Thermodynamics of boroxine formation from the aliphatic boronic acid monomers R-B(OH)2 (R = H, H3C, H2N, HO, and F): a computational investigation.

Boroxines are the six-membered cyclotrimeric dehydration products of organoboronic acids, 3R–B(OH)2 → R3B3O3 + 3H2O, and in recent years have emerged as a useful class of organoboron molecules with applications in organic synthesis both as reagents and catalysts, as structural components in boronic-acid-derived pharmaceutical agents, and as anion acceptors and electrolyte additives for battery materials [Korich, A. L.; Iovine, P.

Structural basis for the stability of a thermophilic methionine adenosyltransferase against guanidinium chloride.

The methionine adenosyltransferase from the thermophile Methanococcus jannaschii is fully and irreversibly unfolded in the presence of guanidinium chloride. Unfolding of this dimeric protein is a three-state process in which a dimeric intermediate could be identified. The less stable secondary structural elements of the protein are the C-terminal ends of β-strands E2 and E6, as deduced from the behavior of tyrosine to tryptophan mutants at residues 72 and 170, which are located in the subunit interface.

Computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, Using H2O and H2O2.

We report results from a computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, using H2O and H2O2 as the reactive oxygen species (ROS) to yield aminomethanol, H2N-CH2-OH; these results complement our study on the protodeboronation of boroglycine to produce methylamine, H2N-CH3 (Larkin et al. J. Phys.

Discovery of novel types of inhibitors of S-adenosylmethionine synthesis by virtual screening.

S-adenosylmethionine (AdoMet) lies at an intersection of nucleotide and amino acid metabolism and performs a multitude of metabolic functions. AdoMet formation is catalyzed by S-adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase (MAT)), which is a target for development of anticancer and antimicrobial agents. High affinity MAT inhibitors have been found through computational docking of more than 200000 compounds for predicted binding to the crystallographically defined nucleotide binding region of the enzyme's active site.

An investigation of the catalytic mechanism of S-adenosylmethionine synthetase by QM/MM calculations.

Catalysis by S-adenosylmethionine synthetase has been investigated by quantum mechanical/molecular mechanical calculations, exploiting structures of the active crystalline enzyme. The transition state energy of +19.1 kcal/mol computed for a nucleophilic attack of the methionyl sulfur on carbon-5' of the nucleotide was indistinguishable from the experimental (solution) value when the QM residues were an uncharged histidine that hydrogen bonds to the leaving oxygen-5' and an aspartate that chelates a Mg2+ ion, and was similar (+18.

Subunit association as the stabilizing determinant for archaeal methionine adenosyltransferases.

Archaea contain a class of methionine adenosyltransferases (MATs) that exhibit substantially higher stability than their mesophilic counterparts. Their sequences are highly divergent, but preserve the essential active site motifs of the family. We have investigated the origin of this increased stability using chemical denaturation experiments on Methanococcus jannaschii MAT (Mj-MAT) and mutants containing single tryptophans in place of tyrosine residues.

A regulatory role of the Bateman domain of IMP dehydrogenase in adenylate nucleotide biosynthesis.

The Bateman domain (CBS subdomain) of IMP dehydrogenase (IMPDH), a rate-limiting enzyme of the de novo GMP biosynthesis, is evolutionarily conserved but has no established function. Deletion of the Bateman domain has no effect on the in vitro IMPDH activity. We report that in vivo deletion of the Bateman domain of IMPDH in Escherichia coli (guaB(DeltaCBS)) sensitizes the bacterium to growth arrest by adenosine and inosine.

A computational characterization of boron-oxygen multiple bonding in HN=CH-CH=CH-NH-BO.

Structures, relative energies, and bonding characteristics for various conformers of 3-imino-N-(oxoboryl)prop-1-en-1-amine, HN=CH-CH=CH-NH-BO, and the corresponding borocycle (-HN=CH-CH=CH-NH-B-)O are discussed using results from second-order Møller-Plesset (MP2) perturbation theory with the Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, and cc-pVTZ basis sets. These MP2 results are compared to those from computationally efficient density functional theory (DFT) calculations using the LDA, PBE, TPSS, BLYP, B3LYP, BVP86, OLYP, O3LYP, and PBE1PBE functionals in conjunction with the economical Pople-type 6-311++G(d,p) basis set to evaluate the suitability of these DFT/6-311++G(d,p) levels for use with larger boron-containing systems. The effects of an aqueous environment were incorporated into the calculations using COSMO methodology.

Shape shifting leads to small-molecule allosteric drug discovery.

Enzymes that regulate their activity by modulating an equilibrium of alternate, nonadditive, functionally distinct oligomeric assemblies (morpheeins) constitute a recently described mode of allostery. The oligomeric equilibrium for porphobilinogen synthase (PBGS) consists of high-activity octamers, low-activity hexamers, and two dimer conformations. A phylogenetically diverse allosteric site specific to hexamers is proposed as an inhibitor binding site.

The CBS subdomain of inosine 5'-monophosphate dehydrogenase regulates purine nucleotide turnover.

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyses the rate-limiting step in guanine nucleotide biosynthesis. IMPDH has an evolutionary conserved CBS subdomain of unknown function. The subdomain can be deleted without impairing the in vitro IMPDH catalytic activity and is the site for mutations associated with human retinitis pigmentosa.

Dimers of boroglycine and methylamine boronic acid: a computational comparison of the relative importance of dative versus hydrogen bonding.

Boronic acids are widely used in materials science, pharmacology, and the synthesis of biologically active compounds. In this Article, geometrical structures and relative energies of dimers of boroglycine, H2N-CH2-B(OH)2, and its constitutional isomer H3C-NH-B(OH)2, were computed using second-order Møller-Plesset perturbation theory and density functional theory; Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the MP2 calculations, and the Pople 6-311++G(d,p) basis set was employed for a majority of the DFT calculations. Effects of an aqueous environment were incorporated into the results using PCM and COSMO-RS methodology.

A computational investigation of the geometrical structure and protodeboronation of boroglycine, H2N-CH2-B(OH)2.

In this article the geometrical structure of the simple, achiral, alpha-amino boronic acid boroglycine, H2N-CH2-B(OH)2, was investigated using density functional theory (DFT), second-order Møller-Plesset (MP2) perturbation theory, and coupled cluster methodology with single- and double-excitations (CCSD); the effects of an aqueous environment were incorporated into the results by using a few explicit water molecules and/or self-consistent reaction field (SCRF) calculations with the IEF polarizable continuum model (PCM). Neutral reaction mechanisms were investigated for the direct protodeboronation (hydrolysis) of boroglycine (H2O+H2N-CH2-B(OH)2-->B(OH)3+H2N-CH3), for which DeltaH degrees 298 was -21.9 kcal/mol at the MP2(FC)/aug-cc-pVDZ level, and for the 1,2-carbon-to-nitrogen shift of the -B(OH)2 moiety (H2N-CH2-B(OH)2-->H3C-NH-B(OH)2), for which the corresponding value of DeltaH degrees 298 was -18.

Metal ion activation of S-adenosylmethionine decarboxylase reflects cation charge density.

S-Adenosylmethionine decarboxylase from Escherichia coli is a pyruvoyl cofactor-containing enzyme that requires a metal cation for activity. We have found that the enzyme is activated by cations of varying charge and ionic radius, such as Li+, A13+, Tb3+, and Eu3+, as well as the divalent cations Mg2+, Mn2+, and Ca2+. All of the activating cations provide kcat values within 30-fold of one another, showing that the charge of the cation does not greatly influence the rate-limiting step for decarboxylase turnover.

Structure of the boronic acid dimer and the relative stabilities of its conformers.

Despite the widespread use of boronic acids in materials science and as pharmaceutical agents, many aspects of their structure and reactivity are not well understood. In this research the boronic acid dimer, [HB(OH)(2)](2), was studied by second-order Møller-Plesset (MP2) perturbation theory and coupled cluster methodology with single and double excitations (CCSD). Pople split-valence 6-31+G*, 6-311G**, and 6-311++G** and Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the calculations.

Structural studies of inhibition of S-adenosylmethionine synthetase by slow, tight-binding intermediate and product analogues.

S-Adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase) catalyzes a two-step reaction in which tripolyphosphate (PPPi) is a tightly bound intermediate. Diimidotriphosphate (O(3)P-NH-PO(2)-NH-PO(3); PNPNP), a non-hydrolyzable analogue of PPPi, is the most potent known inhibitor of AdoMet synthetase with a K(i) of 2 nM. The structural basis for the slow, tight-binding inhibition by PNPNP has been investigated by spectroscopic methods.

Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of S-adenosylmethionine synthesis from ATP and Met.

S-Adenosylmethionine synthetase (MAT) catalyzes formation of S-adenosylmethionine (SAM) from ATP and l-methionine (Met) and hydrolysis of tripolyphosphate to PP(i) and P(i). Escherichia coli MAT (eMAT) has been crystallized with the ATP analogue AMPPNP and Met, and the crystal structure has been determined at 2.5 A resolution.

Catalytic properties of the archaeal S-adenosylmethionine decarboxylase from Methanococcus jannaschii.

S-Adenosylmethionine decarboxylase (AdoMetDC) is a pyruvoyl cofactor-dependent enzyme that participates in polyamine biosynthesis. AdoMetDC from the Archaea Methanococcus jannaschii is a prototype for a recently discovered class that is not homologous to the eucaryotic enzymes or to a distinct group of microbial enzymes. M.

Methylthioadenosine phosphorylase regulates ornithine decarboxylase by production of downstream metabolites.

The gene encoding methylthioadenosine phosphorylase (MTAP), the initial enzyme in the methionine salvage pathway, is deleted in a variety of human tumors and acts as a tumor suppressor gene in cell culture (Christopher, S. A., Diegelman, P.

Conformational dynamics of the active site loop of S-adenosylmethionine synthetase illuminated by site-directed spin labeling.

S-adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase, methionine adenosyltransferase, a.k.a.

The arrangement of first- and second-shell water molecules in trivalent aluminum complexes: results from density functional theory and structural crystallography.

The structural and energetic features of a variety of gas-phase aluminum ion hydrates containing up to 18 water molecules have been studied computationally using density functional theory. Comparisons are made with experimental data from neutron diffraction studies of aluminum-containing crystal structures listed in the Cambridge Structural Database. Computational studies indicate that the hexahydrated structure Al[H(2)O](6)(3+) (with symmetry T(h)()), in which all six water molecules are located in the innermost coordination shell, is lower in energy than that of Al[H(2)O](5)(3+).

The active site loop of S-adenosylmethionine synthetase modulates catalytic efficiency.

Crystallographic studies of Escherichia coli S-adenosylmethionine synthetase (ATP:L-methionine S-adenosyltransferase, MAT) have defined a flexible polypeptide loop that can gate access to the active site without contacting the substrates. The influence of the length and sequence of this active site loop on catalytic efficiency has been characterized in a mutant in which the E. coli MAT sequence (DRADPLEQ) has been replaced with the distinct sequence of the corresponding region of the otherwise highly homologous rat liver enzyme (HDLRNEEDV).

S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group.

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes with proteins.

Enzymatic properties of S-adenosylmethionine synthetase from the archaeon Methanococcus jannaschii.

S-Adenosylmethionine synthetase (ATP:l-methionine S-adenosyltransferase, MAT) catalyzes a unique enzymatic reaction that leads to formation of the primary biological alkylating agent. MAT from the hyperthermophilic archaeon Methanococcus jannaschii (MjMAT) is a prototype of the newly discovered archaeal class of MAT proteins that are nearly unrecognizable in sequence when compared with the class that encompasses both the eucaryal and bacterial enzymes. In this study the functional properties of purified recombinant MjMAT have been evaluated.