Transition state analogues for nucleotidyl transfer reactions: Structure and stability of pentavalent vanadate and phosphate ester dianions

Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase

Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.

Antidiabetic, Chemical, and Physical Properties of Organic Vanadates as Presumed Transition-State Inhibitors for Phosphatases

Studies of antidiabetic vanadium compounds, specifically the organic vanadate esters, are reviewed with regard to their chemistry and biological properties. The compounds are described from the perspective of how the fundamental chemistry and properties of organic vanadate esters impact their effects as inhibitors for phosphatases based on the structural information obtained from vanadium-phosphatase complexes. Vanadium compounds have been reported to have antidiabetic properties for more than a century. The structures and properties of organic vanadate complexes are reviewed, and the potency of such vanadium coordination complexes as antidiabetic agents is described. Because such compounds form spontaneously in aqueous environments, the reactions with most components in any assay or cellular environment has potential to be important and should be considered. Generally, the active form of vanadium remains elusive, although studies have been reported of a number of promising vanadium compounds. The description of the antidiabetic properties of vanadium compounds is described here in the context of recent characterization of vanadate-phosphatase protein structures by data mining. Organic vanadate ester compounds are generally four coordinate or five coordinate with the former being substrate analogues and the latter being transition-state analogue inhibitors. These studies demonstrated a framework for characterization of five-coordinate trigonal bipyramidal vanadium inhibitors by comparison with the reported vanadium-protein phosphatase complexes. The binding of the vanadium to the phosphatases is either as a five-coordinate exploded transition-state analogue or as a high energy intermediate, respectively. Even if potency as an inhibitor requires trigonal bipyramidal geometry of the vanadium when bound to the protein, such geometry can be achieved upon binding from compounds with other geometries. Desirable properties of ligands are identified and analyzed. Ligand interactions, as reported in one peptidic substrate, are favorable so that complementarity between phosphatase and coordinating ligand to the vanadium can be established resulting in a dramatic enhancement of the inhibitory potency. These considerations point to a frameshift in ligand design for vanadium complexes as phosphatase inhibitors and are consistent with other small molecule having much lower affinities. Combined, these studies do suggest that if effective delivery of potentially active antidiabetic compound such a the organic vanadate peptidic substrate was possible the toxicity problems currently reported for the salts and some of the complexes may be alleviated and dramatic enhancement of antidiabetic vanadium compounds may result.

Quantum mechanical analysis of nonenzymatic nucleotidyl transfer reactions: kinetic and thermodynamic effects of β-γ bridging groups of dNTP substrates

Rate (k) and equilibrium (K) constants for the reaction of tetrahydrofuranol with a series of Mg²⁺ complexes of methyl triphosphate analogues, CH₃O-P(O₂)-O-P(O₂)-X-PO₃^4–, X = O, CH₂, CHCH₃, C(CH₃)₂, CFCH₃, CHF, CHCl, CHBr, CFCl, CF₂, CCl₂, and CBr₂, forming phosphate diester and pyrophosphate or bisphosphonate in aqueous solution were evaluated by B3LYP/TZVP//HF/6-31G* quantum chemical calculations and Langevin dipoles and polarized continuum solvation models. The calculated log k and log K values were found to depend linearly on the experimental pK_a4 of the conjugate acid of the corresponding pyrophosphate or bisphosphonate leaving group. The calculated slopes of these Brønsted linear free energy relationships were β_lg = −0.89 and β_eq = −0.93, respectively. The studied compounds also followed the linear relationship Δlog k = 0.8Δlog K, which became less steep, Δlog k = 0.6Δlog K, after the range of studied compounds was extended to include analogues that were doubly protonated on γ-phosphate, CH₃O-P(O₂)-O-P(O₂)-X-PO₃H₂^2–. The scissile P_α–O_lg bond length in studied methyl triphosphate analogues slightly increases with decreasing pK_a of the leaving group; concomitantly, the CH₃OP_α(O₂) moiety becomes more positive. These structural effects indicate that substituents with low pK_a can facilitate both P_α–O_lg bond breaking and the P_α–O_nuc bond forming process, thus explaining the large negative β_lg calculated for the transition state geometry that has significantly longer P_α–O_nuc distance than the P_α–O_lg distance.

Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases

In vertebrates, membrane-bound ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) on the cell surface are responsible for signal conversion and termination in purinergic signaling by extracellular nucleotides. Here we present apo and complex structures of the rat NTPDase2 extracellular domain and Legionella pneumophila NTPDase1, including a high-resolution structure with a transition-state analog. Comparison of ATP and ADP binding modes shows how NTPDases engage the same catalytic site for hydrolysis of nucleoside triphosphates and diphosphates. We find that this dual specificity is achieved at the expense of base specificity. Structural and mutational studies indicate that a conserved active-site water is replaced by the phosphate product immediately after phosphoryl transfer. Partial base specificity for purines in LpNTPDase1 is based on a different intersubunit base binding site for pyrimidine bases. A comparison of the bacterial enzyme in six independent crystal forms shows that NTPDases can undergo a domain closure motion of at least 17°.

Empirical valence bond simulations of the chemical mechanism of ATP to cAMP conversion by anthrax edema factor

The two-metal catalysis by the adenylyl cyclase domain of the anthrax edema factor toxin was simulated using the empirical valence bond (EVB) quantum mechanical/molecular mechanical approach. These calculations considered the energetics of the nucleophile deprotonation and the formation of a new P-O bond in aqueous solution and in the enzyme-substrate complex present in the crystal structure models of the reactant and product states of the reaction. Our calculations support a reaction pathway that involves metal-assisted transfer of a proton from the nucleophile to the bulk aqueous solution followed by subsequent formation of an unstable pentavalent intermediate that decomposes into cAMP and pyrophosphate (PPi). This pathway involves ligand exchange in the first solvation sphere of the catalytic metal. At 12.9 kcal/mol, the barrier for the last step of the reaction, the cleavage of the P-O bond to PPi, corresponds to the highest point on the free energy profile for this reaction pathway. However, this energy is too close to the value of 11.4 kcal/mol calculated for the barrier of the nucleophilic attack step to reach a definitive conclusion about the rate-limiting step. The calculated reaction mechanism is supported by reasonable agreement between the experimental and calculated catalytic rate constant decrease caused by the mutation of the active site lysine 346 to arginine.

An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity

We show how a restricted reaction surface can be used to facilitate the calculation of biologically important contributions of active site geometries and dynamics to DNA polymerase fidelity. Our analysis, using human DNA polymerase beta (pol β), is performed within the framework of an electrostatic linear free energy response (EFER) model. The structure, dynamics, and energetics of pol β-DNA-dNTP interactions are computed between two points on the multidimensional reaction free energy surface. "Point 1" represents a ground state activation intermediate (GSA), which is obtained by deprotonating the terminal 3'OH group of the primer DNA strand. "Point 2" is the transition state (PTS) for the attack of the 3'O(-) (O(nuc)) on the P(α) atom of dNTP substrate, having the electron density of a dianionic phosphorane intermediate. Classical molecular dynamics simulations are used to compute the geometric and dynamic contributions to the formation of right and wrong O(nuc)-P chemical bonds. Matched dCTP·G and mismatched dATP·G base pairs are used to illustrate the analysis. Compared to the dCTP·G base pair, the dATP·G mismatch has fewer GSA configurations with short distances between O(nuc) and P(α) atoms and between the oxygen in the scissile P-O bond (O(lg)) and the nearest structural water. The thumb subdomain conformation of the GSA complex is more open for the mismatch, and the H-bonds in the mispair become more extended during the nucleophilic attack than in the correct pair. The electrostatic contributions of pol β and DNA residues to catalysis of the right and wrong P-O(nuc) bond formation are 5.3 and 3.1 kcal/mol, respectively, resulting in an 80-fold contribution to fidelity. The EFER calculations illustrate the considerable importance of Arg183 and an O(lg)-proximal water molecule to pol β fidelity.

Pyrovanadolysis, a pyrophosphorolysis-like reaction mediated by pyrovanadate, Mn2+, and DNA polymerase of bacteriophage T7

DNA polymerases catalyze the 3'-5'-pyrophosphorolysis of a DNA primer annealed to a DNA template in the presence of pyrophosphate (PP(i)). In this reversal of the polymerization reaction, deoxynucleotides in DNA are converted to deoxynucleoside 5'-triphosphates. Based on the charge, size, and geometry of the oxygen connecting the two phosphorus atoms of PP(i), a variety of compounds was examined for their ability to carry out a reaction similar to pyrophosphorolysis. We describe a manganese-mediated pyrophosphorolysis-like activity using pyrovanadate (VV) catalyzed by the DNA polymerase of bacteriophage T7. We designate this reaction pyrovanadolysis. X-ray absorption spectroscopy reveals a shorter Mn-V distance of the polymerase-VV complex than the Mn-P distance of the polymerase-PP(i) complex. This structural arrangement at the active site accounts for the enzymatic activation by Mn-VV. We propose that the Mn(2+), larger than Mg(2+), fits the polymerase active site to mediate binding of VV into the active site of the polymerase. Our results may be the first documentation that vanadium can substitute for phosphorus in biological processes.

On the energetics of ATP hydrolysis in solution

ATP hydrolysis is the driving force of many life processes, yet the exact nature of and contributions to the energetics of this reaction are far from being clear. In particular, it is unclear how much of the driving force of this reaction is due to the separation of the already dissociated ADP + P(i) moieties rather than to the chemical event. This fundamental issue is explored here by ab initio calculations that use different solvation models, and it is found that, while the calculations are sensitive to the theoretical approach used, it is quite likely that the dissociation of the charged fragments makes a significant contribution to the energetics of ATP hydrolysis.

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models

Phosphate hydrolysis is ubiquitous in biology. However, despite intensive research on this class of reactions, the precise nature of the reaction mechanism remains controversial. Herein, we have examined the hydrolysis of three homologous phosphate diesters. The solvation free energy was simulated by means of either an implicit solvation model (COSMO), hybrid quantum mechanical/molecular mechanical free energy perturbation (QM/MM-FEP) or a mixed solvation model in which N water molecules were explicitly included in the ab initio description of the reacting system (where N=1-3), with the remainder of the solvent being implicitly modelled as a continuum. Here, both COSMO and QM/MM-FEP reproduce DeltaG(obs) within an error of about 1 kcal mol(-1). However, we demonstrate that in order to obtain any kind of reliable results from a mixed model, it is essential to carefully select the explicit water molecules from short QM/MM runs that act as a model for the true infinite system. Additionally, the mixed models tend to be increasingly unstable and miss larger entropic contributions as more explicit water molecules are placed into the system. Thus, our analysis indicates that this approach provides an unreliable way for modelling phosphate hydrolysis in solution.

Linear energy relationships for the octahedral preference of Mg, Ca and transition metal ions

The geometry, atomic charges, force constants, and relative energies of the symmetric and distorted M(2+)(H(2)O)(4)(F(-))(2), M(3+)(H(2)O)(4)(F(-))(2), M(2+)(H(2)O)(3)(F(-))(2), and M(3+)(H(2)O)(3)(F(-))(2) metal complexes, M = Mg, Ca, Co, Cu, Fe, Mn, Ni, Zn, Cr, V, were calculated by using the B3LYP/TZVP density functional method in both gas phase and aqueous solution, modeled using the polarized continuum model. The deformation energy associated with moving one water ligand 12 degrees from the initial "octahedral" arrangement, in which all O-M-O, O-M-F, and F-M-F angles are either 90 degrees or 180 degrees, was calculated to examine the angular ligand flexibility. For all M(2+)(H(2)O)(4)(F(-))(2) complexes, this distortion increased the energy of the complex in proportion to the electrostatic potential-derived (ESP) charge of the metal, and in proportion to D(-10), where D is the distance from the distorted ligand to its closest neighbor. The octahedral stability was further examined by calculating the energies for the removal of a water ligand from the octahedral complex to form a square-pyramidal or trigonal-bipyramidal complex. The octahedral preference, defined as the negative of the corresponding binding energy of the ligand, was found to linearly correlate with the ESP charge of the metal in both the gas phase and aqueous solution. The obtained results indicate that quantum-mechanical covalent effects are of secondary importance for both the flexibility and the octahedral preference of M(2+)(H(2)O)(4)(F(-))(2) and M(3+)(H(2)O)(4)(F(-))(2) complexes. This conclusion and supporting data are important for the development of consistent molecular mechanical force fields of the studied metal ions.

Dineopentyl phosphate hydrolysis: evidence for stepwise water attack

Phosphate ester hydrolysis is ubiquitous in biology, playing a central role in energy production, signaling, biosynthesis, and the regulation of protein function among other things. Although the mechanism of action of the enzymes regulating this reaction has been the focus of intensive research in the past few decades, the correct description of this apparently simple reaction remains controversial. A clear understanding of the mechanism that takes place in solution is crucial to be able to evaluate whether proposals for the enzyme-catalyzed mechanisms are reasonable. For the pH-independent hydrolysis of phosphate diesters, several kinetically equivalent mechanisms are plausible, including hydroxide attack on the neutral phosphate. However, it is very difficult to measure the rate of this reaction directly by experimental methods, so it has been evaluated by examining the rate of hydrolysis of neutral phosphate triesters, where a methyl group has replaced a proton. This may not be an accurate model of the neutral phosphate diester and does not provide information about a reaction pathway that is concerted with nucleophilic attack to generate a similar phosphorane. We have carefully mapped out free energy surfaces for both hydroxide and water attack on the dineopentyl phosphate anion and for water attack on the neutral diester. In doing so, we have accurately reproduced existing experimental data and demonstrate that water attack proceeds through an associative mechanism with proton transfer to the phosphate to generate a phosphorane intermediate. Our data show that the substrate-as-base mechanism is viable for phosphate ester hydrolysis, which may have important implications for the studies of phosphate ester hydrolysis by enzymes.

51V solid-state NMR and density functional theory studies of vanadium environments in V(V)O2 dipicolinic acid complexes

(51)V solid-state NMR and density functional theory (DFT) investigations are reported for a series of pentacoordinate dioxovanadium(V)-dipicolinate [V(V)O(2)-dipicolinate] and heptacoordinate aquahydroxylamidooxovanadium(V)-dipicolinate [V(V)O-dipicolinate] complexes. These compounds are of interest because of their potency as phosphatase inhibitors as well as their insulin enhancing properties and potential for the treatment of diabetes. Experimental solid-state NMR results show that the electric field gradient tensors in the V(V)O(2)-dipicolinate derivatives are affected significantly by substitution on the dipicolinate ring and range from 5.8 to 8.3 MHz. The chemical shift anisotropies show less dramatic variations with respect to the ligand changes and range between -550 and -600 ppm. To gain insights on the origins of the NMR parameters, DFT calculations were conducted for an extensive series of the V(V)O(2)- and V(V)O-dipicolinate complexes. To assess the level of theory required for the accurate calculation of the (51)V NMR parameters, different functionals, basis sets, and structural models were explored in the DFT study. It is shown that the original x-ray crystallographic geometries, including all counterions and solvation water molecules within 5 A of the vanadium, lead to the most accurate results. The choice of the functional and the basis set at a high level of theory has a relatively minor impact on the outcome of the chemical shift anisotropy calculations; however, the use of large basis sets is necessary for accurate calculations of the quadrupole coupling constants for several compounds of the V(V)O(2) series. These studies demonstrate that even though the vanadium compounds under investigations exhibit distorted trigonal bipyramidal coordination geometry, they have a "perfect" trigonal bipyramidal electronic environment. This observation could potentially explain why vanadate and vanadium(V) adducts are often recognized as potent transition state analogs.

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

The hydrolysis of phosphate esters is crucially important to biological systems, being involved in, among other things, signaling, energy transduction, biosynthesis, and the regulation of protein function. Despite this, there are many questions that remain unanswered in this important field, particularly with regard to the preferred mechanism of hydrolysis of phosphate esters, which can proceed through any of multiple pathways that are either associative or dissociative in nature. Previous comparisons of calculated and observed linear free energy relationships (LFERs) for phosphate monoester dianions with different leaving groups showed that the TS character gradually changes from associative to dissociative with the increasing acidity of the leaving group, while reproducing the experimental LFER. Here, we have generated ab initio potential energy surfaces for the hydrolysis of phosphate diesters in solution, with a variety of leaving groups. Once again, the reaction changes from a compact concerted pathway to one that is more expansive in character when the acidity of the leaving group increases. When such systems are examined in solution, it is essential to take into consideration the contribution of solute to the overall activation entropy, which remains a major computational challenge. The popular method of calculating the entropy using a quasi-harmonic approximation appears to markedly overestimate the configurational entropy for systems with multiple occupied energy wells. We introduce an improved restraint release approach for evaluating configurational entropies and apply this approach to our systems. We demonstrate that when this factor is taken into account, it is possible to reproduce the experimental LFER for this system with reasonable accuracy.

Probing the two-metal ion mechanism in the restriction endonuclease BamHI

The choreography of restriction endonuclease catalysis is a long-standing paradigm in molecular biology. Bivalent metal ions are required almost for all PD..D/ExK type enzymes, but the number of cofactors essential for the DNA backbone scission remained ambiguous. On the basis of crystal structures and biochemical data for various restriction enzymes, three models have been developed that assign critical roles for one, two, or three metal ions during the phosphodiester hydrolysis. To resolve this apparent controversy, we investigated the mechanism of BamHI catalysis using quantum mechanical/molecular mechanical simulation techniques and determined the activation barriers of three possible pathways that involve a Glu-113 or a neighboring water molecule as a general base or an external nucleophile that penetrated from bulk solution. The extrinsic mechanism was found to be the most favorable with an activation free energy of 23.4 kcal/mol, in reasonable agreement with the experimental data. On the basis of the effect of the individual metal ions on the activation barrier, metal ion A was concluded to be pivotal for the reaction, while the enzyme lacking metal ion B still has moderate efficiency. Thus, we propose that the catalytic scheme of BamHI does not involve a general base for nucleophile generation and requires one obligatory metal ion for catalysis that stabilizes the attacking nucleophile and coordinates it throughout the nucleophilic attack. Such a model may also explain the variation in the number of metal ions in the crystal structures and thus could serve as a framework for a unified catalytic scheme of type II restriction endonucleases.

Chelation of Vanadium(V) by Difluoromethylene Bisphosphonate, a Structural Analogue of Pyrophosphate

The structural and functional analogy between difluoromethylene bisphosphonate (CF2PP) and pyrophosphate (PPi) is investigated in a reaction with V(V) in the form of vanadate. The reaction of CF2PP with vanadate was investigated using 1.00 M KCl as supporting electrolyte over the ranges 3 < or = [CF2PP] < or = 60 mM and 2.06 < or = pH < or = 11.80. 51V, 19F, and 31P NMR spectroscopic studies showed that a 1:1 species was formed with an H+-dependent formation constant of 110 M-1 at pH 7.22. Results of solution experiments and ab initio calculations are consistent with CF2PP coordinating V(V) in a bidentate manner, as previously reported for PPi. Below pH 4, a minor complex forms, which is consistent with a 1:2 stoichiometry. This complex was also observed with pyrophosphate. The X-ray crystal structure of the monoprotonated difluoromethylene bisphosphonate anion (H[CF2PP]3-)-toludine complex is presented. The H[CF2PP]3- anion crystallized in the triclinic space group P with a = 12.7629(7) A, b = 13.3992(7) A, c = 17.1002(9) A, and V = 2584.4(2) A3, and Z = 2. Sheets of the layers of anions are connected through a network of H-bonds and separated by a layer of toludine cations. The structural features are investigated, and the CF2PP anion was found to be longer and wider than the corresponding PPi. Given the larger size of this anion compared to PPi, the chelation affinity upon CF2 substitution was found to be 4-5-fold reduced at neutral pH.

On Use of the Amber Potential with the Langevin Dipole Method

Inclusion of solvent effects in biomolecular simulations is most ideally done using explicit methods, as they are able to capture the heterogeneous environment typical of biomolecules and systems involving them (e.g., proteins at solid interfaces). Common explicit methods based on molecular solvent models (e.g., TIP and SPC models) and molecular dynamic or Monte Carlo simulation are computationally expensive and are, therefore, not well-suited to situations where many simulations are required (e.g., in the ab initio structure prediction or design contexts). In such cases, more coarse-grained explicit approaches such as the Langevin dipole (LD) method of Warshel and co-workers are more appropriate. The recent incarnations of the LD method appear to produce good solvation free energy estimates. These incarnations use charges and solute structures obtained from high-level quantum mechanics simulations. As such an approach is clearly not possible for larger solutes or when many structures are to be considered, an alternative must be sought. One possibility is to use structures and charges derived from an existing analytical potential model-we report on such a coupling here with the Amber potential model. The accuracy and computational performance of this hybrid approach, which we term LD-Amber to distinguish it from previous incarnations of the LD method, was assessed by comparing results obtained from the approach with those from experiment and other theoretical methods for the solvation of 18 amino acid analogues and the alanine dipeptide. This comparison shows that the LD-Amber approach can yield results in line with experiment both qualitatively and quantitatively and is as accurate as other explicit methods while being computationally much cheaper.

Theoretical Evaluation of the Substrate-Assisted Catalysis Mechanism for the Hydrolysis of Phosphate Monoester Dianions

Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4-dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous S(N)2(P) reactions of F- with the monoanion of the monoester 2,4-dinitrophenyl phosphate and its diester analogue, methyl 2,4-dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH- and F- can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving-group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (beta(lg)=-0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pK(a)<11 are involved, as in alkaline phosphatase, then the S(N)2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of beta(lg) (-0.95) is predicted for the substrate-assisted catalysis mechanism.