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PubMed2006

Improvement of graft function and animal survival by fat emulsion in liver transplant rats.

Nutritional supports are required for liver transplant patients. However, no systematical assessment has been made of the optimal composition of energy yielding substrates in these patients. This study is to evaluate whether mixed energy system consisting of carbohydrate and lipid emulsions is more advantageous over single energy source of glucose for nutritional support in liver transplant recipients and whether structured lipid emulsion (STG) is superior to medium-chain triglyceride/long-chain triglycerides (MCT/LCT) and long-chain triglycerides (LCT) using a total parenteral nutrition model. Liver transplant rats were randomly divided to four groups according to the energy source, i.e. glucose (GLU), MCT/LCT, STG and LCT groups. Sham operated rats served as control. Hepatic function and lipid profile were determined to investigate the roles of lipid emulsion in hepatic function and lipid metabolism. Morphological changes of liver were observed, and nitrogen balance was determined. The results showed that infusion of lipid emulsion was well tolerated. The 1-week survival rate in the lipid emulsion groups was significantly higher than in the GLU group (100% versus 50%, P<0.05); compared with the GLU group, hepatic function recovered quickly and returned to normal level, and morphological alterations were less severer in the lipid emulsion groups, especially in the STG group; the lipid emulsions groups had normal serum TG and TC levels, especially STG and MCT/LCT groups; the lipid emulsions groups achieved a positive nitrogen balance on day 7 compared with the GLU group, and the STG group had the highest nitrogen balance. In conclusion, lipid emulsion is beneficial in improving hepatic function and the recipients' survival and does not influence the lipid metabolism. Mixed energy system consisting of carbohydrate and lipid is more advantageous over single energy source of glucose after liver transplantation, and STG is superior to MCT/LCT and LCT.

Animals↗

PubMed2004

Quantitative analysis of [Dmt(1)]DALDA in ovine plasma by capillary liquid chromatography-nanospray ion-trap mass spectrometry.

The synthetic opioid peptide analog Dmt-D-Arg-Phe-Lys-NH(2) ([Dmt(1)]DALDA; [Dmt= 2',6'-dimethyltyrosine) is a highly potent and selective mu opioid-receptor agonist. A very sensitive and robust capillary liquid chromatography/nanospray ion-trap (IT) mass spectrometry method has been developed to quantify [Dmt(1)]DALDA in ovine plasma, using deuterated [Dmt(1)]DALDA as the internal standard. The standard MS/MS spectra of d(0)- and d(5)-[Dmt(1)]DALDA were obtained, and the collision energy was experimentally optimized to 25%. The product ion [ M + 2H-NH(3)](2+) (m/z 312.2) was used to identify and to quantify the synthetic opioid peptide analog in ovine plasma samples. The MS/MS detection sensitivity for [Dmt(1)]DALDA was 625 amol. A calibration curve was constructed, and quantitative analysis was performed on a series of ovine plasma samples.

Animals↗

PubMed2006

CRF and stress in fish.

The endocrine stress response is pivotal in vertebrate physiology. The stress hormone cortisol-the end product of the endocrine stress axis-(re-)directs energy flows for optimal performance under conditions where homeostasis may be or become at risk. Key players in the continuous adaptation process are corticotropin-releasing factor (CRF) from the hypothalamic nucleus preopticus (NPO), pituitary adrenocorticotropic hormone (ACTH) and cortisol produced by the interrenal cells in the headkidney (adrenal equivalent of fish). CRF is a member of a large family of related peptides that signals through CRF-receptor subtypes specific for central and peripheral actions of the peptide. CRF is "chaperoned" by a unique and phylogenetically very well-conserved binding protein (CRFBP); the functions of the CRFBP can only be speculated on so far, but its mRNA and protein abundance are important indicators of the central CRF-system activity, and indeed its mRNA levels are altered by restraint stress. Moreover, the unique structure and size of the CRFBP provide good tools in phylogenetic studies, that date the CRF-system to at least one billion years old. Pro-opiomelanocortin is produced and processed to ACTH and endorphin in the hypothalamic NPO and pituitary pars distalis ACTH-cells, to MSH and acetylated endorphins in the pituitary pars intermedia MSH-cells. ACTH is the prime corticotrope in acute stress conditions. In carp, MSH, considered a mild corticotrope in chronic stress responses in other fish, lacks corticotropic effects (in line with the absence of the melanocortin-5 receptor in headkidney); yet, an unknown corticotropic signal substance in the pars intermedia of carp awaits elucidation. Interesting observations were made on the CRF control of pituitary cells. CRF stimulates ACTH-cells, but only when these cells experience a mild dopaminergic block. Endorphin, produced in the NPO and transported via axons to the pituitary gland in vivo, reverses the stimulatory CRF action on MSH-cells to a differential inhibition of N-acetyl beta-endorphin release in vitro (MSH release is not affected). We speculate that the consistently observed elevation of plasma MSH during chronic stress may exert central actions related to feeding and leptin regulated processes. A BOLD-fMRI study revealed the functional anatomy of the stress response at work in a paradigm, where carp were exposed to a sudden water temperature drop. In carp (and other fish), the endocrine stress axis is already operational in very early life stages, viz., around hatching and comprises hypothalamic, pituitary, and interrenal signaling to adjust the physiology of the hatchling to its dynamically changing environment. Understanding of stress during early life stages is critical as the consequent rises in cortisol may have long lasting effects on survival and fish quality.

Animals↗

PubMed2002

Metal ion-induced lateral aggregation of filamentous viruses fd and M13.

We report a detailed comparison between calculations of inter-filament interactions based on Monte-Carlo simulations and experimental features of lateral aggregation of bacteriophages fd and M13 induced by a number of divalent metal ions. The general findings are consistent with the polyelectrolyte nature of the virus filaments and confirm that the solution electrostatics account for most of the experimental features observed. One particularly interesting discovery is resolubilization for bundles of either fd or M13 viruses when the concentration of the bundle-inducing metal ion Mg(2+) or Ca(2+) is increased to large (>100 mM) values. In the range of Mg(2+) or Ca(2+) concentrations where large bundles of the virus filaments are formed, the optimal attractive interaction energy between the virus filaments is estimated to be on the order of 0.01 kT per net charge on the virus surface when a recent analytical prediction to the experimentally defined conditions of resolubilization is applied. We also observed qualitatively distinct behavior between the alkali-earth metal ions and the divalent transition metal ions in their action on the charged viruses. The understanding of metal ions-induced reversible aggregation based on solution electrostatics may lead to potential applications in molecular biology and medicine.

Bacteriophage M13↗

PubMed2001

Structure-activity relationships in the deacetylation of O-glucosides of N-hydroxy-N-arylacylamides by mammalian liver microsomes.

Structure-activity relationships in the deacylation of O-glucosides of N-hydroxy-N-aryl-acylamides were investigated to provide insights into the metabolic activation of carcinogenic/mutagenic O-glycosides of N-hydroxy-N-arylacylamides. In the subcellular fractions obtained from porcine liver, the deacetylation activity toward O-glucoside of N-hydroxyacetanilide (GAc) was mainly localized in the microsomes. Both the 2-chloro (2ClGAc) and 2-methyl (2MeGAc) derivatives of GAc were not deacetylated by the microsomes. Other compounds having either 3- or 4-substituent (chloro or methyl), however, were deacetylated and showed higher V(max)/K(m) values than that of GAc. 4-Methyl derivative (4MeGAc) was shown to competitively inhibit the deacetylation activity toward GAc, and the K(i) value of 4MeGAc was comparable with its K(m) value obtained in the microsome-catalyzed deacetylation. These apparent K(m) values were shown to correspond to their lipophilicities estimated from retention times on high-performance liquid chromatography (HPLC). As for the effect of acyl groups, the order of V(max)/K(m) values was N-propionyl derivative (GPr)>GAc>N-butyryl derivative (GBu). From the optimized structures and energy levels of the frontier orbitals of these compounds, calculated by the semi-empirical AM1 method, the effects of 2-substituents and acyl groups on the deacetylation activity is thought to be due to a steric factor. From the energy levels of the frontier orbitals of GAc and its 3- or 4-substituted derivatives, the compound having a lower level of LUMO was shown to be deacetylated effectively. There were marked species differences in the microsomal deacetylation activity toward GAc, and the highest activity was found in the rabbit, followed by the porcine, hamster, rat and then bovine liver microsomes.

Aniline Compounds↗

PubMed1988

The perfection of substrate-channelling in interacting enzyme systems: energetics and evolution.

Some implications of substrate channelling in interacting enzyme systems are considered, with regard to the energetics and evolution of enzyme action. The transient time, a key analytical parameter relating to the phenomenon of channelling, is the basis of our kinetic study. Bounds on the kinetics of multienzyme complexes are established using (apparent) rate constants emanating from the transient-time formulation of coupled reactions. From a transition state representation of the rate process, it is shown how dynamically and statically organized enzyme systems lead to the modification of current ideas on the evolutionary optimization of the energy profile of enzyme catalysis in situ.

Biological Evolution↗

PubMed1996

Use of computational fluid dynamics in the design of surgical procedures: application to the study of competitive flows in cavo-pulmonary connections.

Computational fluid dynamic methods based on a finite-element technique were applied to the study of (1) competition of flows in the inferior and superior venae cavae in total cavopulmonary connection, and (2) competition between flow in the superior vena cava and forward flow from a stenosed pulmonary artery in bidirectional cavopulmonary anastomosis. Models corresponding to various degrees of offsetting and shape of the inferior vena caval anastomosis were simulated to evaluate energy dissipation and flow distribution between the two lungs. A minimal energy loss with optimal flow distribution between the two lungs was obtained by enlarging the inferior vena caval anastomosis toward the right pulmonary artery. This modified technique of total cavopulmonary connection is described. A computational model of the operation was developed in an attempt to understand the mechanisms of postoperative failure. In tight pulmonary artery stenosis (75%), the pulsatile forward flow is primarily directed to the left pulmonary artery, with little influence on superior vena caval pressure and the right pulmonary artery. Pulsatile forward flows corresponding to 15%, 30%, 45%, and 60% of the systemic artery output increased the mean pulmonary artery and superior vena caval pressures by 1, 1.7, 2.4, and 3.6 mm Hg, respectively. Although the modeling studies were not able to determine the cause of postoperative failure, they emphasize the impact of local geometry on flow dynamics. More simulations are required for further investigation of the problem.

Anastomosis, Surgical↗

PubMed2003

Insertion of X-ray structures of proteins in membranes.

Few structures of membrane proteins are known and their relationships with the membrane are unclear. In a previous report, 20 X-ray structures of transmembrane proteins were analyzed in silico for their orientation in a 36A-thick membrane [J. Mol. Graph. Model. 20 (2001) 235]. In this paper, we use the same approach to analyze how the insertion of the X-ray structures varies with the bilayer thickness. The protein structures are kept constant and, at each membrane thickness, the protein is allowed to tilt and rotate in order to accommodate at their best. The conditions are said to be optimal when the energy of insertion is minimal. The results show that most helix bundles require thicker membranes than porin barrels. Moreover, in a few instances, the ideal membrane thickness is unrealistic with respect to natural membranes supporting that the X-ray structure requires adaptation to stabilize in membrane. For instance, the squalene cyclase could adapt by bending the side chains of its ring of lysine and arginine in order to increase the hydrophobic surface in contact with membranes. We analyzed the distribution of amino acids in the water, interface and acyl chain layers of the membrane and compared with the literature.

Carrier Proteins↗

PubMed2000

Genetics of the metabolic syndrome.

The clustering of cardiovascular risk factors such as abdominal obesity, hypertension, dyslipidaemia and glucose intolerance in the same persons has been called the metabolic or insulin-resistance syndrome. In 1998 WHO proposed a unifying definition for the syndrome and chose to call it the metabolic syndrome rather than the insulin-resistance syndrome. Although insulin resistance has been considered as a common denominator for the different components of the syndrome, there is still debate as to whether it is pathogenically involved in all of the different components of the syndrome. Clustering of the syndrome in families suggests a genetic component. It is plausible that so-called thrifty genes, which have ensured optimal storage of energy during periods of fasting, could contribute to the phenotype of the metabolic syndrome. Common variants in a number of candidate genes influencing fat and glucose metabolism can probably, together with environmental triggers, increase susceptibility to the syndrome. Among these, the genes for beta 3-adrenergic receptor, hormone-sensitive lipase, lipoprotein lipase, IRS-1, PC-1, skeletal muscle glycogen synthase, etc. appear to increase the risk of the metabolic syndrome. In addition, novel genes may be identified by genome-wide searches.

Carrier Proteins↗

PubMed2003

Modeling anhydrous and aqua copper(II) amino acid complexes: a new molecular mechanics force field parametrization based on quantum chemical studies and experimental crystal data.

This paper presents the vacuum structures of aquacopper(II) bis(amino acid) complexes with glycine, sarcosine, N,N-dimethylglycine, and N-tert-butyl-N-methylglycine estimated using the B3LYP method. The differences between the B3LYP vacuum structures and experimental crystal structures suggested considerable influence of crystal lattice packing effects on the changes in the complexes' geometries. A previously developed molecular mechanics force field for modeling anhydrous copper(II) amino acidates was reoptimized to simulate these changes and predict the properties of both trans and cis anhydrous and aqua copper(II) amino acid complexes. The modeling included experimental molecular and crystal structures of 13 anhydrous and 10 aqua copper(II) amino acidates with the same atom types (Cu(II), C, H, N, and O) but various copper(II) coordination polyhedron geometries, crystal symmetries, and intermolecular interactions. The empirical parameters of the selected potential energy functions were optimized on the B3LYP vacuum copper(II) coordination geometries of three anhydrous copper(II) amino acidates and on experimental crystalline internal coordinates and unit cell dimensions of six anhydrous and six aqua copper(II) amino acid complexes. The respective equilibrium structures were calculated in vacuo and in simulated crystalline environment. The efficacy of the final force field, FFW, was examined. The total root-mean-square deviations between the experimental and theoretical crystal values were 0.018 A in the bond lengths, 2.2 degrees in the valence angles, 5.5 degrees in the torsion angles, and 0.395 A in the unit cell lengths. FFW reproduced the unit cell volumes in the range from -8.1 to 9.6%. The means of Cu to axial water oxygen distances were 2.4 +/- 0.1 A (experiment) and 2.6 +/- 0.1 A (FFW). This paper describes the ability of the molecular mechanics model and FFW force field to simulate the flexibility of the metal coordination polyhedron. The new force field proved effective in predicting the most stable molecular conformation of copper(II) amino acidato systems in vacuo.

Journal Article↗

PubMed2006

Catalytic mechanism of dopamine beta-monooxygenase mediated by Cu(III)-oxo.

Mechanisms of dopamine hydroxylation by the Cu(II)-superoxo species and the Cu(III)-oxo species of dopamine beta-monooxygenase (DBM) are discussed using QM/MM calculations for a whole-enzyme model of 4700 atoms. A calculated activation barrier for the hydrogen-atom abstraction by the Cu(II)-superoxo species is 23.1 kcal/mol, while that of the Cu(III)-oxo, which can be viewed as Cu(II)-O*, is 5.4 kcal/mol. Energies of the optimized radical intermediate in the superoxo- and oxo-mediated pathways are 18.4 and -14.2 kcal/mol, relative to the corresponding reactant complexes, respectively. These results demonstrate that the Cu(III)-oxo species can better mediate dopamine hydroxylation in the protein environment of DBM. The side chains of three amino acid residues (His415, His417, and Met490) coordinate to the Cu(B) atom, one of the copper sites in the catalytic core that plays a role for the catalytic function. The hydrogen-bonding network between dopamine and the three amino acid residues (Glu268, Glu369, and Tyr494) plays an essential role in substrate binding and the stereospecific hydroxylation of dopamine to norepinephrine. The dopamine hydroxylation by the Cu(III)-oxo species is a downhill and lower-barrier process toward the product direction with the aid of the protein environment of DBM. This enzyme is likely to use the high reactivity of the Cu(III)-oxo species to activate the benzylic C-H bond of dopamine; the enzymatic reaction can be explained by the so-called oxygen rebound mechanism.

Animals↗

PubMed1999

Examination of the Stabilities of Group 14 (C, Si, Ge, Sn, Pb) Congeners of Dihydroxycarbene and Dioxirane. Comparison to Formic Acid and Hydroperoxycarbene Congeners.

The relative energetics of four XH(2)O(2) (X = C, Si, Ge, Sn, Pb) isomers, dihydroxycarbene, formic acid, dioxirane, and hydroperoxycarbene, were determined using the BLYP and B3LYP density functionals with DZP and TZ2P basis sets, as well as CCSD and CCSD(T) single-point energies at the BLYP/TZ2P optimized geometries. Relative to dihydroxycarbene, formic acid was 41.8 kcal/mol lower in energy while dioxirane and hydroperoxycarbene were 51.3 and 63.6 kcal/mol higher, respectively, with CCSD(T). Furthermore, using an effective core potential (ECP) the dihydroxy congener was shown to be the most stable isomer for X = Si-Pb. The formic acid and dioxirane congeners become increasingly less stable as one descends group 14. Our results show that divalency is preferred for Si-Pb (dihydroxy congeners are the most stable) but the tetravalent formic acid congeners remain more stable than the hydroperoxy congeners, showing that divalency is not universally preferred among these isomers.

Journal Article↗

PubMed2005

Reactions of POxCly- ions with H and H2 from 298 to 500 K.

Rate constants and product branching ratios for POxCly- ions reacting with H and H2 were measured in a selected ion flow tube (SIFT) from 298 to 500 K. PO2Cl-, PO2Cl2-, POCl2-, and POCl3- were all unreactive with H2, having a rate constant with an upper limit of <5 x 10(-12) cm3 s(-1). PO2Cl2- did not react with H atoms either, having a similar rate constant limit of <5 x 10(-12) cm3 s(-1). The rate constants for PO2Cl-, POCl2-, and POCl3- reacting with H showed no temperature dependence over the limited range of 298-500 K and were approximately 10-20% of the collision rate constant. Cl abstraction by H to form HCl was the predominant product channel for PO2Cl-, POCl2-, and POCl3-, with a small amount of Cl- observed from POCl2- + H. Reactions of O2 and O3 with the POCl- products ions from the reaction of POCl2- + H were observed to yield predominantly PO3- and PO2-, respectively. POCl- reacted with O2 and O3 with rate constants of 8.9 +/- 1.1 x 10(-11) and 5.2 +/- 3.3 x 10(-10) cm3 s(-1), respectively. No associative electron detachment in the reactions with H atoms was observed with any of the reactant ions; however, detachment was observed with a PO- secondary product ion at high H atom concentrations. Results of new G3 theoretical calculations of optimized geometries and energies for the products observed are discussed.

Journal Article↗

PubMed2005

The isobutylene-isobutane alkylation process in liquid HF revisited.

Details on the mechanism of HF catalyzed isobutylene-isobutane alkylation were investigated. On the basis of available experimental data and high-level quantum chemical calculations, a detailed reaction mechanism is proposed taking into account solvation effects of the medium. On the basis of our computational results, we explain why the density of the liquid media and stirring rates are the most important parameters to achieve maximum yield of alkylate, in agreement with experimental findings. The ab initio Car-Parrinello molecular dynamics calculations show that isobutylene is irreversibly protonated in the liquid HF medium at higher densities, leading to the ion pair formation, which is shown to be a minimum on the potential energy surface after optimization using periodic boundary conditions. The HF medium solvates preferentially the fluoride anion, which is found as solvated [FHF](-) or solvated F(-.)(HF)(3). On the other hand, the tert-butyl cation is weakly solvated, where the closest HF molecules appear at a distance of about 2.9 Angstrom with the fluorine termination of an HF chain.

Journal Article↗

PubMed2005

Exploring intramolecular reactions in complex systems with metadynamics: the case of the malonate anions.

We have determined the optimized structures, relative energies and intramolecular reactions for two anionic forms of malonic acid, anion malonate(-1) (HO(2)CCH(2)CO(2)(-)) and malonate(-2) ((-)O(2)CCH(2)CO(2)(-)). For this purpose we employed accurate quantum chemistry calculations using second-order Möller-Plesset perturbation theory and Density Functional Theory with an aug'-cc-p-VTZ basis set to determine the structures and energies, and a novel metadynamics method based on Car-Parrinello molecular dynamics for the thermal reactions. For both malonates, we found new isomers (keto and enol structures) characterized by CO(2) rotations and intramolecular proton transfers. These proton transfers characterize the keto-enol tautomerism that takes place both in the monoanion and dianion. In all cases, the keto tautomer is the more stable configuration. The metadynamics method allows the system to explore the potential energy surface in a few picoseconds, crossing activation barriers of 20-50 kcal/mol.

Journal Article↗

PubMed2006

Thermochemical properties of HxNO molecules and ions from ab initio electronic structure theory.

Coupled-cluster calculations through noniterative triple excitations were used to compute optimized structures, atomization energies at 0 K, and heats of formation at 0 and 298 K for NH2O, HNOH, NH2O-, NH2OH+, NH3OH+, HNO-, and HON. These molecules are important in the gas-phase oxidation of NH3, as well as its solution-phase chemistry. The O-H, N-H, and N-O bond energies of these molecules are given and compared. The N-H and O-H bond energies are quite low, and, for NH2OH, the O-H bond is weaker than the N-H bond (by 7.5 kcal/mol). The energetics for a variety of ionic chemical processes in the gas phase, including the electron affinities of NH2O and HNO, the proton affinities of NH2O and NH2OH, and the acidities of NH2OH and NH2O, are given. The compounds are weak bases and weak acids in the gas phase. Solvation effects were included at the PCM and COSMO levels. The COSMO model gave better values than the PCM model. The relative values for pKa for NH2O and NH2OH are in good agreement with the experimental values, showing both compounds to be very strong bases in aqueous solution with NH2OH being the stronger base by 1.8 pK units at the COSMO level, compared to the experimental pK difference of 1.1+/-0.3 pK units. We predict that NH2OH+ will not be formed in aqueous solution, because it is a very strong acid. Based on the known acidity of NH3OH+, we predict pKa(NH2OH+)=-5.4 at the COSMO level, which is in good agreement with the experimental estimate of pKa(NH2OH+)=-7+/-2.

Journal Article↗

PubMed2006

Insights into photodissociation dynamics of propionyl chloride from ab initio calculations and molecular dynamics simulations.

The potential energy surfaces of isomerization, dissociation, and elimination reactions for CH3CH2COCl in the S0 and S1 states have been mapped with the different ab initio calculations. Mechanistic photodissociation of CH3CH2COCl at 266 nm has been characterized through the computed potential energy surfaces, the optimized surface crossing structure, intrinsic reaction coordinate, and ab initio molecular dynamics calculations. Photoexcitation at 266 nm leads to the CH3CH2COCl molecules in the S1 state. From this state, the C-Cl bond cleavage proceeds in a time scale of picosecond in the gas phase. The barrier to the C-Cl bond cleavage on the S1 surface is significantly increased by effects of the matrix and the internal conversion to the ground state prevails in the condensed phase. The HCl eliminations as a result of internal conversion to the ground state become the dominant channel upon photodissociation of CH3CH2COCl in the argon matrix at 10 K.

Journal Article↗

PubMed2006

Experimental and theoretical studies on carbon-nitrogen clusters C2nN7-.

C(2n)N7(-) cluster ions are produced by laser ablating on the K(3)[Fe(CN)6] sample. DFT calculations have been performed for these cluster anions. Various isomeric structures of these clusters are optimized and their energies are compared to find the most stable isomers. The most stable structure for C8N7(-) is similar to that of adenine by theoretical calculation, which is in agreement with the collision-induced dissociation (CID) experimental results. With the increasing even numbers of C atoms from 8 to 16, the N atoms in the double-ring structure are gradually substituted by C atoms from the six-membered ring to the five-membered ring. All these C(2n)N7(-) (n = 3-9) clusters exhibit planar aromatic characters. The energy difference and incremental binding energy analyses show that C(2n)N7(-) (n = 4-8) clusters are more stable than C6N7(-) and C18N7(-), which are consistent with the observed mass spectrum.

Journal Article↗