Dynamics of non-covalent interactions during the P-O bond cleavage reaction by ribonuclease A

In this work, an atomistic-scale investigation of the phosphodiester P-O bond cleavage reaction by the enzyme ribonuclease A was carried out using computer simulation techniques. It is shown that during the reaction the network of non-covalent interactions in the active center of the ribonuclease changes significantly, while the role of these non-covalent interactions is different: coordination of the corresponding groups, electron density transfer, and ligand holding in the active center. It is shown that the process of proton transfer from Asp121 to His119 is the first stage of this reaction; at the same time, the hydrogen bond between the phosphate ligand and the imino group of Arg39 is broken, which, although keeping the ligand in the active center, does not allow the ligand to orient itself more conveniently for subsequent proton transfers. Furthermore, the key step of this reaction occurs: proton transfer with the participation of imidazole rings His12 and His119, in which the guiding role is played by several hydrogen bonds with the participation of Phe120, and the role of an electron density carrier is played by the pnictogen bond between the oxygen of the phosphate ligand and the pyridine-like nitrogen of the imidazole ring His119, which was detected for the first time.

Enzyme Mimics: Advances and Applications

Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti-biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications.

Optimizing the high-field relaxivity by self-assembling of macrocyclic Gd(III) complexes

Using recognition moieties that bind to the inner co-ordination sphere of a monomeric DO3A-type di-aqua complex, dimeric poly(aminocarboxylate) gadolinium(III) compounds can be formed with greatly enhanced relaxivities, arising from optimized contributions of inner- and second spheres of hydration.

Luminescent chiral lanthanide(III) complexes as potential molecular probes

This perspective gives an introduction into the design of luminescent lanthanide(iii)-containing complexes possessing chiral properties and used to probe biological materials. The first part briefly describes general principles, focusing on the optical aspect (i.e. lanthanide luminescence, sensitization processes) of the most emissive trivalent lanthanide ions, europium and terbium, incorporated into molecular luminescent edifices. This is followed by a short discussion on the importance of chirality in the biological and pharmaceutical fields. The second part is devoted to the assessment of the chiroptical spectroscopic tools available (typically circular dichroism and circularly polarized luminescence) and the strategies used to introduce a chiral feature into luminescent lanthanide(iii) complexes (chiral structure resulting from a chiral arrangement of the ligand molecules surrounding the luminescent center or presence of chiral centers in the ligand molecules). Finally, the last part illustrates these fundamental principles with recent selected examples of such chiral luminescent lanthanide-based compounds used as potential probes of biomolecular substrates.

Sequestration, fluorometric detection, and mass spectroscopy analysis of lanthanide ions using surface modified magnetic microspheres for microfluidic manipulation

Several methods for rapid sequestration, fluorometric detection, and the subsequent mass spectroscopic analysis of lanthanide ions using surface modified polystyrene magnetic microspheres are demonstrated. Mixed-ligand antenna complexes of Eu(3+) in which one of the ligands is attached to the surface of the microspheres have been used as a means for the sequestration, immobilization, and detection of these ions. Using the ion-exchange properties of these microspheres, this scheme has been extended to the detection of nonluminescent ions. The principles of these assays form the basis for operation of a portable microfluidic device for general analytical and nuclear forensics applications and indicate the manner in which the established methods of analytical chemistry, such as liquid-liquid extraction and ion-exchange chromatography, can be adapted for such miniature devices.

PARACEST properties of a dinuclear neodymium(III) complex bound to DNA or carbonate

A dinuclear Nd(III) macrocyclic complex of 1 (1,4-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-p-xylene) and mononuclear complexes of 1,4,7-tris-1,4,7,10-tetraazacyclododecane, 2, and 1,4,7-tris[(N-N-diethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane, 3, are prepared. Complexes of 1 and 2 give rise to a PARACEST (paramagnetic chemical exchange saturation transfer) peak from exchangeable amide protons that resonate approximately 12 ppm downfield from the bulk water proton resonance. The dinuclear Nd(III) complex is promising as a PARACEST contrast agent for MRI applications, because it has an optimal pH of 7.5 and the rate constant for amide proton exchange (2700 s(-1)) is nearly as large as it can be within slow exchange conditions with bulk water. Dinuclear Ln(2)(1) complexes (Ln(III) = Nd(III), Eu(III)) bind tightly to anionic ligands including carbonate, diethyl phosphate, and DNA. The CEST amide peak of Nd(2)(1) is enhanced by certain DNA sequences that contain hairpin loops, but decreases in the presence of diethyl phosphate or carbonate. Direct excitation luminescence studies of Eu(2)(1) show that double-stranded and hairpin-loop DNA sequences displace one water ligand on each Eu(III) center. DNA displaces carbonate ion despite the low dissociation constant for the Eu(2)(1) carbonate complex (K(d) = 15 microM). Enhancement of the CEST effect of a lanthanide complex by binding to DNA is a promising step toward the preparation of PARACEST agents containing DNA scaffolds.

A new approach in the preparation of dendrimer-based bifunctional diethylenetriaminepentaacetic acid MR contrast agent derivatives

In this paper, we report a new method to prepare and characterize a contrast agent based on a fourth-generation (G4) polyamidoamine (PAMAM) dendrimer conjugated to the gadolinium complex of the bifunctional diethylenetriamine pentaacetic acid derivative (1B4M-DTPA). The method involves preforming the metal-ligand chelate in alcohol prior to conjugation to the dendrimer. The dendrimer-based agent was purified by a Sephadex G-25 column and characterized by elemental analysis. The analysis and SE-HPLC data gave a chelate to dendrimer ratio of 30:1 suggesting conjugation at approximately every other amine terminal on the dendrimer. Molar relaxivity of the agent measured at pH 7.4 displayed a higher value than that of the analogous G4 dendrimer based agent prepared by the postmetal incorporation method (r(1) = 26.9 vs 13.9 mM(-1) s(-1) at 3 T and 22 degrees C). This is hypothesized to be due to the higher hydrophobicity of this conjugate and the lack of available charged carboxylate groups from noncomplexed free ligands that might coordinate to the metal and thus also reduce water exchange sites. Additionally, the distribution populations of compounds that result from the postmetal incorporation route are eliminated from the current product simplifying characterization as quality control issues pertaining to the production of such agents for clinical use as MR contrast agents. In vivo imaging in mice showed a reasonably fast clearance (t(1/2) = 24 min) suggesting a viable agent for use in clinical application.

Synthesis and luminescence properties of a trinucleotide-europium(III) complex conjugate

Two trinucleotide conjugates of the macrocyclic ligand 1,4,7-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane are prepared. One contains only DNA (1) and the second is a chimeric RNA/DNA conjugate (2). The synthetic methodology used to prepare the trinucleotide macrocyclic ligand conjugates is based on the introduction of a convertible nucleoside which has an electrophilic function to facilitate the attachment of any nucleophilic ligand to the 5-position of the 3-nucleoside unit. The convertible nucleoside is first treated with the macrocyclic ligand, 1,4,7,10-tetraazacyclododecane, followed by alkylation of the three remaining amine groups to give a conjugated macrocyclic ligand with three pendent amide groups. Addition of an equivalent of EuCl3 to trinucleotide (1) or (2) yields the complexes Eu(1) and Eu(2), respectively. Studies using time-resolved and steady state direct excitation luminescence spectroscopy show that Eu(III) binds to the macrocyclic moiety in 1 and in 2. The excitation peak frequency for the 7Fo5Do transition and the unexpectedly low number of water ligands in Eu(1) and Eu(2) are consistent with additional interactions of the Eu(III) macrocycle with one of the phosphate diester groups. Studies show that Eu(2) undergoes cleavage at the uridine nucleotide. The unique point of attachment of the macrocyclic complex will enable the preparation of new lanthanide nucleic acid conjugates with useful properties.

Spectroscopic system for direct lanthanide photoluminescence spectroscopy with nanomolar detection limits

A new spectroscopic system for direct photoluminescence of lanthanide ions (Ln(III)) through electronic transitions within the 4f(n) manifold is described. The system is based on an injection seeded frequency tripled (lambda = 355 nm) Nd:YAG pump laser coupled with a master oscillator power oscillator (MOPO). The MOPO delivers an average pulse energy of approximately 60 mJ/pulse, is continuously tunable from 425 to 690 nm (Signal) and 735 to 1800 nm (Idler) with a linewidth of <0.2 cm(-1), and has a pulse duration of 10-12 ns. Aqueous solutions containing two polyaminocarboxylate complexes, ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA), and Ln(3+) aqua ion for several lanthanides including Eu(III), Tb(III), Dy(III), and Sm(III)) are used as steady-state and time-resolved photoluminescence standards. The versatility of the instrument is demonstrated by excitation scans over a broad visible range for aqueous solutions of complexes of Eu(III), Dy(III), Sm(III), and Tb(III). The Eu(III) excitation band ((7)F(o)-->(5)D(o)) is recorded over a range of complex concentrations that are 1000-fold less than reported previously, including Eu(EDTA) (1.00 nM), Eu(DTPA) (1.00 nM), and Eu(III) aqua ion (50.0 nM). Emission spectra are recorded in the visible range for Ln(III) complexes at pH 6.5 and 1.00 mM. Excited-state lifetimes for the standards were constant as a function of concentration from 10.0 nM to 1.00 mM for Eu(EDTA) and Eu(DTPA) and from 100 nM to 1.00 mM for Eu(III) aqua ion. Photoluminescence lifetimes in H(2)O and D(2)O are recorded and used to calculate the number of bound water molecules for all complexes.

Correlation of relaxivity with coordination number in six-, seven-, and eight-coordinate Mn(II) complexes of pendant-arm cyclen derivatives

The syntheses and characterization of several complexes of Mn(II) with cyclen derivatives having variable numbers of pendant N-acetic acid or N-acetamide arms are reported. X-ray crystallographic results are presented for Mn(DOTAM)Cl(2) x 2 H(2)O (monoclinic C2/c, a = 18.5798(15), b = 13.6006(11), c = 10.5800(8) A, beta = 110.490(1) degrees, Z = 4), [Mn(DO3AM)][MnCl(4)] x EtOH (monoclinic P2(1)/n, a = 8.366(8), b = 19.483(2), c = 16.3627(16) A, beta = 99.254(2) degrees, Z = 4), and Mn(H(2)DOTA) (monoclinic C2/c, a = 16.374(3), b = 6.6559(13), c = 16.750(3) A, beta = 98.381(3) degrees, Z = 4), which exhibit 8-, 7-, and 6-coordinate Mn(II), respectively. (1)H relaxivity data in water at 20 MHz and 37 degrees C is presented and interpreted in terms of a mechanism involving transient binding of water in an associative intermediate. Relaxivity studies in mixed water/methanol solvents are consistent with this interpretation.

A promising change in the selection of the circular polarization excitation used in the measurement of Eu(III) circularly polarized luminescence

A judicious change in the selected transition used for circular polarization excitation will overcome the low oscillator strength limitation of the currently allowed magnetic-dipole (5)D1 <-- (7)F2 (Eu(III)) transition chosen for circularly polarized luminescence (CPL) measurement. The proposed allowed magnetic-dipole (5)D1 <-- (7)F0 (Eu(III)) transition will facilitate the detection of CPL from the Eu(III) systems of interest. CPL on the acetonitrile solution of the chiral tris complex of Eu(III) with (R,R)-N,N'-bis(1-phenylethyl)-2,6-pyridinedicarboxamide ([Eu((R,R)-1)3](3+)), recently suggested as an effective and reliable CPL calibrating agent, confirms the feasibility of the proposed experimental procedure. A comparable CPL activity exhibited by the acetonitrile solution of [Eu((R,R)-1)3](3+) following direct excitation in the spectral range of the (5)D1 <-- (7)F0 transition and upon indirect excitation through the ligand absorption bands (lambda(exc) = 308 nm) was observed. This confirms that the recommended magnetic-dipole allowed absorption transition, (5)D1 <-- (7)F0, is the transition to be considered in the measurement of CPL. This work provides critical direction for the continued instrumental improvements that can be done for developing CPL into a biomolecular structural probe.

Phosphate binding energy and catalysis by small and large molecules

Catalysis is an important process in chemistry and enzymology. The rate acceleration for any catalyzed reaction is the difference between the activation barriers for the uncatalyzed (Delta G(HO)(#)) and catalyzed (Delta G(Me)(#)) reactions, which corresponds to the binding energy (Delta G(S)(#) = Delta G(Me)(#)-Delta G(HO)(#)) for transfer of the reaction transition state from solution to the catalyst. This transition state binding energy is a fundamental descriptor of catalyzed reactions, and its evaluation is necessary for an understanding of any and all catalytic processes. We have evaluated the transition state binding energies obtained from interactions between low molecular weight metal ion complexes or high molecular weight protein catalysts and the phosphate group of bound substrate. Work on catalysis by small molecules is exemplified by studies on the mechanism of action of Zn2(1)(H2O). A binding energy of Delta G(S)(#) = -9.6 kcal/mol was determined for Zn2(1)(H2O)-catalyzed cleavage of the RNA analogue HpPNP. The pH-rate profile for this cleavage reaction showed that there is optimal catalytic activity at high pH, where the catalyst is in the basic form [Zn2(1)(HO-)]. However, it was also shown that the active form of the catalyst is Zn2(1)(H2O) and that this recognizes the C2-oxygen-ionized substrate in the cleavage reaction. The active catalyst Zn2(1)(H2O) shows a high affinity for oxyphosphorane transition state dianions and a stable methyl phosphate transition state analogue, compared with the affinity for phosphate monoanion substrates. The transition state binding energies, Delta G(S)(#), for cleavage of HpPNP catalyzed by a variety of Zn2+ and Eu3+ metal ion complexes reflect the increase in the catalytic activity with increasing total positive charge at the catalyst. These values of Delta G(S)(#) are affected by interactions between the metal ion and its ligands, but these effects are small in comparison with Delta G(S)(#) observed for catalysis by free metal ions, where the ligands are water. Enzymes are unique in having evolved mechanisms to effectively utilize binding interactions with nonreacting fragments of the substrate in stabilization of the reaction transition state. Orotidine 5'-monophosphate decarboxylase, alpha-glycerol phosphate dehydrogenase, and triosephosphate isomerase catalyze dissimilar decarboxylation, hydride transfer, and proton transfer reactions, respectively. Each enzyme derives ca. 12 kcal/mol of transition state stabilization from protein interactions with the nonreacting phosphate group, which is larger than the highest approximately 10 kcal/mol transition state stabilization that we have determined for small-molecule catalysis of phosphate diester cleavage in water. Each of these enzymes catalyze the slow reaction of a truncated substrate that lacks the phosphate group, and in each case, the reaction of the truncated substrate is strongly activated by the allosteric binding of the second substrate "piece" phosphite dianion, HPO3(2-). We propose a modular design for these enzymes with a classical active site that recognizes the reactive substrate fragment and a separate phosphodianion binding site. The second site is created, in part, by flexible protein loops that wrap around the substrate phosphodianion group and bury the substrate in an environment with an optimal local dielectric constant for the catalyzed reaction and with the most favorable positioning of the catalytic side chains. This design is easily generalized to a wide variety of enzyme-catalyzed reactions.