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F A Momany

Publications and source records attributed to F A Momany.

At least 19 recordsLinked to original sources
PubMed2004

B3LYP/6-311++G** study of monohydrates of alpha- and beta-D-glucopyranose: hydrogen bonding, stress energies, and effect of hydration on internal coordinates.

Twenty-six monohydrates of alpha- and beta-D-glucopyranose were studied using gradient methods at the B3LYP/6-311++G** level of theory. Geometry optimization was carried out with the water molecules at different configurations around the glucose molecule. A new nomenclature for hydrated carbohydrates was developed to describe the water configurations. Zero-point vibrational energy, enthalpy, entropy, and relative free energy were obtained using the harmonic approximation. Hydrogen-bond energies for the monohydrates range from approximately -5 to -12 kcal/mol, and the average relative free energy is approximately 5 kcal/mol. The 1-hydroxy position is the most energetically favored site for hydration, and the region between the two and three positions is the next-most favored site. A water molecule approaching alpha-D-glucose between the 1- and 2-hydroxy positions pulls the 2-hydroxyl hydrogen atom away from the 1-hydroxy oxygen atom, thus increasing the hydrogen-bond length and also increasing the alpha-D-glucose energy. The increase in energy that occurs with a similar interaction on the beta-anomer is much less effective since the hydrogen bond is much longer. Using the calculated free energies of all 26 configurations, the anomer population (alpha/beta) increases in the beta-anomer population relative to the in vacuo case by approximately 10% at the expense of the alpha-anomer, giving an (alpha/beta) ratio of approximately 50/50. This result arises from entropy contributions favoring the beta-anomer more than the alpha-anomer. From analysis of donor and acceptor hydrogen-bond lengths, excellent correlation is found between the DFT calculated distances and those taken from carbohydrate structures in the Cambridge Crystallographic Data Bank.

Carbohydrate Conformation↗
PubMed2004

B3LYP/6-311++G** study of alpha- and beta-D-glucopyranose and 1,5-anhydro-D-glucitol: 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations.

Geometry optimization, at the B3LYP/6-311++G** level of theory, was carried out on 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations of alpha- and beta-D-glucopyranose. Similar calculations on 1,5-anhydro-D-glucitol allowed examination of the effect of removal of the 1-hydroxy group on the energy preference of the hydroxymethyl rotamers. Stable minimum energy boat conformers of glucose were found, as were stable skew boats, all having energies ranging from approximately 4-15 kcal/mol above the global energy 4C1 chair conformation. The 1C4 chair electronic energies were approximately 5-10 kcal/mol higher than the 4C1 chair, with the 1C4 alpha-anomers being lower in energy than the beta-anomers. Zero-point energy, enthalpy, entropy, and relative Gibbs free energies are reported at the harmonic level of theory. The alpha-anomer 4C1 chair conformations were found to be approximately 1 kcal/mol lower in electronic energy than the beta-anomers. The hydroxymethyl gt conformation was of lowest electronic energy for both the alpha- and beta-anomers. The glucose alpha/beta anomer ratio calculated from the relative free energies is 63/37%. From a numerical Hessian calculation, the tg conformations were found to be approximately 0.4-0.7 kcal/mol higher in relative free energy than the gg or gt conformers. Transition-state barriers to rotation about the C-5-C-6 bond were calculated for each glucose anomer with resulting barriers to rotation of approximately 3.7-5.8 kcal/mol. No energy barrier was found for the path between the alpha-gt and alpha-gg B(3,O) boat forms and the equivalent 4C1 chair conformations. The alpha-tg conformation has an energy minimum in the 1S3 twist form. Other boat and skew-boat forms are described. The beta-anomer boats retained their starting conformations, with the exception of the beta-tg-(3,O)B boat that moved to a skew form upon optimization.

Carbohydrate Conformation↗
PubMed2001

Molecular dynamics simulations on the mycotoxin fumonisin B1.

The solution conformational properties of the mycotoxin fumonisin B(1) have been studied using molecular dynamics methodology. Fumonisins have been shown to inhibit sphinganine (sphingosine) N-acyltransferase (ceramide synthase) and show a wide range of toxic effects in many animals. This study of the solution properties of fumonisin B(1) attempts to add to the structural models necessary for the understanding of the binding and activity properties. The computational method uses a box with periodic boundaries, filled with explicit TIP3P water molecules, the substrate fumonisin B(1), and selected counterions for charge neutrality. The starting structure of fumonisin B(1) is added to the box by excluding water molecules. The explicit image method using 12-A cutoffs is applied to the system and molecular dynamics are carried out on different starting conformations at 300 K in 100-picosecond (ps) steps. Examination of the resulting equilibrated conformations suggests that the structure is relatively extended and that previous computational studies in vacuo, showing a compact folded structure, may not be consistent with the solution structure.

Acyltransferases↗
PubMed2001

Male-specific sesquiterpenes from Phyllotreta and Aphthona flea beetles.

It was previously reported that males of the crucifer flea beetle, Phyllotreta cruciferae, feeding on host foliage are attractive to both males and females in the field. Based on this evidence for an aggregation pheromone, volatiles were collected from male and female P. cruciferae feeding on cabbage (Brassica oleracea) and analyzed. For comparison, volatiles were also collected from males and females of three other flea beetle species, Aphthona flava, A. czwalinae, and A. cyparissiae, all feeding on their host, leafy spurge foliage (Euphorbia esula). Six male-specific compounds were isolated from P. cruciferae, and the same compounds plus two additional ones were isolated from males of Aphthona flava, A. czwalinae, and A. cyparissiae. The blends of compounds were relatively consistent within species, but there were characteristic differences between species. Compound structures were studied by mass spectrometry, NMR spectroscopy, UV spectroscopy, polarimetry, chiral and achiral gas chromatography, molecular modeling, and microchemical tests. Three of the compounds were identified as (+)-ar-himachalene; (+)-trans-alpha-himachalene; (+)-y-cadinene. Two others were new enantiomers of himachalene hydrocarbons that were previously identified from the fir trees, Abies alba and Abies nordmanniana. Finally, there were two himachalene alcohols and one norsesquiterpene ketone that is a himachalene analog. Only (+)-ar-himachalene and (+)-y-cadinene are previously known natural products. Electrophysiological activity was demonstrated for five of the compounds. The chemical and electrophysiological patterns are consistent with, but do not prove, a pheromonal function.

Animals↗
PubMed2000

Tryptophan 67 in the human VPAC(1) receptor: crucial role for VIP binding.

The human receptor subtype for VIP and PACAP, referred to as VPAC(1) receptor, has a large N-terminal extracellular domain which is critical for VIP binding. We further investigated this domain by mutating 12 amino acid residues which could participate in the formation of a tight bend (W67) or a coiled coil motif. They were changed to alanine (A) and the cDNAs were transiently transfected into Cos cells. All mutants but W67A exhibited K(d) values similar to that of the wild-type receptor. For the W67A mutant, no specific (125)I-VIP binding could be observed. Mutants at the W67 site were further characterized after stable transfection of epitope-tagged VPAC(1) receptor-GFP fusion proteins into CHO cells. W67A, W67E, W67H, and W67K mutants neither bound VIP nor mediated adenylyl cyclase activation by VIP. The W67F mutant mediated stimulation of adenylyl cyclase only at high VIP concentrations. Microscopic analysis and antibody binding experiments showed that all mutants were similarly expressed at the cell surface of CHO cells. Therefore tryptophan 67 in the human VPAC(1) receptor plays a crucial role in VIP binding due, in part, to its aromatic moiety.

Animals↗
PubMed2000

Computational studies on carbohydrates: in vacuo studies using a revised AMBER force field, AMB99C, designed for alpha-(1-->4) linkages.

Modifications to the AMBER force field [W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, P.A. Kollman, J. Am. Chem. Soc., 117 (1995) 5179-5197] have been made to improve our ability to reproduce observed molecular properties of alpha-linked carbohydrates when calculated using empirical potential-energy functions. Molecular structures and energies obtained using gradient-optimized density functional methods with ab initio basis sets (B3LYP/6-31G*) on ten minimum-energy conformations of maltose [F.A. Momany, J.L. Willett, J. Comp. Chem., submitted for publication] were used to refine the empirical potentials. Molecular dynamics simulations on beta-maltose (i.e., the beta anomer of maltose), cyclohexamylose (alpha-cyclodextrin), cycloheptamylose (beta-cyclodextrin) and larger cyclomaltooligosaccharide structures were carried out and compared with experimental structural studies to test the new potentials. Ring-puckering potential during dynamics as well as conformational transitions to 'flipped' structures were examined. Results of the tests described here suggest that the revised AMBER parameters (AMB99C) are very good for computational studies of alpha-(1-->4)-linked carbohydrates.

Amylose↗
PubMed2000

Computational studies on carbohydrates: solvation studies on maltose and cyclomaltooligosaccharides (cyclodextrins) using a DFT/ab initio-derived empirical force field, AMB99C.

An empirical force field, denoted AMB99C, has been used to study molecular properties of alpha-(1-->4)-linked carbohydrates in solution. AMB99C was parameterized using structural and energetic parameters from density functional ab initio methodology. In this work we examine the solution behavior of the beta anomer of maltose and cyclohexa-, cyclohepta-, and cyclooctaamyloses (alpha-, beta-, and gamma-cyclodextrins or alpha-, beta-, and gamma-CDs, respectively), as well as of two larger (DP 10, epsilon-CD; DP 21) cyclomaltooligosaccharides, CA10 and CA21. Experimental data used for comparison purposes include X-ray structures, small-angle scattering radius of gyration values, NMR nuclear Overhauser enhancements (NOEs), and proton coupling constants. Molecular dynamics simulations were carried out using explicit water molecules (TIP3P) to establish equilibrium populations of conformations in solution, and these results are compared with other calculated values and a variety of experimental parameters, such as average H-1-H-4' distances between the rings in beta-maltose, and the primary hydroxyl groups' conformational populations. Medium-to-large cyclomaltooligosaccharide molecules were studied to test for glucose ring puckering and stability of kinked and 'flipped' conformations. The results of the solvation studies are in excellent agreement with experimental structural parameters.

Carbohydrate Conformation↗
PubMed1985

Variables determining the growth hormone response of His-D-Trp-Ala-Trp-D-Phe-Lys-NH2 in the rat.

Previous studies of His-D-Trp-Ala-Trp-D-Phe-Lys-NH2 (GH-RP-6) have shown this synthetic hexapeptide to be a potent and specific stimulator of GH secretion both in vivo and in vitro. In this study the variables determining the in vivo responses were examined in the rat. The magnitude of the GH response to sc GH-RP-6 was dependent on the age and sex of the rat. Animals less than 15 days of age had much larger responses than did rats 21 days and older. At 10 days of age the male rat had a larger GH response than the female. At 21 days of age, bis(4-methyl 1-homo-piperazinyl-thiocarbonyl) disulfide (Fla-63)-pretreated females had larger responses than did Fla-63-pretreated males. In the Fla-63-pretreated adult rat, sc GH-RP-6 stimulated GH release in the female but not in the male. In the 10-day-old male, the ED50 for sc GH-RP-6 was 0.4 micrograms, and the maximal serum GH response was 800 ng/ml. In the 21-day-old female Fla-63-pretreated rat, the ED50 for sc GH-RP-6 was 3.0 micrograms, and the maximal GH response was 200 ng/ml. In the 21-day-old female pentobarbital-anesthetized rat, iv GH-RP-6 had an ED50 of 0.5 micrograms and a maximal serum GH response of 2500 ng/ml. A marked dose- and time-dependent decrease of subsequent GH-RP-6 responses occurred after a single sc GH-RP-6 injection. Decreases in pituitary GH or increases in somatostatin secretion would not explain this decreased response because the GH response of MRZ 2549, an opiate agonist, was unchanged by GH-RP-6 pretreatment. In contrast to the acute effect of GH-RP-6, chronic daily injections of GH-RP-6 resulted in an enhancement of the GH-RP-6 response.

Age Factors↗
PubMed1984

Conformational energy studies and in vitro and in vivo activity data on growth hormone-releasing peptides.

A series of growth hormone-releasing peptides have been designed and tested for both in vitro and in vivo activity. In vitro activity at 1-10 ng/ml was obtained for the pentapeptide, His-DTrp-Ala-Trp-DPhe-NH2 (I) and the hexapeptide, His-DTrp-Ala-Trp-DPhe-Lys-NH2 (II). These peptides, as well as others to be described, are active in releasing GH in vivo at low microgram dosages. In this manuscript, the conformational properties and in vitro and in vivo activity of a series of small peptides are reported. Results of the biological studies are reported in an accompanying paper.

Animals↗
PubMed1984

On the in vitro and in vivo activity of a new synthetic hexapeptide that acts on the pituitary to specifically release growth hormone.

His-DTrp-Ala-Trp-DPhe-LysNH2, [His1,Lys6] GHRP, is a new synthetic hexapeptide which specifically elicits a dosage-related release of GH in vitro and in vivo without a concomitant release of LH, FSH, TSH, or PRL and, in limited in vivo studies, insulin or glucagon. Our results indicate that this small peptide has the attributes of a hypophysiotropic hormone. In vitro the minimum and maximum active dosages ranged from 1-10 ng/ml in the pituitary incubate assay. It was active in rats, monkeys, lambs, calves, and under special experimental conditions chicks, indicating its lack of species dependency. It was active when administered iv, sc, or ip to rats. After iv injection, GH levels rose within 2 min, peaked at +10-20 min, and by 2 h usually had returned to normal. It was not possible to directly compare the potencies of [His1,Lys6]GHRP, and the GH-releasing factors GHRF-44 and GHRF-40 after a single sc injection in rats because the time course of the GH response of these peptides was different. The GH response of [His1,Lys6]GHRP was longer in duration than either of these larger peptides. Both SRIF-14 and SRIF-28 inhibited the GH response of the hexapeptide; however, SRIF-28 was about four times more active than SRIF-14 in vitro and 7.5 times more active in vivo. When this small peptide was administered sc once or twice daily to immature rats for 9 or 25 days, the BW gain increased above the control. At the end of the weight gain studies the pituitary remained fully responsive to the peptide. Thus, [His1,Lys6] GHRP may be a valuable peptide for investigating the function of the pituitary somatotrophs and, in addition, it has the potential for increasing BW gain of a variety of normal animals by inducing GH release via a direct pituitary site of action.

Animals↗
PubMed1981

Conformational energy calculations on enkephalins and enkephalin analogs. Classification of conformations to different configurational types.

Conformational energy calculations were carried out on the peptide enkaphalins (ENK) and selected analogs to find those conformers of low energy. The analogs studied include [D-Ala2]Enk-NH2, [D-Ala2]Enk, [D-Met2, Pro5]Enk-NH2, [D-Ala2, D-Phe5]Enk, [D-Ala2, D-Leu5]Enk, [D-Ala2, (N-Me)Phe4, Met5] Enk-NH2 and [D-Ala2, (N-Me)Met5]Enk-NH2. When the low-energy conformers for all the analogs are compared, different allowed backbone conformations are found which orient the functional side-chains such that three classifications of structures appear. Each classification shows a unique configuration of side-chain positions in space even though different backbone conformations are found within each classification.

Endorphins↗
PubMed1981

Design, synthesis, and biological activity of peptides which release growth hormone in vitro.

Experimental observations showed that the analogs [D-Trp2]- and [D-Phe2]methionine enkephalin amide were weakly active in releasing GH from rat pituitary in vitro. These observations were used to design more active GH-releasing factors. Conformational energy calculations were carried out, and energetically favored conformations of these polypeptides were found. Structural similarities as well as structural differences between active and inactive analogs were examined, and new sequences were predicted. Progressively more active analogs were designed, then synthesized, and tested. This cycle of steps was repeated, each time using structural and chemical concepts as design guides, until a series of very active analogs resulted. The most active analog to date, Tyr-D-Trp-Ala-Trp-D-Phe-NH2, was shown to release GH in vitro at 10-30 ng/ml medium, which is approximately 10(3) times more active than the two starting enkephalin-based analogs. From the structure-activity data, a mechanism for binding at the receptors is formulated, and a comparison is made between the structural relationships of the GH-releasing peptide analogs and the GH inhibitor, somatostatin.

Animals↗