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Eric J Toone

Publications and source records attributed to Eric J Toone.

13 recordsLinked to original sources
PubMed2006

Mechanism of the Class I KDPG aldolase.

In vivo, 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible, stereospecific retro-aldol cleavage of KDPG to pyruvate and D-glyceraldehyde-3-phosphate. The enzyme is a lysine-dependent (Class I) aldolase that functions through the intermediacy of a Schiff base. Here, we propose a mechanism for this enzyme based on crystallographic studies of wild-type and mutant aldolases. The three dimensional structure of KDPG aldolase from the thermophile Thermotoga maritima was determined to 1.9A. The structure is the standard alpha/beta barrel observed for all Class I aldolases. At the active site Lys we observe clear density for a pyruvate Schiff base. Density for a sulfate ion bound in a conserved cluster of residues close to the Schiff base is also observed. We have also determined the structure of a mutant of Escherichia coli KDPG aldolase in which the proposed general acid/base catalyst has been removed (E45N). One subunit of the trimer contains density suggesting a trapped pyruvate carbinolamine intermediate. All three subunits contain a phosphate ion bound in a location effectively identical to that of the sulfate ion bound in the T. maritima enzyme. The sulfate and phosphate ions experimentally locate the putative phosphate binding site of the aldolase and, together with the position of the bound pyruvate, facilitate construction of a model for the full-length KDPG substrate complex. The model requires only minimal positional adjustments of the experimentally determined covalent intermediate and bound anion to accommodate full-length substrate. The model identifies the key catalytic residues of the protein and suggests important roles for two observable water molecules. The first water molecule remains bound to the enzyme during the entire catalytic cycle, shuttling protons between the catalytic glutamate and the substrate. The second water molecule arises from dehydration of the carbinolamine and serves as the nucleophilic water during hydrolysis of the enzyme-product Schiff base. The second water molecule may also mediate the base-catalyzed enolization required to form the carbon nucleophile, again bridging to the catalytic glutamate. Many aspects of this mechanism are observed in other Class I aldolases and suggest a mechanistically and, perhaps, evolutionarily related family of aldolases distinct from the N-acetylneuraminate lyase (NAL) family.

Aldehyde-Lyases↗
PubMed2005

Nitrosonium-catalyzed decomposition of s-nitrosothiols in solution: a theoretical and experimental study.

The decomposition of S-nitrosothiols (RSNO) in solution under oxidative conditions is significantly faster than can be accounted for by homolysis of the S-N bond. Here we propose a cationic chain mechanism in which nitrosation of nitrosothiol produces a nitrosated cation that, in turn, reacts with a second nitrosothiol to produce nitrosated disulfide and the NO dimer. The nitrosated disulfide acts as a source of nitrosonium for nitrosothiol nitrosation, completing the catalytic cycle. The mechanism accounts for several unexplained facets of nitrosothiol chemistry in solution, including the observation that the decomposition of an RSNO is accelerated by O(2), mixtures of O(2) and NO, and other oxidants, that decomposition is inhibited by thiols and other antioxidants, that decomposition is dependent on sulfur substitution, and that decomposition often shows nonintegral kinetic orders.

Catalysis↗
PubMed2005

A small-molecule inhibitor of isoprenylcysteine carboxyl methyltransferase with antitumor activity in cancer cells.

Many key regulatory proteins, including members of the Ras family of GTPases, are modified at their C terminus by a process termed prenylation. This processing is initiated by the addition of an isoprenoid lipid, and the proteins are further modified by a proteolytic event and methylation of the C-terminal prenylcysteine. Although the biological consequences of prenylation have been characterized extensively, the contributions of prenylcysteine methylation to the functions of the modified proteins are not well understood. This reaction is catalyzed by the enzyme isoprenylcysteine carboxyl methyltransferase (Icmt). Recent genetic disruption studies have provided strong evidence that blocking Icmt activity has profound consequences on oncogenic transformation. Here, we report the identification of a selective small-molecule inhibitor of Icmt, 2-[5-(3-methylphenyl)-1-octyl-1H-indol-3-yl]acetamide (cysmethynil). Cysmethynil treatment results in inhibition of cell growth in an Icmt-dependent fashion, demonstrating mechanism-based activity of the compound. Treatment of cancer cells with cysmethynil results in mislocalization of Ras and impaired epidermal growth factor signaling. In a human colon cancer cell line, cysmethynil treatment blocks anchorage-independent growth, and this effect is reversed by overexpression of Icmt. These findings provide a compelling rationale for development of Icmt inhibitors as another approach to anticancer drug development.

Acetamides↗
PubMed2005

C-nitroso compounds: synthesis, physicochemical properties and biological activities.

Because of the chemical and physical properties of nitric oxide, its effective use and delivery for therapeutic application represents a significant challenge. Accordingly, current understanding of nitric oxide biology largely stems from the use of nitric oxide prodrugs and adducts whose biological activities are based on their ability to release nitric oxide or a redox-related species. Among the structurally diverse ensemble of nitric oxide donor compounds reported to date are the C-nitroso compounds. These compounds have only recently been investigated with respect to their potential as nitric oxide donors, although they have been known and studied for over 120 years. Here, we consider the synthesis and physico-chemical properties of the C-nitroso compounds and the available data regarding their biological activities. Synthetic methods reviewed include direct substitution of H by NO, oxidative approaches, and the addition of various oxides of nitrogen across multiple bonds. The electronic spectra of C-nitroso compounds and the mechanism and thermodynamics of monomer-dimer equilibration are described. The physico-chemical and biological properties of two related classes of compounds, the diazetine dioxides and the furoxans, are also described.

Animals↗
PubMed2004

A bacterial selection for the directed evolution of pyruvate aldolases.

A novel bacterial in vivo selection for pyruvate aldolase activity is described. Pyruvate kinase deficient cells, which lack the ability to biosynthetically generate pyruvate, require supplementation of exogenous pyruvate when grown on ribose. Supplementation with pyruvate concentrations as low as 50 microM rescues cell growth. A known substrate of the KDPG aldolases, 2-keto-4-hydroxy-4-(2'-pyridyl)butyrate (KHPB), also rescues cell growth, consistent with retroaldol cleavage by KDPG aldolase and rescue through pyruvate release. An initial round of selection against 2-keto-4-hydroxyoctonate (KHO), a nonsubstrate for wild-type aldolase, produced three mutants with intriguing alterations in protein sequence. This selection system allows rapid screening of mutant enzyme libraries and facilitates the discovery of enzymes with novel substrate specificities.

Aldehyde-Lyases↗
PubMed2003

Solid-phase synthesis for the identification of high-affinity bivalent lectin ligands.

The development of carbohydrate-based therapeutics has been frustrated by the low affinities that characterize protein-carbohydrate complexation. Because of the oligomeric nature of most lectins, the use of multivalency may offer a successful strategy for the creation of high-affinity ligands. The solid-phase evaluation of libraries of peptide-linked multivalent ligands facilitates rapid examination of a large fraction of linker structure space. If such solid-phase assays are to replicate solution binding behavior, the potential for intermolecular bivalent binding on bead surfaces must be eliminated. Here we report the solid-phase synthesis and analysis of peptide-linked, spatially segregated mono- and bivalent ligands for the legume lectin concanavalin A. Bead shaving protocols were used for the creation of beads displaying spatially segregated binding sequences on the surface of Tentagel resins. The same ligands were also synthesized on PEGA resin to determine the effect of ligand presentation on solid-phase binding. While we set out to determine the lower limit of assay sensitivity, the unexpected observation that intermolecular bivalent ligand binding is enhanced for bivalent ligands relative to monovalent ligands allowed direct observation of the level of surface blocking required to prevent intermolecular bivalent ligand binding. For a protein with binding sites separated by 65 A, approximately 99.9% of Tentagel(1) surface sites and 99.99% of the total sites on a PEGA bead must be blocked to prevent intermolecular bivalent binding. We also report agglutination and calorimetric solution-phase binding studies of mono- and bivalent peptide-linked ligands.

Amino Acid Sequence↗
PubMed2003

Additivity and the physical basis of multivalency effects: a thermodynamic investigation of the calcium EDTA interaction.

To better understand the origin of multivalency effects in ligand binding, the binding of a series of mono-, bi-, tri- and tetravalent carboxylate ligands to Ca(II) was examined by isothermal titration calorimetry (ITC). The data are inconsistent with an entropic origin of enhanced affinity, but rather show that at least in this instance the multivalency effect is enthalpic in origin. Analysis of binding data using the Jencks model shows the addition of incremental carboxylate "ligands" produces an unfavorable interaction entropy that is more than offset by a strongly favorable interaction enthalpy. The most likely source of this interaction enthalpy is the relief of repulsive Coulombic interactions in the unbound state. The conformational entropy penalty arising from the restriction of flexible dihedrals is negligible, within experimental error. On the other hand, an enthalpic contribution from linker restriction contributes strongly to the overall thermodynamics of ligand binding. Together, these data suggest that enthalpic effects dominate ligand binding, and design strategies should seek to optimize these interactions. The incorporation of unfavorable interactions in the unbound ligand that are relieved during binding provides an important mechanism by which to enhance ligand affinities.

Calcium↗
PubMed2003

Nitroxyl disulfides, novel intermediates in transnitrosation reactions.

A novel anionic RSN(O)SR species, the intermediate in transnitrosation reactions, was explored computationally with B3LYP and CBS-QB3 methods. The species resembles a nitroxyl coordinated to a highly distorted disulfide, and it differs significantly from intermediates in nucleophilic acyl substitution. Reactions of the following species were computed for comparison: MeS(-) + MeSNO; MeO(-) + MeONO; MeS(-) + MeSCHO; MeO(-) + MeOCHO. The last two have very different intermediates from the first two. Mass spectrometric experimental evidence is presented that is consistent with the formation of a nitroxyl disulfide in the gas phase. The calculated proton affinity and redox potentials of the intermediate are also reported.

Disulfides↗
PubMed2002

Cloning, isolation and characterization of the Thermotoga maritima KDPG aldolase.

The Thermotoga maritima aldolase gene has been cloned into a T7 expression vector and overexpressed in Escherichia coli. The preparation yields 470 UL(-1) of enzyme at a specific activity of 9.4 U mg(-1). During retroaldol cleavage of KDPG, the enzyme shows a k(cat) that decreases with decreasing temperature. A more than offsetting decrease in K(m) yields an enzyme that is more efficient at 40 degrees C than at 70 degrees C. The substrate specificity of the enzyme was evaluated in the synthetic direction with a range of aldehyde substrates. Although the protein shows considerable structural homology to KDPG aldolases from mesophilic sources, significant differences in substrate specificity exist. A preparative scale reaction between 2-pyridine carboxaldehyde and pyruvate provided product of the same absolute configuration as mesophilic enzymes, but with diminished stereoselectivity.

Aldehyde-Lyases↗
PubMed2002

The decomposition of thionitrites.

The mechanism of thionitrite decomposition, both in vivo and in vitro, remains unclear. Thionitrite stability is highly variable; it is a complex function of thionitrite structure and environmental condition. Several recent advances clarify the role of unimolecular homlytic decomposition, metal-catalyzed reductive decomposition and higher-order enzymatic and non-enzymatic processes to the overall observed stability of thionitrites.

Aldehyde Oxidoreductases↗
PubMedDate not supplied

Binding of warfarin influences the acid-base equilibrium of H242 in sudlow site I of human serum albumin.

Sudlow Site I of human serum albumin (HSA) is located in subdomain IIA of the protein and serves as a binding cavity for a variety of ligands. In this study, the binding of warfarin (W) is examined using computational techniques and isothermal titration calorimetry (ITC). The structure of the docked warfarin anion (W-) to Site I is similar to that revealed by X-ray crystallography, with a calculated binding constant of 5.8 x 10(5) M(-1). ITC experiments (pH 7.13 and I = 0.1) carried out in three different buffers (MOPs, phosphate and Tris) reveal binding of W- is accompanied by uptake of 0.30+/-0.02 protons from the solvent. This measurement suggests that the binding of W- is stabilized by an ion-pair interaction between protonated H242 and the phenoxide group of W-.

Acid-Base Equilibrium↗