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Metabolomics may have the capacity to revolutionize disease diagnosis through the identification of scores of metabolites that vary during environmental, pathogenic, or toxicological insult. NMR spectroscopy has become one of the main tools for measuring these changes since an NMR spectrum can accurately identify metabolites and their concentrations. The predominant approach in analyzing NMR data has been through the technique of spectral binning. However, identification of spectral areas in an NMR spectrum is insufficient for diagnostic evaluation, since it is unknown whether areas of interest are strictly caused by metabolic changes or are simply artifacts. In this paper, we explore differences in gender, diurnal variation, and age in a human population. We use the example of gender differences to compare traditional spectral binning techniques (NMR spectral areas) to novel targeted profiling techniques (metabolites and their concentrations). We show that targeted profiling produces robust models, generates accurate metabolite concentration data, and provides data that can be used to help understand metabolic differences in a healthy population. Metabolites relating to mitochondrial energy metabolism were found to differentiate gender and age. Dietary components and some metabolites related to circadian rhythms were found to differentiate time of day urine collection. The mechanisms by which these differences arise will be key to the discovery of new diagnostic tests and new understandings of the mechanism of disease.

Pseudomonas fluorescens strain KU-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-NBA) via the formation of 3-hydroxyanthranilate (3-HAA), a known antioxidant and reductant. The initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-HAA are catalyzed by a NADPH-dependent 2-NBA nitroreductase (NbaA) and 2-hydroxylaminobenzoate mutase (NbaB), respectively. The 216-amino-acid protein NbaA is 78% identical to a plasmid-encoded hypothetical conserved protein of Polaromonas strain JS666; structurally, it belongs to the homodimeric NADH:flavin mononucleotide (FMN) oxidoreductase-like fold family. Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. Mutational analysis supports the roles of Asn40, Asp76, and Glu113, which are predicted to form the binding site for a divalent metal ion implicated in FMN binding, and a role in NADPH binding for the 10-residue insertion in the [beta]5-[alpha]2 loop. The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g., Pseudomonas putida strain TW3. Coexpression of nbaB with nbaA in Escherichia coli produced a small amount of 3-HAA from 2-NBA, supporting the functionality of the nbaB gene. We also showed by gene knockout and chemotaxis assays that nbaY, a chemoreceptor NahY homolog located downstream of the nbaA gene, is responsible for strain KU-7 being attracted to 2-NBA. NbaY is the first chemoreceptor in nitroaromatic metabolism to be identified, and this study completes the gene elucidation of 2-NBA metabolism that is localized within a 24-kb chromosomal locus of strain KU-7. doi:10.1128/JB.01098-06

The equilibrium geometries at 54 small molecules containing linear or near-linear N-H..N bonds (sample M) are optimized at the MP2/6-31G(d,p) level and the values of p' and p' of the parameters p(sub c) at the bond-critical points(p' in the N-H, p' in the H..N bond) are compounded from the results of the optimizations.

The equilibrium geometries of the isoelectronic Z[Ph.sup.0, [+ or -] 1.sub.4] (Z = B, C, N) molecules have been optimized, in [S.sub.4] and [D.sub.2d] symmetries, at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels, with the phenyl rings constrained to be planar. The ground-state conformations of all three species are shown to be of [S.sub.4] symmetry, but the difference of the energies of the [S.sub.4] and the [D.sub.2d] conformations is estimated to amount to only ~1 kcal [mol.sup.-1], with a barrier to concerted rotational reorientation of the phenyl rings of ~5.0 kcal [mol.sup.-1] for B[Ph.sup.1.sub.4], ~6.4 kcal [mol.sup.-1] for C[Ph.sub.4], and ~7.9 kcal [mol.sup.-1] for N[Ph.sup.+.sub.4]. A redetermination of the crystal structure of C[Ph.sub.4] from -60[degrees]C X-ray data agrees with the results of previous determinations at ambient temperature; the C[Ph.sub.4] molecule in the crystal is slightly compressed along the [S.sub.4] axis relative to the free molecule, otherwise the geometries of the two are essentially the same. Correlations between the optimized geometric parameters of the Z[Ph.sup.0, [+ or -] 1.sub.4] molecules have been examined and analyzed in detail, as have the substitution-induced changes in the geometry of the phenyl ring. The results confirm and strengthen the conclusions from the statistical studies by Domenicano et al. on the geometry of benzene rings monosubstituted by atoms of elements from the first row of the Periodic system. Key words: tetraphenylborate, tetraphenylmethane, tetraphenylammonium, ab initio molecular geometries.

A study of the proline-catalyzed direct aldol reaction between acetone and acetaldehyde using density functional theory is presented. The results show that the aldol reaction between acetone and acetaldehyde, in which proline acts as an enzyme mimic illustrates the potential of small organic molecules to act as chiral catalysts in asymmetric synthesis and the complementary nature of theoretical calculations.

Trends exhibited in distance relationships and properties at the bond critical point (BCP) in linear or non-linear N-H...N hydrogen bonds are investigated by optimizing geometry of such bonds in a large number of suitable simple chemical species at the RHF/6-31G** level. Results obtained for several experimental parameters are discussed in detail along with the implications of the findings.

Research into the aminolysis of 6-chloropyrimidine and 2-amino-6-chloropyrimidine is presented. This work shows the significance of a well-selected proton acceptor and the catalytic possibilities connected with the formation of multiple hydrogen bonds.

Density functional theory was used to study the effects of hydrogen bonding on the aminolysis of 6-chloropyrimidine.

The cis-trans isomerization of N-acetylproline methylamide is investigated by using density functional theory. The study demonstrates the important role the intramolecular N... HN hydrogen bond plays in the cis-trans isomerization of proline-containing molecules and the catalytic possibilities of hydrogen bonding.

The equilibrium geometries of the isoelectronic ZPh[sub 4] [sup 0, ±1] (Z = B, C, N) molecules have been optimized, in S[sub 4] and D[sub 2] [sub d] symmetries, at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels, with the phenyl rings constrained to be planar. The ground-state conformations of all three species are shown to be of S[sub 4] symmetry, but the difference of the energies of the S[sub 4] and the D[sub 2] [sub d] conformations is estimated to amount to only ~1 kcal mol[sup –1] , with a barrier to concerted rotational reorientation of the phenyl rings of ~5.0 kcal mol[sup –1] for BPh[sup –] [sub 4] , ~6.4 kcal mol[sup –1] for CPh[sub 4] , and ~7.9 kcal mol[sup –1] for NPh[sup +] [sub 4] . A redetermination of the crystal structure of CPh[sub 4] from –60°C X-ray data agrees with the results of previous determinations at ambient temperature; the CPh[sub 4] molecule in the crystal is slightly compressed along the S[sub 4] axis relative to the free molecule, otherwise the geometries of the two are essentially the same. Correlations between the optimized geometric parameters of the ZPh[sub 4] [sup 0, ±1] molecules have been examined and analyzed in detail, as have the substitution-induced changes in the geometry of the phenyl ring. The results confirm and strengthen the conclusions from the statistical studies by Domenicano et al. on the geometry of benzene rings monosubstituted by atoms of elements from the first row of the Periodic system.Key words: tetraphenylborate, tetraphenylmethane, tetraphenylammonium, ab initio molecular geometries.Opérant au niveau HF/6-31G(d,p) et B3LYP/6-31G(d,p) de la théorie et en contraignant les noyaux phényles à être plans, on a optimisé les géométries à l'équilibre des molécules isoélectroniques ZPh[sub 4] [sup 0, ±1] (Z = B, C, N) dans les symétries S[sub 4] et D[sub 2d] . On démontre que les conformations des trois espèces à l'état fondamental sont de symétrie S[sub 4] ; toutefois, on a évalué que la différence d'énergie entre les conformations S[sub 4] et D[sub 2d] n'est que d'environ 1 kcal mol[sup –1] alors que la barrière à la réorientation rotationnelle des noyaux phényles d'environ 5,0 kcal mol[sup –1] pour le BPh[sup –] [sub 4] , d'environ 6,4 kcal mol[sup –1] pour le CPh[sub 4] et d'environ 7,9 kcal mol[sup –1] pour le NPh[sup +] [sub 4] . Une redétermination de la structure cristalline du CPh[sub 4] à partir de données de rayons X obtenues à –60°C est en accord avec les déterminations antérieures à la température ambiante; par rapport à la molécule libre, la molécule de CPh[sub 4] dans le cristal est légèrement comprimée le long de l'axe S[sub 4] , mais autrement les géométries des deux sont essentiellement les mêmes. On a examiné les corrélations entre les paramètres géométriques optimisés des molécules de ZPh[sub 4] [sup 0, ±1] et on les a analysées en détail comme on l'a fait pour les changements dans la géométrie du noyau phényle induits par une substitution. Les résultats confirment et renforcent les conclusions obtenues par les études statistiques de Domenicano et ses collaborateurs sur les géométries des noyaux benzéniques monosubstitués par des atomes d'éléments de la première rangée du tableau périodique.Mots clés : tétraphénylborate, tétraphénylméthane, tétraphénylammonium, géométries moléculaires ab initio.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Pseudomonas fluorescens strain KU-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-NBA) via the formation of 3-hydroxyanthranilate (3-HAA), a known antioxidant and reductant. The initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-HAA are catalyzed by a NADPH-dependent 2-NBA nitroreductase (NbaA) and 2-hydroxylaminobenzoate mutase (NbaB), respectively. The 216-amino-acid protein NbaA is 78% identical to a plasmid-encoded hypothetical conserved protein of Polaromonas strain JS666; structurally, it belongs to the homodimeric NADH:flavin mononucleotide (FMN) oxidoreductase-like fold family. Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. Mutational analysis supports the roles of Asn40, Asp76, and Glu113, which are predicted to form the binding site for a divalent metal ion implicated in FMN binding, and a role in NADPH binding for the 10-residue insertion in the β5-α2 loop. The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g., Pseudomonas putida strain TW3. Coexpression of nbaB with nbaA in Escherichia coli produced a small amount of 3-HAA from 2-NBA, supporting the functionality of the nbaB gene. We also showed by gene knockout and chemotaxis assays that nbaY, a chemoreceptor NahY homolog located downstream of the nbaA gene, is responsible for strain KU-7 being attracted to 2-NBA. NbaY is the first chemoreceptor in nitroaromatic metabolism to be identified, and this study completes the gene elucidation of 2-NBA metabolism that is localized within a 24-kb chromosomal locus of strain KU-7. [ABSTRACT FROM AUTHOR]

Objective: To identify risk factors for loss to cardiology follow-up among children and young adults with congenital heart disease., Methods: We used a matched case-control design. Cases were born before January, 2001 with moderate or complex congenital heart disease and were previously followed up in the paediatric or adult cardiology clinic, but not seen for 3 years or longer. Controls had been seen within 3 years. Controls were matched 3:1 to cases by year of birth and congenital heart disease lesion. Medical records were reviewed for potential risk factors for loss to follow-up. A subset of cases and controls participated in recorded telephone interviews., Results: A total of 74 cases (66% male) were compared with 222 controls (61% male). A history of missed cardiology appointments was predictive of loss to follow-up for 3 years or longer (odds ratio 13.0, 95% confidence interval 3.3-51.7). Variables protective from loss to follow-up were higher family income (odds ratio 0.87 per $10,000 increase, 0.77-0.98), cardiac catheterisation within 5 years (odds ratio 0.2, 95% confidence interval 0.1-0.6), and chart documentation of the need for cardiology follow-up (odds ratio 0.4, 95% confidence interval 0.2-0.8). Cases lacked awareness of the importance of follow-up and identified primary care physicians as their primary source of information about the heart, rather than cardiologists. Unlike cases, controls had methods to remember appointments., Conclusions: A history of one or more missed cardiology appointments predicted loss to follow-up for 3 or more years, as did lack of awareness of the need for follow-up. Higher family income, recent catheterisations, and medical record documentation of the need for follow-up were protective.

We present a binding free energy function that consists of force field terms supplemented by solvation terms. We used this function to calibrate the solvation model along with the binding interaction terms in a self-consistent manner. The motivation for this approach was that the solute dielectric-constant dependence of calculated hydration gas-to-water transfer free energies is markedly different from that of binding free energies (J. Comput. Chem. 2003, 24, 954). Hence, we sought to calibrate directly the solvation terms in the context of a binding calculation. The five parameters of the model were systematically scanned to best reproduce the absolute binding free energies for a set of 99 protein-ligand complexes. We obtained a mean unsigned error of 1.29 kcal/mol for the predicted absolute binding affinity in a parameter space that was fairly shallow near the optimum. The lowest errors were obtained with solute dielectric values of Din = 20 or higher and scaling of the intermolecular van der Waals interaction energy by factors ranging from 0.03 to 0.15. The high apparent Din and strong van der Waals scaling may reflect the anticorrelation of the change in solvated potential energy and configurational entropy, that is, enthalpy-entropy compensation in ligand binding (Biophys. J. 2004, 87, 3035-3049). Five variations of preparing the protein-ligand data set were explored in order to examine the effect of energy refinement and the presence of bound water on the calculated results. We find that retaining water in the final protein structure used for calculating the binding free energy is not necessary to obtain good results; that is the continuum solvation model is sufficient. Virtual screening enrichment studies on estrogen receptor and thymidine kinase showed a good ability of the binding free energy function to recover true hits in a collection of decoys.