroferrin, but different from that of the native enzyme, which uses a terminal Fe(III)-bound nucleophile to initiate catalysis. Binuclear Fe(III)Ni(II) biomimetics with coordination environments similar to the coordination environment of uteroferrin were generated to provide both experimental benchmarks (structural and spectroscopic) and further insight into the catalytic mechanism of hydrolysis. The data are consistent with a reaction mechanism employing an Fe(III)-bound terminal hydroxide as a nucleophile, similar to that proposed for native uteroferrin and various related isostructural biomimetics. Thus, only in the uteroferrin-catalyzed reaction are the precise details of the catalytic mechanism sensitive to the metal ion composition, illustrating the significance of the dynamic ligand environment in the protein active site for the optimization of the catalytic efficiency. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Transition metal ion complexes with associates of porphyrin bound to a hydrophobic-hydrophilic copolymer.

The interaction of dimeric forms of meso-tetraphenylporphine with Mn2+ as well as the interaction of associated forms of meso-tetra(p-aminophenyl)porphine bound to a hydrophobic-hydrophilic copolymer with Mn2+ and Fe3+ were studied by absorption, luminescence, Raman, and EPR spectroscopies. Both dimeric and associated forms of these porphyrins produced Mn2+ complexes. Manganese ions in these complexes undergo clusterization, which is accompanied by transformation of the six-line EPR signal of Mn2+ into a broad single-line signal. The EPR signal of Mn2+ in these clusters is characterized by a g-factor value typical of a free electron with half-width DeltaHpp = 50 mT. The interaction of the two-component complex with Fe3+ produces a donor-acceptor complex. The electronic spectrum of the donor-acceptor complex contains a broad band with a maximum at 760 nm. The molar extinction coefficient of the complex at 760 nm is 9.1.104 M-1.cm-1, and the rate constant for its formation is Kdac = (3.9 +/- 0.6).106 M-1. The constants for Mn2+ binding to the organic compounds used in this work were also determined.     

Modified activity of Aeromonas aminopeptidase: metal ion substitutions and role of substrates

Aeromonas aminopeptidase contains two nonidentical metal binding sites that have been shown by both spectroscopy and kinetics to be capable of interacting with one another [Prescott, J.M., Wagner, F.W., Holmquist, B., & Vallee, B.L. (1985) Biochemistry 24, 5350-5356]. The effects of metal ion substitutions on the susceptibility of the p-nitroanilides of L-alanine, L-valine, and L-leucine--substrates that are hydrolyzed at widely differing rates by native Aeromonas aminopeptidase--were studied by determining values of kcat and Km for the 16 metalloenzymes that result from all possible combinations of Zn2+, Co2+, Ni2+, and Cu2+ in each of the two sites. The different combinations of metal ions and substrates yield a broad range in kinetic values; kcat varies by more than 1800-fold, Km by 3000-fold, and kcat/Km ratios by more than 10,000. L-Leucine-p-nitroanilide is by far the most susceptible of the three substrates, and the hyperactivation previously observed with aminopeptidase containing either Ni2+ or Cu2+ in the first binding site and Zn2+ in the second site occurs only with the two poorer substrates, L-alanine-p-nitroanilide and L-valine-p-nitroanilide. Although the enzyme with Zn2+ in both sites hydrolyzes the substrates with N-terminal alanine and valine poorly, it is extremely effective toward L-leucine-p-nitroanilide. Neither metal binding site can be identified as controlling either Km or kcat; both parameters are influenced by the identity of the metal ions, by the site each occupies, and, most strongly, by the substrate.(ABSTRACT TRUNCATED AT 250 WORDS)     

On the role of chirality in structure-odor relationships

The influence of chirality on odors was studied on 16 enantiomericpairs according to the dispersion/hydrogen bonding theory ofreceptor-odorant interaction. Comparisons of molecular structures were made by superimpositionof optimized conformations, using the Alchemy II package. Thequality of fit was assessed using the RMS parameter includedin Alchemy II and a new index for hydrogen bonding: the anglebetween H-bonds in the two molecules. In the case of camphoraceous odorants where an interaction modelwas already known superimposition according to the model ledto correct predictions of the high similarity of odors observedin enantiomeric pairs. For several urinous odorants comparisons were made using d-androstenoneas a reference compound for the urinous odor. Correct predictionswere obtained for l-androstenone, both enantiomers of androsta-4,16-dienone, and (+)-2-methyl-4-(5,5,6-exo-trimethy1-2-exonorbornyl)-cyclobexane.The (–) enantiomer of the latter compound was correctlypredicted only if it was assumed that its weak intensity isdue to a partial interaction with the hydrophobic zone of thereceptor. For ambergris odorants which have a complex odor (–)-Ambroxwas selected as the reference compound. The odors of (+)-Ambroxand enantiomers of four other compounds (ambergris or woody)were correctly predicted by superimposition. For nootkatone and three derivatives which have a grapefruitnote for one enantiomer and a woody note for the other no modelsor reference compounds were available. The superimpositionswere made between grapefruit enantiomers, on the one hand, andwoody enantiomers on the other hand. Woody and grapefruit characterswere correctly predicted in all cases. The limits of this approach based on molecular modelling arediscussed.     

Geometrical and algebraic approach to central molecular chirality: a chirality index and an Aufbau description of tetrahedral molecules

On the basis of empirical Fischer projections, we develop an algebraic approach to the central molecular chirality of tetrahedral molecules. The elements of such an algebra are obtained from the 24 projections which a single chiral tetrahedron can generate in S and R absolute configurations. They constitute a matrix representation of the O4 orthogonal group. According to this representation, given a molecule with n chiral centres, it is possible to define an "index of chirality chi identical with {n, p}", where n is the number of stereogenic centres of the molecule and p the number of permutations observed under rotations and superimpositions of the tetrahedral molecule to its mirror image. The chirality index not only assigns the global chirality of a given tetrahedral chain, but indicates also a way to predict the same property for new compounds, which can be built up consistently.     

Relative reactivity of hydroxyl groups in inositol derivatives: role of metal ion chelation

O-Alkylation of myo-inositol derivatives containing more than one hydroxyl group via their alkali metal alkoxides (sodium or lithium) preferentially occurs at a hydroxyl group having a vicinal cis-oxygen atom. In general the observed selectivity is relatively higher for lithium alkoxides than for the corresponding sodium alkoxide. The observed regioselectivity is also dependent on other factors such as the solvent and reaction temperature. A perusal of the results presented in this article as well as those available in the literature suggests that chelation of metal ions by inositol derivatives plays a significant role in the observed regioselectivity. Steric factors associated with the axial or equatorial disposition of the reacting hydroxyl groups do not contribute much to the outcome of these O-alkylation reactions. These results could serve as guidelines in planning synthetic strategies involving other carbohydrates and their derivatives.     

Catalytic role of the metal ion of carboxypeptidase A in ester hydrolysis.

The mechanism of action of bovine pancreatic carboxypeptidase. Aalpha (peptidyl-L-amino acid hydrolase; EC 3.4.12.2) has been investigated by application of cryoenzymologic methods. Kinetic studies of the hydrolysis of the specific ester substrate O-(trans-p-chlorocinnamoyl)-L-beta-phenyllactate have been carried out with both the native and the Co2+-substituted enzyme in the 25 to --45 degrees C temperature range. In the --25 to --45 degrees C temperature range with enzyme in excess, a biphasic reaction is observed for substrate hydrolysis characterized by rate constants for the fast (kf) and the slow (ks) processes. In Arrhenius plots, ks extrapolates to kcat at 25 degrees C for both enzymes in aqueous solution, indicating that the same catalytic rate-limiting step is observed. The slow process is analyzed for both metal enzymes, as previously reported (Makinen, M. W., Yamamura, K., and Kaiser, E. T. (1976) Proc Natl. Acad. Sci. U. S. A. 73, 3882-3886), to involve the deacylation of a mixed anhydride acyl-enzyme intermediate. Near --60 degrees C the acyl-enzyme intermediate of both metal enzymes can be stabilized for spectral characterization. The pH and temperature dependence of ks reveals a catalytic ionizing group with a metal ion-dependent shift in pKa and an enthalpy of ionization of 7.2 kcal/mol for the native enzyme and 6.2 kcal/mol for the Co2+ enzyme. These parameters identify the ionizing catalytic group as the metal-bound water molecule. Extrapolation of the pKa data to 25 degrees C indicates that this ionization coincides with that observed in the acidic limb of the pH profile of log(kcat/Km(app)) for substrate hydrolysis under steady state conditions. The results indicate that in the esterolytic reaction of carboxypeptidase. A deacylation of the mixed anhydride intermediate is catalyzed by a metal-bound hydroxide group.     

Exploring the role of chirality in nucleic acid recognition

The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.     

Enhancers of the non-peroxidative metal porphyrin chemiluminescence reaction

Metal porphyrins catalyse luminol chemiluminescence at pH 13 without added peroxide. The effects of 22 different surface active compounds on this reaction were studied using six metal porphyrins and one metal porphyrin conjugate. The most active catalyst was Mn-meso-tetra(4-sulphonatophenyl)porphine. Tween-20 enhanced the activity of this catalyst best at a Tween-20 to luminol ratio of 74:1. However, lauryl sulphate enhanced best at an optimum lauryl sulphate to luminol ratio of over 1000:1 and both detergents enhanced the reaction when present below their critical micelle concentrations. Negatively charged aliphatic compounds such as fatty acids enhanced the reaction but positive-charged aliphatic compounds inhibited it. Small differences in enhancer structure resulted in differing enhancement. For example, linoleic acid enhanced Mn-meso-tetraphenyl porphine more than 10-fold, yet linolenic acid inhibited this catalyst. Conjugation of a metal porphyrin to antibody did not influence its enhancement by detergents. The results indicate that the enhancement mechanism does not require formation of pure detergent micelles but that direct association between enhancer and catalyst may be important.     

Chiral memory: induction, amplification, and switching in porphyrin assemblies

The interaction between the tetra-anionic porphyrin H2TPPS and its copper derivative, CuTPPS, with the tetra-cationic porphyrin H2T4 and its copper derivative, CuT4, leads, in aqueous solution, to the formation of remarkably stable and kinetically inert heteroaggregates. The aggregation process is under hierarchic control and, in the presence of a suitable chiral mold, leads to the formation of chiral porphyrin heteroassemblies as stable and inert as the achiral ones. Because of these properties, the chirality of the porphyrin "imprinted" heteroaggregates not only survives the disruption of the template, but also to its complete removal from the solution. Notably, the template-free chiral porphyrin system is an excellent mold for its own self-replication. The relevant characteristics of these chiral heteroaggregates together with the knowledge of the forces that guide the aggregation processes permitted us to design a new but similar system. This system not only is able to store chiral information, but also is capable to release and restore it reversibly, in a cyclic manner. This has been achieved by modulating the charges carried by one of the two coupled porphyrins through protonation under various pH conditions. The role of the central metal ion and the template-free chiral structure of the CuT4-H2TPPS heteroaggregate, determined through EDXD analysis, are also presented.     

Investigation of the role of the substrate metal ion in the yeast inorganic pyrophosphatase reaction

The substrate activities of a series of tripositive metal ion-pyrophosphate complexes with yeast inorganic pyrophosphatase were examined. While the Michaelis constants for these complexes were shown to be between one and two orders of magnitude greater than that of the natural substrate, [Mg(H2O)4PPi]2-, the turnover numbers were in general comparable to that of [Mg(H2O)4PPi]2-. These data suggest that the nature of the metal ion cofactor effects substrate binding but in most cases not catalysis. Thus, the role of the metal ion in catalysis is probably restricted to that of an electron sink.     

Magnesium ion exerts a central role in the regulation of inhibitory adenosine receptors.

Guanine nucleotides and Mg2+ differentially regulate agonist binding to adenosine (Ri) receptors in fat-cell plasma membranes. GTP alone decreases binding of the agonist ligand [3H]N6-cyclohexyladenosine (CHA) by increasing the dissociation constant (Kd). Mg2+ alone also decreases [3H]CHA binding, which is associated with a decrease in the number of receptors and in the dissociation constant. In the presence of Mg2+, the effect of GTP is to increase [3H]CHA binding by increasing the total number of receptors. It thus appears that Mg2+ acts specifically at a bivalent-cation site which, with GTP, regulates agonist binding. This putative Mg site is highly sensitive to alkylating agents. Mild treatment with N-ethylmaleimide (NEM) abolishes the characteristic GTP effect on agonist binding in the presence of Mg2+. In addition, the effect of Mg2+ alone is also eliminated. The effect of GTP alone is largely unaltered. Studies of the adenylate cyclase activity indicate that this NEM treatment also abolishes the inhibition of basal activity by adenosine analogues, whereas guanylyl imidodiphosphate inhibition of forskolin-stimulated activity is only slightly impaired at this NEM concentration. These observations indicate that a Mg2+ 'site' or 'component' is required for the integration of receptor (Ri) occupancy with regulation of catalytic activity (C). The regulatory role of Mg2+ is more demonstrable in receptor-GTP-regulatory-protein (Ri-Ni) interactions than in GTP-regulatory-protein-catalytic-unit (Ni-C) interactions.     

Isotope effect studies of chicken liver NADP malic enzyme: role of the metal ion and viscosity dependence

The role of the metal ion in the oxidative decarboxylation of malate by chicken liver NADP malic enzyme and details of the reaction mechanism have been investigated by 13C isotope effects. With saturating NADP and the indicated metal ion at a total concentration 10-fold higher than its Km, the following primary 13C kinetic isotope effects at C4 of malate [13(V/Kmal)] were observed at pH 8.0: Mg2+, 1.0336; Mn2+, 1.0365; Cd2+, 1.0366; Zn2+, 1.0337; Co2+, 1.0283; Ni2+, 1.025. Knowing the partitioning of the intermediate oxalacetate between decarboxylation to pyuvate and reduction to malate allows calculation of the intrinsic carbon isotope effect for decarboxylation. For Mg2+ as activator, this was 1.049 with NADP and 1.046 with 3-acetylpyridine adenine dinucleotide phosphate, although the intrinsic primary deuterium isotope effects on dehydrogenation were 5.6 and 4.2, and the partition ratios of the oxalacetate intermediate for decarboxylation as opposed to hydride transfer were 0.11 and 3.96 (the result of the different redox potentials of NADP and the acetylpyridine analogue). The close agreement of the intrinsic 13C isotope effects with each other and with the 13C isotope effect for the Mg2+-catalyzed nonenzymatic decarboxylation of oxalacetate of 1.0489 [Grissom, C. B., & Cleland, W. W. (1986) J. Am. Chem. Soc. 108, 5582] indicates a similarity of transition states for these reactions. It was not possible to calculate reasonable intrinsic carbon isotope effects with the other metal ions by use of the partitioning ratio of oxalacetate because of decarboxylation by another mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)     

Supramolecular chirality induction in bis(zinc porphyrin) by amino acid derivatives: rationalization and applications of the ligand bulkiness effect

The achiral syn conformer (face-to-face) of the ethane-bridged bis(zinc porphyrin) (syn-ZnD) transforms into the corresponding chiral extended anti bis-ligated species (anti-ZnD.L2) in the presence of enantiopure ligands (L: amino acid derivatives). The mechanism of the supramolecular chirality induction is based on chiral ligand binding to zinc porphyrins and subsequent formation of either right- or left-handed screw structures in anti-ZnD.L2. The screw structure formation arises from steric interactions between the bulkiest substituent at the asymmetric carbon of the ligand and the peripheral ethyl groups of the neighboring porphyrin ring directed towards the covalent bridge. The sign and amplitude of the induced circular dichroism (CD) are dependent on the steric bulk of the substituents at the chiral center. The greater difference in size between the chiral center's substituents gives the stronger induced CD signal. Rationalization of the ligand bulkiness effect on chirality induction by amino acid derivatives, application of this supramolecular system for the determination of ligand absolute configuration, and relative bulkiness of the substituents at the asymmetric carbon are discussed.