X-ray studies on crystalline complexes involving amino acids and peptides. XV. Crystal structures of L-lysine D-glutamate and L-lysine D-aspartate monohydrate and the effect of chirality on molecular aggregation

L-Lysine D-glutamate crystallizes in the monoclinic space group P2(1) with a = 4.902, b = 30.719, c = 9.679 A, beta = 90 degrees and Z = 4. The crystals of L-lysine D-aspartate monohydrate belong to the orthorhombic space group P2(1)2(1)2(1) with a = 5.458, b = 7.152, c = 36.022 A and Z = 4. The structures were solved by the direct methods and refined to R values of 0.125 and 0.040 respectively for 1412 and 1503 observed reflections. The glutamate complex is highly pseudosymmetric. The lysine molecules in it assume a conformation with the side chain staggered between the alpha-amino and the alpha-carboxylate groups. The interactions of the side chain amino groups of lysine in the two complexes are such that they form infinite sequences containing alternating amino and carboxylate groups. The molecular aggregation in the glutamate complex is very similar to that observed in L-arginine D-aspartate and L-arginine D-glutamate trihydrate, with the formation of double layers consisting of both types of molecules. In contrast to the situation in the other three LD complexes, the unlike molecules in L-lysine D-aspartate monohydrate aggregate into alternating layers as in the case of most LL complexes. The arrangement of molecules in the lysine layer is nearly the same as in L-lysine L-aspartate, with head-to-tail sequences as the central feature. The arrangement of aspartate ions in the layers containing them is, however, somewhat unusual. Thus the comparison between the LL and the LD complexes analyzed so far indicates that the reversal of chirality of one of the components in a complex leads to profound changes in molecular aggregation, but these changes could be of more than one type.

Theoretical and Experimental Studies on an Ammonia-Based Loop Heat Pipe With a Flat Evaporator

An ammonia loop heat pipe (LHP) with a flat plate evaporator is developed and tested. The device uses a nickel wick encased in an aluminum-stainless steel casing. The loop is tested for various heat loads and different sink temperatures, and it demonstrated reliable startup characteristics. Results with the analysis of the experimental observation indicate that the conductance between the compensation chamber and the heater plate can significantly influence the operating temperatures of the LHP. A mathematical model is also presented which is validated against the experimental observations.

Optimization of an ammonia reactor using regression analysis

This paper presents an optimization algorithm for an ammonia reactor based on a regression model relating the yield to several parameters, control inputs and disturbances. This model is derived from the data generated by hybrid simulation of the steady-state equations describing the reactor behaviour. The simplicity of the optimization program along with its ability to take into account constraints on flow variables make it best suited in supervisory control applications.

Dehydrogenation of ammonia borane in fluoro alcohols

Dehydrogenation of ammonia borane was carried out in fluor alcohol solvent in order to obtain compounds that are more likely candidates suitable for regeneration. Even though ammonia borane undergoes self-dissociation in 2,2,2-trifluoroethanol to liberate H-2, decent hydrogen release rates were obtained by using Co-Co2B, Ni-Ni3B, and Co-Ni-B nanocomposites as catalysts. These catalysts are magnetic in nature and hence can be separated from the reaction mixture using a magnet for re-use. The final by-product NH4+ B(OCH2CF3)(4)(-) obtained after the catalytic dehydrogenation of ammonia borane was thoroughly characterized using H-1, B-11, and C-13 NMR and IR spectroscopies. The FTIR data showed that the B-O bond in NH4+ B(OCH2CF3)(4)(-) is slightly weaker compared to boric acid. Preliminary investigations on the regenerative routes for ammonia borane from the by-product NH4+ B(OCH2CF3)(4)(-) showed indications of the formation of BNHx species. (C) 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

Design and fabrication of an automated thermal desorption gas-solid reaction system: Oxidation of ammonia and methanol over YBa2Cu3O7−δ(123) oxide systems

A fully automated, versatile Temperature Programmed Desorption (TDP), Temperature Programmed Reaction (TPR) and Evolved Gas Analysis (EGA) system has been designed and fabricated. The system consists of a micro-reactor which can be evacuated to 10−6 torr and can be heated from 30 to 750°C at a rate of 5 to 30°C per minute. The gas evolved from the reactor is analysed by a quadrupole mass spectrometer (1–300 amu). Data on each of the mass scans and the temperature at a given time are acquired by a PC/AT system to generate thermograms. The functioning of the system is exemplified by the temperature programmed desorption (TPD) of oxygen from YBa2Cu3−xCoxO7 ± δ, catalytic ammonia oxidation to NO over YBa2Cu3O7−δ and anaerobic oxidation of methanol to CO2, CO and H2O over YBa2Cu3O7−δ (Y123) and PrBa2Cu3O7−δ (Pr123) systems.

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M. tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the selfbiotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over selfbiotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-59 AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis.

Selectivities in the formation of pyridines and pyrimidines by ammonia-induced cyclocondensations of vinamidiniums

Arylvinamidines (2-, 3- or 4-aryl-4-(N,N-dimethyl)amino-1-azabuta-1,3-dienes), generated from 1,1,5,5-tetramethyl-2- or -3-phenyl-1,5-diazapentadienium salts, cyclocondense orientation-specifically under two regioselections forming 1-4' + 4-3' and 1-2' + 4-1' bonds on exposure to ammonia. The initial cyclates aromatise eliminatively to give mixtures of diarylpyridines and arylpyrimidines. The 2-arylvinamidines do not participate as 2-centre reactants and their 4-aryl isomers not as 4-centre reactants in the cyclocondensations which appear to be stepwise and not concerted. Reasons for the selective participation appear to be that the required eliminations from the initial cyclates are disfavoured in the first case and that a geometric factor prevents cyclate-formation in the second.

Small Ubiquitin-related Modifier Ligase Activity of Mms21 Is Required for Maintenance of Chromosome Integrity during the Unperturbed Mitotic Cell Division Cycle in Saccharomyces cerevisiae

The SUMO ligase activity of Mms21/Nse2, a conserved member of the Smc5/6 complex, is required for resisting extrinsically induced genotoxic stress. We report that the Mms21 SUMO ligase activity is also required during the unchallenged mitotic cell cycle in Saccharomyces cerevisiae. SUMO ligase-defective cells were slow growing and spontaneously incurred DNA damage. These cells required caffeine-sensitive Mec1 kinase-dependent checkpoint signaling for survival even in the absence of extrinsically induced genotoxic stress. SUMO ligase-defective cells were sensitive to replication stress and displayed synthetic growth defects with DNA damage checkpoint-defective mutants such as mec1, rad9, and rad24. MMS21 SUMO ligase and mediator of replication checkpoint 1 gene (MRC1) were epistatic with respect to hydroxyurea-induced replication stress or methyl methanesulfonate-induced DNA damage sensitivity. Subjecting Mms21 SUMO ligase-deficient cells to transient replication stress resulted in enhancement of cell cycle progression defects such as mitotic delay and accumulation of hyperploid cells. Consistent with the spontaneous activation of the DNA damage checkpoint pathway observed in the Mms21-mediated sumoylation-deficient cells, enhanced frequency of chromosome breakage and loss was detected in these mutant cells. A mutation in the conserved cysteine 221 that is engaged in coordination of the zinc ion in Loop 2 of the Mms21 SPL-RING E3 ligase catalytic domain resulted in strong replication stress sensitivity and also conferred slow growth and Mec1 dependence to unchallenged mitotically dividing cells. Our findings establish Mms21-mediated sumoylation as a determinant of cell cycle progression and maintenance of chromosome integrity during the unperturbed mitotic cell division cycle in budding yeast.

Ammonia Channeling in Plasmodium falciparum GMP Synthetase: Investigation by NMR Spectroscopy and Biochemical Assays

GMP synthetase, a class I amidotransferase, catalyzes the last step of the purine biosynthetic pathway, where ammonia from glutamine is incorporated into xanthosine 5'-monophospate to yield guanosine 5'-monnophosphate as the main product. Combined biochemical, structural, and computational studies of glutamine amidotransferases have revealed the existence of physically separate active sites connected by molecular tunnels that efficiently transfer ammonia from the glutaminase site to the synthetase site. Here, we have investigated aspects of ammonia channeling in P. falciparum GMP synthetase using biochemical assays in conjunction with N-15-edited proton NMR spectroscopy. Our results suggest that (1) ammonia released from glutamine is not equilibrated with the external medium (2) saturating concentrations of glutamine do not obliterate the incorporation of external ammonia into GMP, and (3) ammonia in the external medium can access the thioester intermediate when the ATPPase domain is bound to substrates. Further, mutation of Cys-102 to alanine confirmed its identity as the catalytic residue in the glutaminase domain, and ammonia-dependent assays on the mutant indicated glutamine to be a partial uncompetitive inhibitor of the enzyme.

Nature of the Oxygen Species at Ni(110) and Ni(100) Surfaces Revealed by Exposure to Oxygen and Oxygen-Ammonia Mixtures: Evidence for the Surface Reactivity of O- Type Species

Adsorption of dioxygen at clean Ni(110) and Ni(100) surfaces gives rise to two prominent features in the O(1s) spectra at 530 and 531 eV due to O2- and O- type species, respectively. Interaction of ammonia with a Ni(100)-O surface where theta(oxygen) < 0.1 ML favors the dissociation of NH3 giving NHn, (n = 1, 2) and N(a) species. This is accompanied by a decrease in the intensity of the 531 eV feature. On the other hand. a Ni(100)-O surface where the oxygen species are mainly of the O2- type is unreactive, Coadsorption studies of NH3-O-2 mixtures show that at Ni(110) surfaces the uptake of both oxygen and ammonia increase with the proportion of oxygen in the NH3-O-2 mixture. The surface concentrations of the O- species and the NHn species also increase with the increase in the O-2/NH3 ratio while the slope of the plot of sigma(N) versus sigma(O-) is around unity. The results demonstrate the high surface reactivity of the O- species and its role in the dissociation of ammonia. Based on these observations, the possibility of the formation of a surface complex between ammonia and oxygen (specifically O-) is suggested. Results from vibrational spectroscopic studies of the coadsorption of NH3-O-2 mixtures are consistent with those from core-level spectroscopic studies.