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PubMed1996

The influence of sub-optimal protein nutrition on insulin hypersecretion evoked by high-energy/high-fat feeding in rats.

Low (8%) protein feeding during pregnancy impairs the functional development of the fetal endocrine pancreas. Continued low-protein feeding post-natally decreases pancreatic insulin content and secretion, whereas transfer to standard diet evoked beta-cell recuperation. Glucose-stimulated insulin secretion (GSIS) and insulin action were examined in vivo at 28 days after transfer from 8% protein diet to a high-energy/high-fat/standard (20%)-protein diet (HEF diet). HEF feeding dramatically enhanced GSIS after intravenous glucose in control rats, but not in rats previously maintained on the low-protein diet. However, glucose disappearance after intravenous glucose, and glucose production and whole-body glucose disposal during euglycaemic-hyperinsulinaemic clamps were unaffected by prior protein malnutrition. In conclusion, impaired insulin secretion after protein malnutrition is exacerbated by high-energy/high-fat feeding, but this response is not linked to enhanced whole-body insulin resistance.

Animal Nutritional Physiological Phenomena↗

PubMed1991

Ab initio calculations of the pyrophosphate hydrolysis reaction.

Ab initio quantum mechanical calculations were used to study the hydrolysis reaction H4P2O7 + H2O in equilibrium with 2H3PO4, as well as some molecular properties of the reactants and products. SCF calculations with several basis sets ranging from minimal to extended with polarization functions were used to look at the basis dependency of the reaction enthalpies and optimized geometries. Although the minimal basis sets yield erratic predictions of the enthalpy, when a more extended basis (3-21G*) was used for the geometry optimization, and the total energies of the reactants and products were computed with this and larger basis sets, we obtained more consistent predictions of the structural properties of the P-O-P bridge and of the heat of the hydrolysis reaction (delta E = -7.39 kcal/mol at the SCF/6-31G** level). A comparison is made with previous estimates performed with smaller basis sets and without taking into account the electron correlation effects, which are calculated in the present work. The inclusion of the zero point energy calculated using the harmonic approximation, and of the electronic correlation energy determined at the MBPT(2) level, raised the computed heat of the reaction to -3.83 kcal/mol, and when an estimate for the thermal energy was added, the value obtained was of -3.38 kcal/mol. In conclusion, we found that the hydrolysis of pyrophosphate should be exothermic in the gas phase. The implications of this result in relation to some recent theories about enzyme catalysis are discussed.

Diphosphates↗

PubMed1990

Improved dose homogeneity in electron arc therapy achieved by a multiple-energy technique.

Improved dose homogeneity throughout the treatment volume defined for electron arc therapy is achieved through superposition of multiple arcs of different electron energy to the same treatment surface. The relative weights for each arc segment and energy are determined by computer optimization which minimizes the variation in radial depth dose across the treatment volume. In addition to the standard electron beam energies of 6 MeV, 9 MeV, 12 MeV, 16 MeV and 20 MeV, a new electron arc field is created by adding bolus to the treatment surface during an additional pass using 6 MeV electrons. This modified field, having maximum dose on the patient surface and a reduced range, supplements the dose delivered by the standard electron arc fields in the buildup region. Through use of this multiple-energy technique, depending on clinical indications, electron arc therapy can be planned and delivered to allow either skin sparing or a uniform dose from the patient's surface to the desired treatment depth.

Electrons↗

PubMed2004

A theoretical study of the conformational behavior of analogues of alpha-L-rhamnose-1-phosphate.

The conformational behavior of methyl(2-O-methyl-alpha-L-rhamnopyranosyl)phosphate, together with a group of potentially more stable analogues, was investigated through a DFT approach at the B3LYP/6-31G(d) level; the energy of all the optimized structures was recalculated using a continuum solvent model, C-PCM, choosing water as the solvent. The compounds exhibited several, sometimes tenths of populated conformations so that the overall properties of flexibility and mobility were evaluated. The analogue in which the pyranose oxygen atom is replaced by a methylene group emerges as the best candidate as a mimic of the reference 1-phosphate, in spite of the fact that it lacks the anomeric and exo-anomeric effects. The other analogues result poorer mimics because of a conformational equilibrium at the pyranose ring or of an excessive rigidity of the aglycone moiety.

Carbohydrate Conformation↗

PubMed2006

Conformational evaluation and detailed 1H and 13C NMR assignments of flavoxate, a urinary tract antispasmodic agent.

1H and 13C NMR chemical shift assignments for the urinary tract antispasmodic flavoxate (1) and flavoxate hydrochloride (2) were obtained from one- and two-dimensional measurements. A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing DFT calculations at the B3LYP/6-31G* level, and a Boltzmann analysis of the total energies, provided accurate molecular models which describe the conformational behavior of flavoxate (1). The electron density surfaces for the global minimum and the second minimum conformers 1a and 1b of this L-type Ca2+ channel inhibitor were calculated. The presence of both conformers in solution was demonstrated in full agreement with 2D NOESY data and NOE difference spectroscopy.

Computer Simulation↗

PubMed1994

Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques.

There is a growing body of low-resolution structural data that can be utilized to devise structural models for large RNAs and ribonucleoproteins. These models are routinely built manually. We introduce an automated refinement protocol to utilize such data for building low-resolution three-dimensional models using the tools of molecular mechanics. In addition to specifying the positions of each nucleotide, the protocol provides quantitative estimates of the uncertainties in those positions, i.e., the resolution of the model. In typical applications, the resolution of the models is about 10-20 A. Our method uses reduced representations and allows us to refine three-dimensional structures of systems as big as the 16S and 23S ribosomal RNAs, which are about one to two orders of magnitude larger than nucleic acids that can be examined by traditional all-atom modeling methods. Nonatomic resolution structural data--secondary structure, chemical cross-links, chemical and enzymatic footprinting patterns, protein positions, solvent accessibility, and so on--are combined with known motifs in RNA structure to predict low-resolution models of large RNAs. These structural constraints are imposed on the RNA chain using molecular mechanics-type potential functions with parameters based on the quality of experimental data. Surface potential functions are used to incorporate shape and positional data from electron microscopy image reconstruction experiments into our models. The structures are optimized using techniques of energy refinement to get RNA folding patterns. In addition to providing a consensus model, the method finds the range of models consistent with the data, which allows quantitative evaluation of the resolution of the model. The method also identifies conflicts in the experimental data. Although our protocol is aimed at much larger RNAs, we illustrate these techniques using the tRNA structure as an example and test-bed.

Anticodon↗

PubMed2000

A theoretical approach to the mechanism of biological oxidation of organophosphorus pesticides.

Organophosphorus pesticides are the most common classes involved in poisonings related to pesticides. We used enzymatic activity of chloroperoxidase on the metabolism of some phosphorothioate pesticides published previously and molecular mechanics methods to perform a theoretical approach of the mechanism of biological oxidation of this class of pesticides. The molecular structure of eight pesticides were optimized by molecular mechanics methods using the CAChe program package for biomolecules, ver. 3.11 (Oxford Molecular Ltd., Campbell, CA). Total energy resulted from the structure optimization process and the partial charges of both phosphorus and sulfur were computed for every pesticide. Phosphorus partial charge and enzymatic activity were significantly related by linear regression analysis (r=0.82, P<0.05). Analyzing our results and using previously reported enzymatic activity of chloroperoxidase on these pesticides, we deduced chemical events involved in activation of the active site of chloroperoxidase and proposed a novel mechanism of oxidation for this class of pesticides. This mechanism will also help to understand the oxidation process of pesticides by cytochrome P450, and production of toxic metabolites.

Chemical Phenomena↗

PubMed2003

Addition of side chains to a known backbone with defined side-chain centroids.

An automatic procedure is proposed for adding side chains to a protein backbone; it is based on optimization of a simplified energy function for peptide side chains, given its backbone and positions of side-chain centroids. The energy is expressed as a sum of the energies of interaction between side chains, and a harmonic penalty function accounting for the preservation of the positions of the C(alpha) atoms and the side-chain centroids. The energy of side-chain interactions is calculated with the soft-sphere ECEPP/3 potential. A Monte Carlo search is carried out to explore all possible side-chain orientations within a fixed backbone and side-chain centroid positions. The initial, usually extended, side-chain conformations are taken directly from the ECEPP/3 database. The procedure was tested on six experimental (X-ray or NMR) structures: immunoglobulin binding protein (PDB code 1IGD, an alpha+beta-protein); transcription factor PML (PDB code 1BOR, a 49-104 fragment of the ring finger domain, predominantly beta-protein); bovine pancreatic trypsin inhibitor (crystal form II) (PDB code 1BPI, an alpha+beta-protein); the monomer of human deoxyhemoglobin (PDB code 1BZ0, an alpha-helical structure); chain A of alcohol dehydrogenase from Drosophila lebanonensis (PDB code 1A4U); as well as on the 10-55 portion of the B domain of staphylococcal protein A (PDB code 1BDD). In all cases except 1BPI, the data for the algorithm (i.e. the backbone or C(alpha) coordinates and the positions of side-chain centroids) were taken from the experimental structures. For protein A, the C(alpha) coordinates and positions of side-chain centroids were also taken from the 1.9-A-resolution model predicted by the UNRES force field. In all comparisons with experimental structures, complete side-chain geometry was reconstructed with a root-mean-square (RMS) deviation of approximately 0.6-0.9 A from the heavy atoms when complete backbone and side-chain-centroid coordinates were used in reconstruction, or approximately 1.0 A when the C(alpha) and centroid coordinates were used.

Algorithms↗

PubMed1999

Stabilization of cellobiase by covalent coupling to soluble polysaccharide.

Cellobiase from Aspergillus niger was glycosylated by covalent coupling to cyanogen bromide activated dextran. The conjugated enzyme retained 62% of the original specific activity exhibited by the native cellobiase. The optimum pH as well as the pH stability of the conjugated form remain almost the same as for the native enzyme. Compared to the native enzyme, the conjugated form exhibited a higher optimal reaction temperature and energy of activation, a higher K(m) (Michaelis constant) and lower Vmax (maximal reaction rate), and improved thermal stability. The thermal deactivation of the native and conjugated cellobiase obeyed the first-order kinetics. The calculated half-life values of heat inactivation at 60, 70 and 80 degrees C was 10.7, 6.25, and 4.05 h, respectively, whereas at these temperatures the native enzyme was less stable (half-life of 3.5, 1.69, and 0.83 h, respectively). The deactivation rate constant at 80 degrees C for the conjugated cellobiase is about 7.9 x 10(-2) h-1, which is lower than that of the native enzyme (36.0 x 10(-2) h-1). The activation energy for denaturation of the native enzyme is about 10.58 kcal/mol, which is 7.25 kcal/mol lower than that of the conjugated enzyme. The effect of different surfactants and some metal ions on the activity of the conjugated cellobiase has been investigated.

Enzyme Stability↗

PubMed2003

The Xplor-NIH NMR molecular structure determination package.

We announce the availability of the Xplor-NIH software package for NMR biomolecular structure determination. This package consists of the pre-existing XPLOR program, along with many NMR-specific extensions developed at the NIH. In addition to many features which have been developed over the last 20 years, the Xplor-NIH package contains an interface with a new programmatic framework written in C++. This interface currently supports the general purpose scripting languages Python and TCL, enabling rapid development of new tools, such as new potential energy terms and new optimization methods. Support for these scripting languages also facilitates interaction with existing external programs for structure analysis, structure manipulation, visualization, and spectral analysis.

Molecular Structure↗

PubMed2001

Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'.

Plants, like other organisms, have developed mechanisms that allow them to sense and respond to changes in levels of carbon and nitrogen metabolites. These mechanisms, in turn, regulate the expression of genes and the activities of proteins involved in C and N transport and metabolism, allowing plants to optimize the use of energy resources. Recent studies, which have involved molecular-genetic, genomic, and cell biological approaches, have begun to uncover the signals and components of C:N sensing and signaling mechanisms in plants. For sugar sensing, analysis of Arabidopsis mutants has revealed intersections with hormone and nitrogen signaling. For nitrogen sensing/signaling, recent progress has identified transcriptional and posttranslational mechanisms of regulation. In all, a complex picture is emerging in which C:N signaling systems are subject to a 'matrix effect' in which downstream responses are dependent upon cell-type, developmental, metabolic, and/or environmental conditions.

Anion Transport Proteins↗

PubMed2006

Tandem parallel fragmentation of peptides for mass spectrometry.

Parallel fragmentations of peptides in the source region and in the collision cell of tandem mass spectrometers are sequentially combined to develop parallel collision-induced-dissociation mass spectrometry (p2CID MS). Compared to MS/MS spectra, the p2CID mass spectra show increased signal intensities (2-400-fold) and number of sequence ions. This improvement is attributed to the fact that p2CID MS virtually samples all the ions generated by electrospray ionization, including intact and fragment ions of different charge states from a peptide. We implement the method using a quadrupole time-of-flight tandem mass spectrometer. The instrument is operated in TOF-MS mode that allows the ions from source region broadband-passing the first mass analyzer to enter the collision cell. Cone voltage and collision energy are investigated to optimize the outcome of the two parallel CID processes. In the in-source parallel CID, elevated cone voltage produces singly charged intact peptide ions and large fragment ions, as well as decreases the charge-state distribution of peptide ions mainly to double and single charges. The in-collision-cell parallel CID is optimized to dissociate the ions from the source region to produce small and medium fragment ions. The method of p2CID MS is especially useful for sequencing of large peptides with labile amide bonds and peptides with C-terminal arginine. It has unique potential for de novo sequencing of peptides and proteome analysis, especially for affinity-enriched subproteomes.

Dynorphins↗

PubMed1996

Detection of radionuclides in capillary electrophoresis using a phosphor-imaging detector.

A capillary electrophoresis (CE) postcolumn radionuclide detector has been developed that uses a commercial phosphor-imaging detector and has been optimized for low-energy beta emitters. Eluant from the separation capillary is deposited on a membrane. Emission from radioactive analytes on the membrane is integrated using the phosphor-imaging system for 10-72 h. Results from the phosphor-imaging system are converted to conventional electropherograms. Modifications to a prior postcolumn CE deposition system have been accomplished by adding a buffer makeup capillary; this increases the electrolyte pH range and improves reproducibility. The limit of detection (LOD) for 35S-labeled analytes is 0.13 amol (8.7 pM or 0.007 Bq), while the LOD for 32P-labeled analytes is 4.9 zmol (0.33 pM or 0.002 Bq), with a linear range for 35S-Met from 1.5 amol to 1.5 fmol.

Animals↗

PubMed1988

Solution-state structure of the Dewar pyrimidinone photoproduct of thymidylyl-(3'----5')-thymidine.

The preparation, spectroscopic investigation, structure determination, conformational analysis, and modeling of the Dewar pyrimidinone photoproduct of thymidylyl-(3'----5')-thymidine, previously referred to as TpT3 [Johns, H. E., Pearson, M. L., LeBlanc, J. C., & Heilleiner, C. W. (1964) J. Mol. Biol. 9, 503-524], is described. TpT3 was prepared in quantitative yield by photolysis of an aqueous solution of the (6-4) photoproduct of TpT with Pyrex-filtered medium-pressure mercury arc light. TpT3 was analyzed by FAB MS, IR, UV, and 1H, 13C, and 31P NMR spectroscopy. The spectroscopic data led to the conclusion that TpT3 results from the photoisomerization of the pyrimidinone ring of the (6-4) product of TpT to its Dewar valence isomer. Torsion angle and interproton distance information derived from coupling constants and NOE data was used to constrain ring conformation searches by utilizing the SYBYL molecular modeling program subroutine SEARCH. Sets of angles derived from the ring search procedure were then used to construct structures whose geometries were optimized by the energy-minimization subroutine MAXIMIN. A two-state model for the solution-state structure of the Dewar photoproduct was chosen which was energetically sound, fit the experimental coupling constants with an RMS deviation of 1.15 Hz, and was consistent with the NOE data. The model for the Dewar photoproduct was compared to a model for the (6-4) photoproduct and the TpT subunits of the Dickerson dodecamer structure by a least-squares fitting procedure. It was concluded that the Dewar photoproduct more closely resembles a B-form TpT unit than does the (6-4) photoproduct.

Chromatography, High Pressure Liquid↗

PubMedDate not supplied

FLAME: a program to flexibly align molecules.

Herein, we describe a method to flexibly align molecules (FLAME = FLexibly Align MolEcules). FLAME aligns two molecules by first finding maximum common pharmacophores between them using a genetic algorithm. The resulting alignments are then subjected to simultaneous optimizations of their internal energies and an alignment score. The utility of the method in pairwise alignment, multiple molecule flexible alignment, and database searching was examined. For pairwise alignment, two carboxypeptidase ligands (Protein Data Bank codes and ), two estrogen receptor ligands ( and ), and two thrombin ligands ( and ) were used as test sets. Alignments generated by FLAME starting from CONCORD structures compared very well to the X-ray structures (average root-mean-square deviation = 0.36 A) even without further minimization in the presence of the protein. For multiple flexible alignments, five structurally diverse D3 receptor ligands were used as a test set. The FLAME alignment automatically identified three common pharmacophores: a base, a hydrogen-bond acceptor, and a hydrophobe/aromatic ring. The best alignment was then used to search the MDDR database. The search results were compared to the results using atom pair and Daylight fingerprint similarity. A similar database search comparison was also performed using estrogen receptor modulators. In both cases, hits identified by FLAME were structurally more diverse compared to those from the atom pair and Daylight fingerprint methods.

Journal Article↗

PubMed2004

Are gas-phase reactions of five-coordinate divalent metal ion complexes affected by coordination geometry?

Five-coordinate metal complex ions of the type [ML](2+) [where M = Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II) and L= 1,9-bis(2-pyridyl)-2,5,8-triazanonane (DIEN-(pyr)(2)) and 1,9-bis(2-imidazolyl)-2,5,8-triazanonane (DIEN-(imi)(2)] have been reacted with acetonitrile in the gas phase using a modified quadrupole ion trap mass spectrometer. The kinetics and thermodynamics of these reactions show that the reactivity of these complexes is affected by metal electronic structure and falls into three groups: Mn(II) and Ni(II) complexes are the most reactive, Fe(II) and Co(II) complexes exhibit intermediate reactivity, and Cu(II) and Zn(II) complexes are the least reactive. To help explain the experimental trends in reactivity, theoretical calculations have been used. Due to the relatively large size of the metal complexes involved, we have utilized a two-layered ONIOM method to perform geometry optimizations and single point energy calculations for the [ML](2+) and [ML + CH(3)CN](2+) systems. The calculations show that the reactant five-coordinate complexes ([ML](2+)) exhibit structures that are slightly distorted trigonal bipyramidal geometries, while the six-coordinate complexes ([ML + CH(3)CN](2+)) have geometries that are close to octahedral. The Delta G values obtained from the ONIOM calculations roughly agree with the experimental data, but the calculations fail to completely explain the trends for the different metal complexes. The failure to consider all possible isomers as well as adequately represent pi-d interactions for the metal complexes is the likely cause of this discrepancy. Using the angular overlap model (AOM) to obtain molecular orbital stabilization energies (MOSE) also fails to reproduce the experimental trends when only sigma interactions are considered but succeeds in explaining the trends when pi interactions are taken into account. These results indicate that the pi-donor character of the CH(3)CN plays a subtle, yet important, role in controlling the reactivity of these five-coordinate complexes. Also, the AOM calculations are consistent with the experimental data when the [ML](2+) complexes have high-spin trigonal bipyramidal configurations. Generally, these results suggest that ion-molecule reactions can be very sensitive to metal complex coordination geometry and thus may have some promise for providing gas-phase coordination structure.

Journal Article↗

PubMed2006

Periodic density functional theory investigation of the uranyl ion sorption on the TiO2 rutile (110) face.

Periodic density functional theory calculations have been performed in order to study the uranyl ion sorption on the TiO2 rutile (110) face. From experimental measurements, two uranyl surface complexes have been observed and the two corresponding sorption sites have been identified. However, from a crystallographic point of view, three different sorption sites can be considered on this face. The corresponding three surface bidentate complexes were modeled and optimized, and their relative energies were calculated. Only 5 kJ/mol separates the two most stable structures, which correspond to the experimental ones. The third surface complex is nearly 10 kJ/mol less stable, in agreement with the fact that it was not observed experimentally.

Journal Article↗

PubMed1997

Ab Initio and Experimental Studies on the Structure and Relative Stability of the cis-Hydride-eta(2)-Dihydrogen Complexes [{P(CH(2)CH(2)PPh(2))(3)}M(H)(eta(2)-H(2))](+) (M = Fe, Ru).

Ab initio calculations (DMOL method) including the estimate of the total energy and the full optimization of the geometrical parameters have been used to study the electronic structures and the coordination geometries of the model systems [{P(CH(2)CH(2)PH(2))(3)}M(H)(L)](+) (M = Fe, L = H(2), C(2)H(4), CO, N(2); M = Ru, L = H(2)). Single crystal X-ray analyses have been carried out on the complexes [(PP(3))Fe(H)(eta(2)-H(2))]BPh(4).0.5THF (1.0.5THF), [(PP(3))Fe(H)(CO)]BPh(4).THF (3.THF), and [(PP(3))Ru(H)(eta(2)-H(2))]BPh(4).0.5THF (5.0.5THF) [PP(3) = P(CH(2)CH(2)PPh(2))(3)]. Crystal data: for 1.0.5THF, triclinic P1 (No. 2), a = 17.626(3) Å, b = 14.605(3) Å, c = 12.824(4) Å, alpha = 90.09(2) degrees, beta = 103.87(2) degrees, gamma = 107.46(2) degrees, Z = 2, R = 0.082; for 3.THF, triclinic P1 (No. 2), a = 12.717(2) Å, b = 14.553(1) Å, c = 17.816(2) Å, alpha = 72.90(1) degrees, beta = 76.82(2) degrees, gamma = 89.71(1) degrees, Z = 2, R = 0.067; for 5.0.5THF, monoclinic P2/1a (No. 14), a = 19.490(5) Å, b = 19.438(2) Å, c = 16.873(5) Å, beta = 110.96(2) degrees, Z = 4, R = 0.074. On the basis of theoretical calculations, X-ray analyses, and multinuclear NMR studies, all of the complexes of the formula [(PP(3))M(H)(L)]BPh(4) [M = Fe, L = H(2) (1), C(2)H(4) (2), CO (3), N(2) (4); M = Ru, L = H(2) (5), C(2)H(4) (6)] are assigned a distorted octahedral structure where the hydride (trans to a terminal phosphorus donor) and the L ligand occupy mutually cis positions. The theoretical calculations indicate that the H(2) ligand in the eta(2)-dihydrogen-hydride derivatives 1 and 5 is placed in the P-M-H plane (parallel orientation) and that there is an attractive interaction between the H and H(2) ligands. XPS measurements, performed on the iron complexes, show that the Fe --> L back-bonding interaction plays a leading role in 3. It is concluded that the stronger metal-H(2) bond in the dihydrogen-hydride complex 1, as compared to the Ru analog 5, is due to the greater d(metal) --> sigma(H-H) back-donation as well as a more efficient interaction between the terminal hydride and an H of the dihydrogen ligand. This cis effect is suggested to contribute to the relative stability of the iron complexes, which increases in the order C(2)H(4) < N(2) < H(2) < CO.

Journal Article↗