Metal ion induced allosteric transition in the catalytic activity of an artificial phosphodiesterase

An artificial phosphodiesterase (1) bearing two kinds of metal binding sites, a catalytic site and a regulatory bipyridine site showed a unique allosteric transition in the catalytic activity against the metal concentration.     

An allosteric synthetic catalyst: metal ions tune the activity of an artificial phosphodiesterase

A trinuclear metal complex of general formula (L-H)M3(Mf)2 represents the first allosteric low molecular weight catalyst. L is a polyaza ligand having a tetradentate and two bidentate metal binding sites, Ms is a "structural" (allosteric) metal, and Mf are functional (catalytic) metals which interact with a substrate. In mononuclear [(L-H)Ms]+ complexes [(L-H)Cu(MeOH)]ClO4 (1a). [(L-H)Cu]NO3 x 2H2O (1b), [(L-H)Ni]ClO4 x 4H2O (2), and [(L-H)Pd]ClO4 x 2H2O (3), prepared from L and M2+ salts, the metal is strongly bound by an in-plane N4-coordination (confirmed by X-ray crystal structure determination of la). Formation of trinuclear complexes [(L-H)MsCu2]5+, with two functional Cu2+ ions coordinated to the bidentate sites of L, was evidenced in solution by photometric titration and by isolation of [(L-H)Cu3][PO4][ClO4]2 x 9H2O (4). The trinuclear complexes catalyze the cleavage of RNA-analogue 2-(hydroxypropyl)-p-nitrophenyl phosphate (HPNP), an activated phosphodiester. From a kinetic analysis of the cleavage rate at various HPNP concentrations, parameters KHPNP (the equilibrium constant for binding of HPNP to [(L-H)MsCu2]5+ and kcat (first-order rate constant for cleavage of HPNP when bound to the catalyst) were derived: KM= 170 (Ms= Cu2+), 340 (Ms = Ni2+), 2,600 (Ms = Pd2+) M(-1), kcat = 17 x 10(-3) (Ms= Cu2+) 3.1 x 10(-3) (Ms=Ni2+), 0.22 x 10(-3) (Ms = Pd2+) s(-1). Obviously, the nature of the allosteric metal ion Ms strongly influences both substrate affinity and reactivity of the catalyst [(L-H)MsCu2]5+. Our interpretation of this observation is that subtle differences in the ionic radius of Ms and in its tendency to distort the N4-Ms coordination plane have a significant influence on the conformation of the catalyst (i.e., preorganization of functional Cu2+ ions) and thus on catalytic activity.     

Immobilization of transition metal ion complexes and their catalytic activity towards the activation of hydrogen peroxide

Transition metal ion-imidazole complexes have been immobilized on silica, silica–alumina (25%Al₂O₃), and alumina supports by adsorption and functionalization methods. The catalytic activity of these supported complexes in the decomposition of H₂O₂ has been studied. The reaction exhibits first-order kinetics with respect to [H₂O₂] and the quantity of catalyst. The rate of reaction decreases as [H₂O₂]₀ increases. The order of catalytic reactivity is strongly dependent on the type of metal ion, support, and the immobilization method. The complex anchored via adsorption exhibited a higher activity compared to the corresponding complex anchored via functionalization of the surface. The reaction proceed via formation of the peroxo-intermediate, which has an inhibiting effect on the reaction rate. The reaction is enthalpy-controlled as is concluded from the isokinetic relationship. A mechanism is proposed involving the generation of HO₂ radicals from the peroxo-intermediate in the rate-determining step.     

Calculation of catalytic activity of transition metal complexes

A method is proposed for calculation of the catalytic activity of the complexes of transition metals. An effective Hamiltonian describing the behavior of the reagents in the presence of the catalyst is formulated, and a catalytic activity index tan2 is introduced. The isomerization of quadricyclane to norbornadiene is considered. It is shown that the index in the case of the catalytically active low-spin complex CoTPP is two orders of magnitude larger than in the case of the catalytically inactive high-spin complex MnTPP and the analogous Fe(III)TPP and MnPc complexes.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 4, pp. 398–406, July–August, 1988.     

First computational evidence for a catalytic bridging hydroxide ion in a phosphodiesterase active site.

Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulates the intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding the structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it is uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand is theoretically determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.     

Fe离子不同形态诱导血清蛋白质分子别构效应的比较分析研究

通过紫外差谱方法研究金属Fe离子不同形态与不同类别血清白蛋白分子的别构效应,并比较分析分子作用机理.考察氧介导条件对Fe离子不同形态分别与人血清白蛋白(Human serum albumin,HSA)、牛血清白蛋白(Bovine serum albumin,BSA)别构效应的影响,建立定量模型方程.结果表明,Fe离子不同形态与血清白蛋白结合反应体系中存在Fe(Ⅱ)-HSA/BSA～Fe(Ⅲ)-HSA/BSA的动态平衡,Fe(Ⅱ)-HSA/BSA～Fe(Ⅲ)-HSA/BSA电子转移效应是别构效应的关键影响因素,导致Fe离子不同形态与血清白蛋白结合反应的别构效应迥异,呈现形态显著性差异.氧介导及无氧条件下的Fe(Ⅱ)-HSA/BSA～Fe(Ⅲ)-HSA/BSA电子转移效应机理不同.无氧条件下,Fe(Ⅲ)与血清白蛋白的相互作用遵循动力学一级反应规律,计算得到结合反应体系的速率常数k及自由能变ΔG≠.     

Metal ion induced FRET OFF-ON in tren/dansyl-appended rhodamine

A series of new fluorescent probes bearing tren-spaced rhodamine B and dansyl groups have been synthesized. Compound 1 exhibits selective changes in the absorption and the emission spectra toward Cu2+ ion over miscellaneous metal cations. Among 1-3, 1 shows the best FRET efficiency through dansyl emission to rhodamine absorption for the Cu2+ ion.     

Reversible stiffening transition in beta-hairpin hydrogels induced by ion complexation

We have previously shown that properly designed lysine and valine-rich peptides undergo a random coil to beta-hairpin transition followed by intermolecular self-assembly into a fibrillar hydrogel network only after the peptide solutions are heated above the intramolecular folding transition temperature. Here we report that these hydrogels also undergo a stiffening transition as they are cooled below a critical temperature only when boric acid is used to buffer the peptide solution. This stiffening transition is characterized by rheology, dynamic light scattering, and small angle neutron scattering. Rheological measurements show that the stiffening transition causes an increase in the hydrogel storage modulus (G') by as much as 1 order of magnitude and is completely reversible on subsequently raising the temperature. Although this reversible transition exhibits rheological properties that are similar to polyol/borax solutions, the underlying mechanism does not involve hydroxyl-borate complexation. The stiffening transition is mainly caused by the interactions between lysine and boric acid/borate anion and is not driven by the changes in the secondary structure of the beta-hairpin peptide. Addition of glucose to boric acid and peptide solution disrupts the stiffening transition due to competitive glucose-borate complexation.     

Metal induced selectivity in phosphate ion binding in E9 DNase

Mass spectrometric and calorimetric data reveal that phosphate ion binding to the active site of colicin E9 DNase is delicately regulated by concomitant binding of specific transition metal ions.     

Distribution and catalytic activity of sulfonic acid groups in organic ion exchangers

The existence of inhomogeneities in the polymer structure of ion exchangers was demonstrated and their influence on catalytic properties was shown. The results are based on the differences in catalytic activity of two ion exchangers with low degrees of sulfonation differing in the distribution of active groups within the polymer particles.     

Dramatically improved catalytic activity of an artificial (S)-selective arylmalonate decarboxylase by structure-guided directed evolution

Using three rounds of structure-guided directed evolution, the catalytic activity of the (S)-selective arylmalonate decarboxylase variant G74C/C188S could be increased up to 920-fold. The best variant had a 220-fold improved activity in the production of (S)-naproxen with excellent enantioselectivity (>99% ee).     

The mechanism of cyclic nucleotide hydrolysis in the phosphodiesterase catalytic site

The cyclic nucleotide phosphodiesterase superfamily of enzymes (PDEs) catalyzes the stereospecific hydrolysis of the second messengers adenosine and guanosine 3',5'- cyclic monophosphate (cAMP, cGMP) to produce 5'-AMP and 5'-GMP, respectively. The PDEs are targets of high-throughput screening to determine selective inhibitors for a variety of therapeutic purposes. The catalytic pocket where the hydrolysis takes place is a highly conserved region and has several residues which are absolutely conserved across the PDE families. In this study, we consider a model cyclic substrate in which the adenine/guanine base has been replaced with a hydrogen atom, and we present results of a quantum computational investigation of the hydrolysis reaction as it occurs within the PDE catalytic site using the ONIOM hybrid (B3LYP/6-31g(d):PM3) method. We characterize the bound substrate, the bound hydrolyzed product, and the transition state which connects them for our model cyclic substrate placed in a truncated model of the PDE4D2 catalytic site. We address the role that the conserved histidine proximal to the bimetal system of the catalytic site, along with its conserved glutamine partner, plays in the generation of the hydroxide nucleophile. Our study provides computational evidence for several key features of the cAMP/cGMP hydrolysis mechanism as it occurs within the protein environment across the PDE superfamily.     

Modeling the framework stability and catalytic activity of pure and transition metal-doped zeotypes

We present a thorough computational study of transition metal-doped zeolite and aluminophosphate (AlPO) frameworks. The structural and electronic chemistry of the dopants is examined with ab initio quantum mechanical calculations, and the results correlated with the Brønsted and Lewis acid strength, and with the redox potential of the dopant ions in the framework. The energetics of doping is provided, and is employed to analyze the mode of dopant incorporation, and its site ordering in the microporous framework. In total, 23 dopant ions are examined in the isostructural framework of chabasite and AlPO-34. These cover most of the isomorphous framework replacements known to occur experimentally, but also framework replacements that have not yet been achieved. In this case, ab initio modeling techniques are employed in a predictive way. Finally, we present a computational study of the alkene epoxidation on titanosilicates, that covers the whole catalytic cycle.     

Metal ion separations using cellulose phosphate as an ion-exchanger

Cellulose phosphate is used as a chelating ion-exchanger to effect the separation of several metal ions. Its exchange rate is much more rapid than that of a chelating ion-exchanger containing phosphonic acid groups on a polystyrene matrix. Weight distribution coefficients as a function of hydrogen ion concentration on cellulose phosphate are given for several metal ions. Successful separations of rare earths and alkaline earths, alkaline earths and alkali metals and aluminium and alkaline earths have been achieved on cellulose phosphate columns.     

Metal ion induced FRET On-Off in naphthyl-pyrenyl pendent tetrahomodioxacalix[4]arene

A novel tetrahomodioxacalix[4]arene (7) bearing both naphthyl- and pyrenyl-amide pendants was synthesized as FRET-based fluorometric sensor for Cu²⁺ ion. Intramolecular FRET from the naphthalene emission to the pyrene absorption affords Cu²⁺ ion selectivity over other metal ions. Upon addition of Cu²⁺ ion, the complex solution of 7 gave a significantly decreased pyrene acceptor emission along with an enhancement of naphthalene donor emission via FRET On-Off event.     

Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method

Finding all required transition state (TS) structures is an important but hard task in theoretical study of complex reaction mechanisms. In the present article, an efficient automated TS search method, artificial force induced reaction (AFIR), was extended to intramolecular reactions. The AFIR method has been developed for intermolecular associative pathways between two or more reactants. Although it has also been applied to intramolecular reactions by dividing molecules manually into fragments, the fragmentation scheme was not automated. In this work, we propose an automated fragmentation scheme. Using this fragmentation scheme and the AFIR method, a fully automated search algorithm for intramolecular pathways is introduced. This version for intramolecular reactions is called single‐component AFIR (SC‐AFIR), to distinguish it from multicomponent AFIR for intermolecular reactions. SC‐AFIR was tested with two reactions, the Claisen rearrangement and the first step of cobalt‐catalyzed hydroformylation, and successfully located all important pathways reported in the literature. © 2013 Wiley Periodicals, Inc.     

Collision induced ion ejection in an FTICR trapped-ion cell

A collision algorithm was used with SimIon to evaluate collision-mediated ion ejection mechanisms in the ICR MS experiment. These mechanisms were characterized based on kinetic energy, ion mass, applied trapping potential, and collision gas mass. It was found that there are three collision-based energy regimes for ion loss from a trapped-ion cell. The first region is characterized by low initial cyclotron kinetic energy, a radial ejection mode, and a very high collision ratio (>100 collisions per ejection). The second region is characterized by a medium to high initial cyclotron kinetic energy leading to axial ejection at low collision ratio (1 to 10 collisions per ejection). The third region is characterized by a high initial cyclotron kinetic energy, a radial ejection mode, and a collision ratio of unity. It was also determined that there is a radial cyclotron mode limit, approximately 40% of the cell radius, after which an ion is ejected after a single collision. This has important consequences on the damping of the FTICR signal, various cooling techniques, ion activation techniques, and the remeasurement experiment.     

Metal controlled enantioselectivity in the catalytic asymmetric hydrosilylation

The asymmetric hydrosilylation of acetophenone with Ph₂SiH₂ has been investigated in the presence of (S)-amphos as the chiral ligand in combination with the cyclooctadiene-rhodium(I), -iridium(I), -palladium(II), and -platinum(II) chloride complexes.

High activity and optical yields up to 50% ee have been obtained. The product configuration induced by the rhodium system is (S), in all other cases it was (R).