Thermodynamics of proton dissociation in dilute aqueous solution. V. An entropy titration study of adenosine, pentoses, hexoses, and related compounds

Stereoselective Conversions of Carbohydrate Anomeric Hydroxyl Group in Basic and Neutral Conditions

The rapidly growing glycoscience has boosted the research on the synthesis of glycans and their conjugates, which are centered on the stereoselective formation of glycosidic bonds. Compared to the mainstream acid-promoted glycosylation method that undergoes the SN1 type mechanism, the basic/neutral conditions give better stereo control via the SN2 mechanism. Anomeric hydroxyl group transformation, whether to form glycosidic bonds directly or to install a leaving group for later glycosylation, is key to carbohydrate synthesis, and the strategies in the stereo control of these reactions under basic/neutral conditions are summarized in this review. Different stereo control strategies that are applicable to protected or unprotected hemiacetals are discussed, and case-by-case studies of literature reports in the past two decades are included. In addition to surveying literature reports, this review aims at providing insights into the strategic considerations in the development of a stereoselective method for the formation of glycosidic bonds.

Selective Anomeric Acetylation of Unprotected Sugars with Acetic Anhydride in Water

Unprotected sugars are selectively acetylated simply by stirring in aqueous solution in the presence of acetic anhydride and a weak base such as sodium carbonate. The reaction is selective for acetylation of the anomeric hydroxyl group of mannose, 2-acetamido, and 2-deoxy sugars and can be performed on a large scale. Competitive intramolecular migration of the 1-O-acetate to the 2-hydroxyl group when these two substituents are cis causes over-reaction and the formation of product mixtures.

Study of base-catalyzed isomerization of d-glucose with a focus on reaction kinetics

We explored the isomerization of d-glucose into d-fructose using the simplest possible base catalyst, aqueous NaOH, to maintain a constant pH value during the reaction. Under the applied mild conditions (T 50–90 °C, pH 9.5–11.5), yields of d-fructose of up to 31% were observed. Selectivity-conversion plots were not significantly influenced by variation of the temperature, pH value or substrate concentration. A reaction network for kinetic modelling includes d-glucose-d-fructose interconversion, co-production of d-mannose and d-allulose (also known as d-psicose) as well as decomposition paths after deprotonation of the hexoses. All four hexoses were employed as substrates in the isomerization. Thermodynamic ionization constants of the saccharides were measured by means of potentiometric titration. In the kinetic studies, pH-independent rate constants as well as activation energies were determined. The obtained kinetic and thermodynamic results as well as selectivity-conversion correlations present a useful benchmark for soluble and solid base catalysts.

Pyridoneimine-catalyzed anomeric aqueous oxa-Michael additions of native mono- and disaccharides

A pyridoneimine-catalyzed oxa-Michael addition of protecting groups-free, native mono- and disaccharides with Michael acceptors in aq. solution is reported. Several mono- and disaccharides are reacted with acceptors, namely, methylvinyl ketone, acrylonitrile and tert-butyl acrylate in aq. solution, the addition catalyzed by n-pentylpyridone imine. The addition occurs site-selectively at the anomeric lactol and the remaining hydroxy functionalities are un-affected. The resulting keto-glycopyranoside products are explored in aldol, allylation and oxime product formation, occurring at either α-methyl moiety or at the keto-moiety, with appropriate synthons. In another direction, the keto-glycopyranoside is functionalized further with amino acids through reductive amination in aq. methanol solution. Formation of hemiacetal anion occurs in the presence of pyridoneimine in aq. Solution, enabling subsequent addition to occur with acceptors. Facile reductive amination of the resulting keto-glycoside provides an avenue for conjugations with amino acids in the present work.

Anomeric alkylations and acylations of unprotected mono- and disaccharides mediated by pyridoneimine in aqueous solutions

A site-specific deprotonation followed by alkylations and acylations of sugar hemiacetals to the corresponding alkyl glycosides and acylated sugars in aqueous solutions is disclosed herein. Pyridoneimine as a new base is developed to mediate the deprotonation of readily available sugar hemiacetals and further reactions with alkylation and acylation agents.

Investigation of the pKa of the Nucleophilic O2' of the Hairpin Ribozyme

Small ribozymes cleave their RNA phosphodiester backbone by catalyzing a transphosphorylation reaction wherein a specific O2' functions as the nucleophile. While deprotonation of this alcohol through its acidification would increase its nucleophilicity, little is known about the pK_a of this O2' in small ribozymes, in part because high pK_a's are not readily accessible experimentally. Herein, we turn to molecular dynamics to calculate the pK_a of the nucleophilic O2' in the hairpin ribozyme and to study interactions within the active site that may impact its value. We estimate the pK_a of the nucleophilic O2' in the wild-type hairpin ribozyme to be 18.5 ± 0.8, which is higher than the reference compound, and identify a correlation between proper positioning of the O2' for nucleophilic attack and elevation of its pK_a. We find that monovalent ions may play a role in depression of the O2' pK_a, while the exocyclic amine appears to be important for organizing the ribozyme active site. Overall, this study suggests that the pK_a of the O2' is raised in the ground state and lowers during the course of the reaction owing to positioning and metal ion interactions.

Applications of Shoda's reagent (DMC) and analogues for activation of the anomeric centre of unprotected carbohydrates

2-Chloro-1,3-dimethylimidazolinium chloride (DMC, herein also referred to as Shoda's reagent) and its derivatives are useful for numerous synthetic transformations in which the anomeric centre of unprotected reducing sugars is selectively activated in aqueous solution. As such unprotected sugars can undergo anomeric substitution with a range of added nucleophiles, providing highly efficient routes to a range of glycosides and glycoconjugates without the need for traditional protecting group manipulations. This mini-review summarizes the development of DMC and some of its derivatives/analogues, and highlights recent applications for protecting group-free synthesis.

Determination of acidity constants for weak acids and bases by isothermal titration calorimetry

The advantage of isothermal titration calorimetry (ITC) to determine the acid dissociation constant (pK_a value) is the simultaneous determination of the binding constant and binding enthalpy, as well as being precise and easy to use. The pK_a can be calculated from the binding constant, and the temperature dependency of the pK_a can be calculated from the binding enthalpy. The use of ITC to study protonation reactions is less common compared to its more conventional use of studying macromolecules and ligands. Water will influence the equilibrium due to autoionization, meaning that both the conjugate base and acid will exist in the sample cell at the beginning of the experiment. These differences are accounted for by optimizing the theoretical model used to estimate the binding constant and binding enthalpy. Through simulations and experimental measurements, we show that ITC can be used to determine the pK_a for ibuprofen, ascorbic acid, 2-morpholin-4-ylethanesulfonic acid and paracetamol. The pK_a values were consistent with potentiometric or spectrophotometric determinations as well as literature values. Optimizing the theoretical model does not lead to an improved determination, so the "one set of sites" model is adequate for the determination of pK_a values.

Scope of the DMC mediated glycosylation of unprotected sugars with phenols in aqueous solution

Activation of reducing sugars in aqueous solution using DMC and triethylamine in the presence of phenols allows direct stereoselective conversion to the corresponding 1,2-trans aryl glycosides without the need for any protecting groups.

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.

An update on anticancer drug development and delivery targeting carbonic anhydrase IX

The expression of carbonic anhydrase (CA) IX is up-regulated in many types of solid tumors in humans under hypoxic and acidic microenvironment. Inhibition of CA IX enzymatic activity with selective inhibitors, antibodies or labeled probes has been shown to reverse the acidic environment of solid tumors and reduce the tumor growth establishing the significant role of CA IX in tumorigenesis. Thus, the development of potent antitumor drugs targeting CA IX with minimal toxic effects is important for the target-specific tumor therapy. Recently, several promising antitumor agents against CA IX have been developed to treat certain types of cancers in combination with radiation and chemotherapy. Here we review the inhibition of CA IX by small molecule compounds and monoclonal antibodies. The methods of enzymatic assays, biophysical methods, animal models including zebrafish and Xenopus oocytes, and techniques of diagnostic imaging to detect hypoxic tumors using CA IX-targeted conjugates are discussed with the aim to overview the recent progress related to novel therapeutic agents that target CA IX in hypoxic tumors.

Selective anomeric acetylation of unprotected sugars in water

High yielding selective acetylation of only the anomeric hydroxyl of unprotected sugars is possible in aqueous solution using 2-chloro-1,3-dimethylimidazolinium chloride (DMC), thioacetic acid, and a suitable base. The reaction, which may be performed on a multi-gram scale, is stereoselective for sugars that possess a hydroxyl group at position-2, exclusively yielding the 1,2-trans products. The use of an iterative reagent addition procedure allows the use of sodium carbonate as the base, avoiding the formation of triethylammonium salts, which may hamper product purification. The glycosyl acetate products may be used as donor substrates for glycosidase-catalysed synthesis. The crude aqueous acetylation reaction mixture may also be used for this purpose.

Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ

Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze the nucleotidyl-transfer reaction in the base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free-energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3′-OH group of the primer DNA strand, and the subsequent formation and cleavage of P–O bonds in four Polβ, two truncated Polλ (tPolλ), and two tPolλ Loop1 mutant (tPolλΔL1) systems differing in the initial X-ray crystal structure and nascent base pair. The average calculated activation free energies of 14, 18, and 22 kcal mol^–1 for Polβ, tPolλ, and tPolλΔL1, respectively, reproduce the trend in the observed catalytic rate constants. The most feasible reaction pathway consists of two successive steps: specific base (SB) proton transfer followed by rate-limiting concerted formation and cleavage of the P–O bonds. We identify linear free-energy relationships (LFERs) which show that the differences in the overall activation and reaction free energies among the eight studied systems are determined by the reaction free energy of the SB proton transfer. We discuss the implications of the LFERs and suggest pK_a of the 3′-OH group as a predictor of the catalytic rate of X-family DNA polymerases.

Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β

Elucidating the catalytic mechanism of DNA polymerase is crucial for a progress in the understanding of the control of replication fidelity. This work tries to advance the mechanistic understanding by analyzing the observed effect of mutations of the acidic groups in the active site of Polymerase β as well as the pH effect on the rate constant. The analysis involves both empirical valence bond (EVB) free energy calculations and considerations of the observed pH dependence of the reaction. The combined analysis indicates that the proton transfer (PT) from the nucleophilic O3' has two possible pathways, one to D256 and the second to the bulk. We concluded based on calculations and the experimental pH profile that the most likely path for the wild-type (WT) and the D256E and D256A mutants is a PT to the bulk, although the WT may also use a PT to Asp 256. Our analysis highlights the need for very extensive sampling in the calculations of the activation barrier and also clearly shows that ab initio QM/MM calculations that do not involve extensive sampling are unlikely to give a clear quantitative picture of the reaction mechanism. Proteins 2016; 84:1644-1657. © 2016 Wiley Periodicals, Inc.

Mixed Anhydride Intermediates in the Reaction of 5(4H)-Oxazolones with Phosphate Esters and Nucleotides

5(4H)‐Oxazolones can be formed through the activation of acylated α‐amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic‐phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono‐substituted phosphate group at the 3’‐ or 5’‐terminus but not at the internal phosphodiester linkages. In addition to the formation of mixed anhydrides, the subsequent intramolecular acyl or phosphoryl transfers taking place at the 3’‐terminus are considered to be particularly relevant to the common prebiotic chemistry of α‐amino acids and nucleotides.

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed.

Visualizing Organophosphate Precipitation at the Calcite-Water Interface by in Situ Atomic-Force Microscopy

Esters of phosphoric acid constitute a large fraction of the total organic phosphorus (OP) in the soil environment and, thus, play an important role in the global phosphorus cycle. These esters, such as glucose-6-phosphate (G6P), exhibit unusual reactivity toward various mineral particles in soils, especially those containing calcite. Many important processes of OP transformation, including adsorption, hydrolysis, and precipitation, occur primarily at mineral-fluid interfaces, which ultimately governs the fate of organophosphates in the environment. However, little is known about the kinetics of specific mineral-surface-induced adsorption and precipitation of organophosphates. Here, by using in situ atomic-force microscopy (AFM) to visualize the dissolution of calcite (1014) faces, we show that the presence of G6P results in morphology changes of etch pits from the typical rhombohedral to a fan-shaped form. This can be explained by a site-selective mechanism of G6P-calcite surface interactions that stabilize the energetically unfavorable (0001) or (0112) faces through step-specific adsorption of G6P. Continuous dissolution at calcite (1014)-water interfaces caused a boundary layer at the calcite-water interface to become supersaturated with respect to a G6P-Ca phase that then drives the nucleation and growth of a G6P-Ca precipitate. Furthermore, after the introduction of the enzyme alkaline phosphatase (AP), the precipitates were observed to contain a mixture of components associated with G6P-Ca, amorphous calcium phosphate (ACP)-hydroxyapatite (HAP) and dicalcium phosphate dihydrate (DCPD). These direct dynamic observations of the transformation of adsorption- and complexation-surface precipitation and enzyme-mediated pathways may improve the mechanistic understanding of the mineral-interface-induced organophosphate sequestration in the soil environment.

RNA synthesis by in vitro selected ribozymes for recreating an RNA world

The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme’s possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory.

Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature

Xyloglucans are structurally complex plant cell wall polysaccharides that are involved in cell growth and expansion, energy metabolism, and signaling. Determining the structure-function relationships of xyloglucans would benefit from the availability of a comprehensive and structurally diverse collection of rigorously characterized xyloglucan oligosaccharides. Here, we present a workflow for the semi-preparative scale generation and purification of neutral and acidic xyloglucan oligosaccharides using a combination of enzymatic and chemical treatments and size-exclusion chromatography. Twenty-six of these oligosaccharides were purified to near homogeneity and their structures validated using a combination of matrix-assisted laser desorption/ionization mass spectrometry, high-performance anion exchange chromatography, and 1H nuclear magnetic resonance spectroscopy. Mass spectrometry and analytical chromatography were compared as methods for xyloglucan oligosaccharide quantification. 1H chemical shifts were assigned using two-dimensional correlation spectroscopy. A comprehensive update of the nomenclature describing xyloglucan side-chain structures is provided for reference.

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.

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.

Chemistry and applications of polysaccharide solutions in strong electrolytes/dipolar aprotic solvents: an overview

Biopolymers and their derivatives are being actively investigated as substitutes for petroleum-based polymers. This has generated an intense interest in investigating new solvents, in particular for cellulose, chitin/chitosan, and starch. This overview focuses on recent advances in the dissolution and derivatization of these polysaccharides in solutions of strong electrolytes in dipolar aprotic solvents. A brief description of the molecular structures of these biopolymers is given, with emphases on the properties that are relevant to derivatization, namely crystallinity and accessibility. The mechanism of cellulose dissolution is then discussed, followed by a description of the strategies employed for the synthesis of cellulose derivatives (carboxylic acid esters, and ethers) under homogeneous reaction conditions. The same sequence of presentation has been followed for chitin/chitosan and starch. Future perspectives for this subject are summarized, in particular with regard to compliance with the principles of green chemistry.

Simultaneous determination of equilibrium constants and enthalpy changes by titration calorimetry: Methods, instruments, and uncertainties

Calorimetric methods have been used to determine equilibrium constants since 1937, but no comprehensive review of the various calorimeters and methods has been done previously. This article reports methods for quantitative comparison of the capabilities of calorimeters for simultaneous determination of equilibrium constants and enthalpy changes, for determining optimal experimental conditions, and for assessing the effects of systematic and random errors on the accuracy and precision of equilibrium constants and enthalpy changes determined by this method.

Uranium(VI) complexes with sugar phosphates in aqueous solution

The complex formation in the aqueous systems of uranium(VI) with glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P) were studied using potentiometric titration, TRLFS, and EXAFS. Two complexes with a uranyl-to-ligand ratio of 1:1 and 1:2 for both sugars were observed. Complex stability constants were determined by potentiometric titration for both complexes to be log β11(G6P)=5.89±0.40, log β12(G6P)=9.45±0.08, log β11(F6P)=5.72±0.21, and log β12(F6P)=9.54±0.09. Stability constants could be determined with TRLFS under the specific experimental conditions only for the 1:1 complexes: log β11(G6P)=6.35±0.28, and log β11(F6P)=5.66±0.17.

The TRLFS measurements results show the UO2G6P complex to exhibit no fluorescence properties. For this system, only a decrease of the fluorescence intensity with increasing ligand concentration was observed. For the UO2F6P system, a red shift of the fluorescence emission bands of about 8 to 9 nm compared to the free uranyl ion was observed. The fluorescence emission wavelengths of the UO2F6P complex were determined to be 483, 496, 518, 542, and 567 nm, and the lifetime of this complex is 0.13±0.05 μs.

Uranium L III-edge EXAFS measurements at pH 3.5, 4.0, and 5.5 yielded a shortened U–Oeq bond distance (2.30±0.02 to 2.37±0.02 Å), compared to the UO2 2+(H2O)5 ion (2.40±0.02 Å), due to a monodentate coordination via the oxygen atoms of the phosphate group.

Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

The relationships between the conformational landscape, nucleotide insertion catalysis and fidelity of DNA polymerase beta are explored by means of computational simulations. The simulations indicate that the transition states for incorporation of right (R) and wrong (W) nucleotides reside in substantially different protein conformations. The protein conformational changes that reproduce the experimentally observed fidelity are significantly larger than the small rearrangements that usually accompany motions from the reactant state to the transition state in common enzymatic reactions. Once substrate binding has occurred, different constraints imposed on the transition states for insertion of R and W nucleotides render it highly unlikely that both transition states can occur in the same closed structure, because the predicted fidelity would then be many orders of magnitude too large. Since the conformational changes reduce the transition state energy of W incorporation drastically they decrease fidelity rather than increase it. Overall, a better agreement with experimental data is attained when the R is incorporated through a transition state in a closed conformation and W is incorporated through a transition state in one or perhaps several partially open conformations. The generation of free energy surfaces for R and W also allow us to analyze proposals about the relationship between induced fit and fidelity.

Nalpha-(1-deoxy-D-fructos-1-yl)-L-histidine ("D-Fructose-L-histidine"): a potent copper chelator from tomato powder

Dried fruits and vegetables are known for their high content of D-fructose-amino acids, or Amadori compounds, which appear at the initial step of the Maillard reaction and may participate in redox reactions mediated by trace metals. In this study, we investigated complexation between Cu(II) and N(alpha)-(1-deoxy-D-fructos-1-yl)-L-histidine (D-fructose-L-histidine, FruHis). The content of FruHis in two types of commercial tomato powders was estimated by GLC-MS, using single ion monitoring of trimethylsilylated FruHis hydroxyoximate, as 40 mg/100 g, whereas the concentration of free histidine in the powder samples was about 53 mg/100 g. The Cu(II)-binding ability of FruHis was studied along with structurally related molecules L-histidine, dipeptide L-carnosine, and N(alpha)-(1-deoxy-D-fructos-1-yl)-L-arginine (FruArg) at 25 degrees C using pH-potentiometric titrations. Analysis of the titration curves showed that formation of Cu(II)-FruHis complex species occurs at pH values as low as 2 and that the complexes were redox stable in the pH range 2-10.5, at least for the time of the experiment. At physiological pH, Cu(II) and FruHis form a dominant coordination species of composition MLH-1 (log beta = 5.67), with a presumably deprotonated anomeric hydroxyl group of the fructose portion. The apparent stability constant of 1:1 complexes formed by FruHis and Cu(II) in neutral aqueous solutions is about 10(4) times higher than similar values calculated for L-histidine, L-carnosine, and FruArg. FruHis nearly completely protected hydroxyl radical-mediated fragmentation of polymeric DNA in the presence of the Cu/H2O2/ascorbate system, whereas neither of the reference compounds could inhibit the DNA fragmentation as efficiently in similar conditions. These results warrant further investigation of FruHis as a potential food-related antioxidant.

Participation of the tRNA A76 hydroxyl groups throughout translation

The free 2'-3' cis-diol at the 3'-terminus of tRNA provides a unique juxtaposition of functional groups that play critical roles during protein synthesis. The translation process involves universally conserved chemistry at almost every stage of this multistep procedure, and the 2'- and 3'-OHs are in the immediate vicinity of chemistry at each step. The cis-diol contribution affects steps ranging from tRNA aminoacylation to peptide bond formation. The contributions have been studied in assays related to translation over a period that spans at least three decades. In this review, we follow the 2'- and 3'-OHs through the steps of translation and examine the involvement of these critical functional groups.

Tri- and Tetranuclear Copper(II) Complexes Consisting of Mononuclear Cu(II) Chiral Building Blocks with a Sugar-Derived Schiff's Base Ligand

A new sugar-derived Schiff's base ligand N-(3-tert-butyl-2-hydroxybenzylidene)-4,6-O-ethylidene-beta-D-glucopyranosylamine (H3L1) has been developed which afforded the coordinatively labile, alcoholophilic trinuclear Cu(II) complex [Cu3(L1)2(CH3OH)(H2O)] (1). Complex 1 has been further used in the synthesis of a series of alcohol-bound complexes with a common formula of [Cu3(L1)2(ROH)2] (R = Me (2), Et (3), nPr (4), nBu (5), nOct (6)). X-ray structural analyses of complexes 2-6 revealed the collinearity of trinuclear copper(II) centers with Cu-Cu-Cu angles in the range of 166-172 degrees . The terminal and central coppers are bound with NO3 and O4 atoms, respectively, and exhibit square-planar geometry. The trinuclear structures of 2-6 can be viewed as the two {Cu(L1)}- fragments capture a copper(II) ion in the central position, which is further stabilized by a hydrogen-bonding interaction between the alcohol ligands and the sugar C-3 alkoxo group. Complex 2 exhibits a strong antiferromagnetic interaction between the Cu(II) ions (J = -238 cm(-1)). Diffusion of methanol into a solution of complex 1 in a chloroform/THF mixed solvent afforded the linear trinuclear complex [Cu(3)(L1)2(CH3OH)2(THF)2] (7). The basic structure of 7 is identical to complex 2; however, THF binding about the terminal coppers (Cu-O(THF) = 2.394(7) and 2.466(7) A) has introduced the square-pyramidal geometry, indicating that the planar trinuclear complexes 2-6 are coordinatively unsaturated and the terminal metal sites are responsible for further ligations. In the venture of proton-transfer reactions, a successful proton transfer onto the saccharide C-3 alkoxo group has been achieved using 4,6-O-ethylidene-d-glucopyranose, resulting in the self-assembled tetranuclear complex, [Cu4(HL1)4] (8), consisting of the mononuclear Cu(II) chiral building blocks, {Cu(HL1)}.

Substrate 2'-hydroxyl groups required for ribozyme-catalyzed polymerization

A polymerase ribozyme has been generated that uses nucleoside triphosphates to elongate an RNA primer by the successive addition of nucleotides complementary to an RNA template. Its polymerization is accurate, with an average error rate less than 3%, and it is general in terms of the sequence and the length of the primer and template RNAs. To begin to understand how the substrate contacts contribute to this accurate and general activity, we investigated which primer and template 2'-hydroxyl groups are involved in substrate recognition. We identified eight positions where 2'-deoxy substitutions can influence polymerization kinetics. All eight are within five nucleotides of the primer 3' terminus. Some, but not all, of the 2'-deoxy effects appear to be sequence dependent. These results begin to build a picture of how the polymerase ribozyme recognizes its substrates.

Ribozyme speed limits

The speed at which RNA molecules decompose is a critical determinant of many biological processes, including those directly involved in the storage and expression of genetic information. One mechanism for RNA cleavage involves internal phosphoester transfer, wherein the 2'-oxygen atom carries out an SN2-like nucleophilic attack on the adjacent phosphorus center (transesterification). In this article, we discuss fundamental principles of RNA transesterification and define a conceptual framework that can be used to assess the catalytic power of enzymes that cleave RNA. We deduce that certain ribozymes and deoxyribozymes, like their protein enzyme counterparts, can bring about enormous rate enhancements.

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

Understanding the chemical step in the catalytic reaction of DNA polymerases is essential for elucidating the molecular basis of the fidelity of DNA replication. The present work evaluates the free energy surface for the nucleotide transfer reaction of T7 polymerase by free energy perturbation/empirical valence bond (FEP/EVB) calculations. A key aspect of the enzyme simulation is a comparison of enzymatic free energy profiles with the corresponding reference reactions in water using the same computational methodology, thereby enabling a quantitative estimate for the free energy of the nucleotide insertion reaction. The reaction is driven by the FEP/EVB methodology between valence bond structures representing the reactant, pentacovalent intermediate, and the product states. This pathway corresponds to three microscopic chemical steps, deprotonation of the attacking group, a nucleophilic attack on the P(alpha) atom of the dNTP substrate, and departure of the leaving group. Three different mechanisms for the first microscopic step, the generation of the RO(-) nucleophile from the 3'-OH hydroxyl of the primer, are examined: (i) proton transfer to the bulk solvent, (ii) proton transfer to one of the ionic oxygens of the P(alpha) phosphate group, and (iii) proton transfer to the ionized Asp654 residue. The most favorable reaction mechanism in T7 pol is predicted to involve the proton transfer to Asp654. This finding sheds light on the long standing issue of the actual role of conserved aspartates. The structural preorganization that helps to catalyze the reaction is also considered and analyzed. The overall calculated mechanism consists of three subsequent steps with a similar activation free energy of about 12 kcal/mol. The similarity of the activation barriers of the three microscopic chemical steps indicates that the T7 polymerase may select against the incorrect dNTP substrate by raising any of these barriers. The relative height of these barriers comparing right and wrong dNTP substrates should therefore be a primary focus of future computational studies of the fidelity of DNA polymerases.

The pK(a) of the internucleotidic 2'-hydroxyl group in diribonucleoside (3'-->5') monophosphates

Ionization of the internucleotidic 2'-hydroxyl group in RNA facilitates transesterification reactions in Group I and II introns (splicing), hammerhead and hairpin ribozymes, self-cleavage in lariat-RNA, and leadzymes and tRNA processing by RNase P RNA, as well as in some RNA cleavage reactions promoted by ribonucleases. Earlier, the pK(a) of 2'-OH in mono- and diribonucleoside (3'-->5') monophosphates had been measured under various nonuniform conditions, which make their comparison difficult. This work overcomes this limitation by measuring the pK(a) values for internucleotidic 2'-OH of eight different diribonucleoside (3'-->5') monophosphates under a set of uniform noninvasive conditions by 1H NMR. Thus the pK(a) is 12.31 (+/-0.02) for ApG and 12.41 (+/-0.04) for ApA, 12.73 (+/-0.04) for GpG and 12.71 (+/-0.08) for GpA, 12.77 (+/-0.03) for CpG and 12.88 (+/-0.02) for CpA, and 12.76 (+/-0.03) for UpG and 12.70 (+/-0.03) for UpA. By comparing the pK(a)s of the respective 2'-OH of monomeric nucleoside 3'-ethyl phosphates with that of internucleotidic 2'-OH in corresponding diribonucleoside (3'-->5') monophosphates, it has been confirmed that the aglycons have no significant effect on the pK(a) values of their 2'-OH under our measurement condition, except for the internucleotidic 2'-OH of 9-adeninyl nucleotide at the 5'-end (ApA and ApG), which is more acidic by 0.3-0.4 pK(a) units.

Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups

The functional groups found among the RNA bases and in the phosphoribose backbone represent a limited repertoire from which to construct a ribozyme active site. This work investigates the possibility that simple RNA phosphodiester and hydroxyl functional groups could catalyze amide bond synthesis. Reaction of amine groups with activated esters would be catalyzed by a group that stabilizes the partial positive charge on the amine nucleophile in the transition state. 2'-Amine substitutions adjacent to 3'-phosphodiester or 3'-hydroxyl groups react efficiently with activated esters to form 2'-amide and peptide products. In contrast, analogs in which the 3'-phosphodiester is replaced by an uncharged phosphotriester or is constrained in a distal conformation react at least 100-fold more slowly. Similarly, a nucleoside in which the 3'-hydroxyl group is constrained trans to the 2'-amine is also unreactive. Catalysis of synthetic reactions by RNA phosphodiester and ribose hydroxyl groups is likely to be even greater in the context of a preorganized and solvent-excluding catalytic center. One such group is the 2'-hydroxyl of the ribosome-bound P-site adenosine substrate, which is close to the amine nucleophile in the peptidyl synthesis reaction. Given ubiquitous 2'-OH groups in RNA, there exists a decisive advantage for RNA over DNA in catalyzing reactions of biological significance.

Coordination properties of adenosine-5'-monophosphate and related ligands towards Me2Sn(IV)2+ in aqueous solution

The coordination of Me2Sn(IV)2+ to adenosine-5'-monophosphate (AMP) and the related compounds D-ribose-5-phosphate (R5P), D-glucose-1-phosphate (G1P) and D-glucose-6-phosphate (G6P) in aqueous solution was investigated by means of potentiometric titration, and 1H-, 31P-NMR and Mössbauer spectroscopic methods in the pH range 2-11 (I=0.1 M NaClO4, 298 K). The complex of AMP and Me2Sn(IV)2+ precipitated at low pH was characterised by elemental analysis, FT-IR and Mössbauer spectroscopic methods. From a comparison of the pK values obtained in the presence and absence of metal ion and the stability constants for the different systems, the coordination of [N] is excluded, while bidentate coordination of the phosphate group is presumed. Mössbauer spectroscopic measurements recorded in the glassy state confirmed bidentate coordination of the phosphate and the formation of mixed hydroxo complexes in the weakly acidic, neutral and strongly basic pH range. With increasing pH, the phosphate groups were replaced by the deprotonated alcoholic [O] atoms of the sugar moiety. The solid complex proved to be tbp structure with bidentate phosphate coordination.

Complexes of aluminium(III) with glucose-6-phosphate in aqueous solutions

The interaction of aluminium(III) with glucose-6-phosphate (GP: LH2) in aqueous solutions has been studied from pH 1 to pH 8, by pH-potentiometry and multinuclear (31P, 27Al, 13C) NMR spectroscopy. Various mononuclear species (MLH2, MLH, ML, ML2H, ML2 and MLH(-3)) and dinuclear complexes M2L2H-n (n=1-4) are formed in the system. NMR clearly indicates that GP is already bound to Al(III) at pH 1. The potentiometric speciation results are confirmed and completed by spectroscopic experiments. Many peaks are observed in the 31P NMR spectra suggesting the formation of isomeric species. An attempt to assign the signals to the corresponding complexes is made, allowing a discussion about their structure. Interestingly enough no metal ion-induced deprotonation and coordination of the alcoholic-OH functions have been observed.

The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction

BACKGROUND

The 2'-hydroxyl of U preceding the cleavage site, U(-1), in the Tetrahymena ribozyme reaction contributes 10(3)-fold to catalysis relative to a 2'-hydrogen atom. Previously proposed models for the catalytic role of this 2'-OH involve coordination of a catalytic metal ion and hydrogen-bond donation to the 3'-bridging oxygen. An additional model, hydrogen-bond donation by the 2'-OH to a nonbridging reactive phosphoryl oxygen, is also consistent with previous results. We have tested these models using atomic-level substrate modifications and kinetic and thermodynamic analyses.

RESULTS

Replacing the 2'-OH with -NH(3)(+) increases the reaction rate approximately 60-fold, despite the absence of lone-pair electrons on the 2'-NH(3)(+) group to coordinate a metal ion. Binding and reaction of a modified oligonucleotide substrate with 2'-NH(2) at U(-1) are unaffected by soft-metal ions. These results suggest that the 2'-OH of U(-1) does not interact with a metal ion. The contribution of the 2'-moiety of U(-1) is unperturbed by thio substitution at either of the nonbridging oxygens of the reactive phosphoryl group, providing no indication of a hydrogen bond between the 2'-OH and the nonbridging phosphoryl oxygens. In contrast, the 10(3)-fold catalytic advantage of 2'-OH relative to 2'-H is eliminated when the 3'-bridging oxygen is replaced by sulfur. As sulfur is a weaker hydrogen-bond acceptor than oxygen, this effect suggests a hydrogen-bonding interaction between the 2'-OH and the 3'-bridging oxygen.

CONCLUSIONS

These results provide the first experimental support for the model in which the 2'-OH of U(-1) donates a hydrogen bond to the neighboring 3'-bridging oxygen, thereby stabilizing the developing negative charge on the 3'-oxygen in the transition state.

Formation of a ternary complex between chitosan and ion pairs of strontium carbonate

This work deals essentially with the study of the interactions between chitosan and an alkaline-earth metal: 85Sr. We showed that addition of carbonate ions is necessary to observe this interaction, but only for pH values over 11. The use of an appropriate calculation software allowed us to determine the nature of the strontium ionic species present in solution. In order to understand the mechanism of interaction, the influence of various parameters on the complexation was studied. Thus, the interaction was maximum for a CO3(2-) concentration close to 10(-2) mol/l, the lowest ionic strength, the most expanded physical form (lyophilisate) and the lowest degree of acetylation of the polymer. We conclude to the formation of a ternary complex between the ion pair Sr2+ CO3(2-) and the amino groups of chitosan. We also showed the presence of interactions between chitosan and carbonate ions which hinder further interactions with strontium ions.