Insights into the Catalytic Mechanism and Transition State Stabilization of 5′‐Methylthioadenosine Nucleosidase using Neutron Crystallography
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Michael T. Banco↗
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Results for “Catalytic mechanisms”
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Modeling of a possible conformational change associated with the catalytic mechanism in the hammerhead ribozyme
Here we describe a possible model of the cleavage mechanism in the hammerhead ribozyme. In this model, the 2' hydroxyl of C17 is moved into an appropriate orientation for an in-line attack on the G1.1 phosphate through a change in its sugar pucker from C3' endo to C2' endo. This conformational change in the active site is caused by a change in the uridine turn placing the N2 and N3 atoms of G5 of the conserved core in hydrogen bonding geometry with the N3 and N2 atoms on the conserved G16.2 residue. The observed conformational change in the uridine turn suggests an explanation for the conservation of G5. In the crystal structure of H.M. Pley et al., Nature 372, 68-74 (1994), G5 is situated 5.3A away from G16.2. However, the uridine turn is sufficiently flexible to allow this conformational change with relatively modest changes in the backbone torsion angles (average change of 14.2 degrees). Two magnesium ions were modeled into the active site with positions analogous to those described in the functionally similar Klenow fragment 3'-5' exonuclease (L.S. Beese and T.A. Steitz, EMBO J. 10, 25-33 (1991)), the Group I intron (T.A. Steitz and J.A. Steitz, P.N.A.S. U.S.A. 90, 6498-6502 (1993); R.F. Setlik et al., J. Biomol. Str. Dyn. 10, 945-972 (1993)) and other phosphotransferases. Comparison of this model with one in which the uridine turn conformation was not changed showed that although the changes in the C17 sugar pucker could be modeled, insufficient space existed for the magnesium ions in the active site.
Non-NASA Center↗
The Conservation of Structure and Mechanism of Catalytic Action in a Family of Thiamin Pyrophosphate (TPP)-dependent Enzymes
Thiamin pyrophosphate (TPP)-dependent enzymes are a divergent family of TPP and metal ion binding proteins that perform a wide range of functions with the common decarboxylation steps of a -(O=)C-C(OH)- fragment of alpha-ketoacids and alpha- hydroxyaldehydes. To determine how structure and catalytic action are conserved in the context of large sequence differences existing within this family of enzymes, we have carried out an analysis of TPP-dependent enzymes of known structures. The common structure of TPP-dependent enzymes is formed at the interface of four alpha/beta domains from at least two subunits, which provide for two metal and TPP-binding sites. Residues around these catalytic sites are conserved for functional purpose, while those further away from TPP are conserved for structural reasons. Together they provide a network of contacts required for flip-flop catalytic action within TPP-dependent enzymes. Thus our analysis defines a TPP-action motif that is proposed for annotating TPP-dependent enzymes for advancing functional proteomics.
Dominiak, P.↗
Modeling study on the cleavage step of the self-splicing reaction in group I introns
A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.
NASA Discipline Exobiology↗
Clays as prebiotic photocatalysts
Clay minerals catalyze peptide bond formation in fluctuating environments. A number of plausible mechanisms have been proposed and tested. The possibility that clays may actually be energizing the reaction by means of electronic excitation, creating mobile or trapped holes and electrons in the lattice, is explored. It has been discovered that clays emit light upon dehydration. The correlation between dehydration-induced, or thermoluminescent, processes and the yield of glycine oligomers after treatments known to affect the luminescent yields is being tested, in an effort to understand the catalytic mechanism
Coyne, L. M.↗
Identification of a dual-specificity protein phosphatase that inactivates a MAP kinase from Arabidopsis
Mitogen-activated protein kinases (MAPKs) play a key role in plant responses to stress and pathogens. Activation and inactivation of MAPKs involve phosphorylation and dephosphorylation on both threonine and tyrosine residues in the kinase domain. Here we report the identification of an Arabidopsis gene encoding a dual-specificity protein phosphatase capable of hydrolysing both phosphoserine/threonine and phosphotyrosine in protein substrates. This enzyme, designated AtDsPTP1 (Arabidopsis thaliana dual-specificity protein tyrosine phosphatase), dephosphorylated and inactivated AtMPK4, a MAPK member from the same plant. Replacement of a highly conserved cysteine by serine abolished phosphatase activity of AtDsPTP1, indicating a conserved catalytic mechanism of dual-specificity protein phosphatases from all eukaryotes.
Non-NASA Center↗
Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation
Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.
Willey, Ronald J.↗
Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments
The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.
NASA Discipline Exobiology↗
ECUT (Energy Conversion and Utilization Technologies Program). Biocatalysis Project
Presented are the FY 1985 accomplishments, activities, and planned research efforts of the Biocatalysis Project of the U.S. Department of Energy, Energy Conversion and Utilization Technologies (ECUT) Program. The Project's technical activities were organized as follows: In the Molecular Modeling and Applied Genetics work element, research focused on (1) modeling and simulation studies to establish the physiological basis of high temperature tolerance in a selected enzyme and the catalytic mechanisms of three species of another enzyme, and (2) determining the degree of plasmid amplification and stability of several DNA bacterial strains. In the Bioprocess Engineering work element, research focused on (1) studies of plasmid propagation and the generation of models, (2) developing methods for preparing immobilized biocatalyst beads, and (3) developing an enzyme encapsulation method. In the Process Design and Analysis work element, research focused on (1) further refinement of a test case simulation of the economics and energy efficiency of alternative biocatalyzed production processes, (2) developing a candidate bioprocess to determine the potential for reduced energy consumption and facility/operating costs, and (3) a techno-economic assessment of potential advancements in microbial ammonia production.
Source record↗
Potential technology transfers of research on low-temperature carbon monoxide-oxygen recombination catalysts
Results from research on catalytic recombination of CO-O2 for stable closed-cycle operation of CO2 lasers hold much promise for a variety of technology transfer. Expansion of CO2 laser remote sensing applications toward chemical detection and pollution monitoring would certainly be expected. However, the catalysts themselves may be especially effective in low-temperature oxidation of a number of chemicals in addition to CO. It is therefore of interest to compare the CO-O2 catalysts with chemical systems designed for chemical sensing, air purification and process catalysis. Success in understanding the catalytic mechanisms of the recombination of CO-O2 could help to shed light on how catalyst systems operate. New directions in low-temperature oxidation catalysts, coatings for chemical sensors and sorbents for air purification could well emerge.
Poziomek, Edward J.↗
Zeolite crystal growth in space
The growth of large, uniform zeolite crystals in high yield in space can have a major impact on the chemical process industry. Large zeolite crystals will be used to improve basic understanding of adsorption and catalytic mechanisms, and to make zeolite membranes. To grow large zeolites in microgravity, it is necessary to control the nucleation event and fluid motion, and to enhance nutrient transfer. Data is presented that suggests nucleation can be controlled using chemical compounds (e.g., Triethanolamine, for zeolite A), while not adversely effecting growth rate. A three-zone furnace has been designed to perform multiple syntheses concurrently. The operating range of the furnace is 295 K to 473 K. Teflon-lined autoclaves (10 ml liquid volume) have been designed to minimize contamination, reduce wall nucleation, and control mixing of pre-gel solutions on orbit. Zeolite synthesis experiments will be performed on USML-1 in 1992.
Sacco, Albert, Jr.↗
The Effect of Diffusional Transport and Surface Catalysis on the Aerothermodynamic Heating for Martian Atmospheric Entry
For the reentry heating of 70-degree blunt sphere-cones entering Mars at velocities in excess of 6 km/sec, a study was performed to determine the magnitude of both convective and catalytic heating on the cone forebody. Case studies of the peak heating conditions for the current NASA Mars Pathfinder entry probe, as well as the peak heating conditions of the proposed NASA Mars 2001 aerobraking orbiter mission were performed. Since the actual behavior of the chemical recombination of Mars atmosphere hypersonic shock layer species on heat shield materials is not known, and no experimental studies of any consequence have been done to determine surface reaction rates for the CO2 system, a parametric analysis of various reaction schemes and surface catalytic mechanistic models was performed. In many cases the actual Mars entry probe will have a heat shield composed of an ablative material which can either partially or completely preclude the existence of catalytic surface recombination phenomena. The extent of this blockage effect has not been examined at this time and is not considered in this effort. Instead only non-ablative computations are performed to separately evaluate the full extent of the surface catalysis and related diffusional phenomena. Parametric studies include peak heating point comparisons of non-catalytic, partially catalytic and fully catalytic total surface heat transfer for three difference surface recombination catalytic mechanisms (with and without simultaneous CO + O and O + O recombination) as well as with different species diffusion models. Diffusion model studies include constant Schmidt number (equal diffusivities) and the bifurcation, approximate multi-component diffusion model. Since the gas phase reaction kinetics for the Mars CO2 based atmosphere have also not been validated, the effect of two different (fast and slow) sets of gas kinetics on heat transfer is presented.
Henline, William D.↗
Ionization and Deionization Processes in Low-Density Plasma Flows
Various plasma relaxation processes that are significant in laboratory plasma flows for aerospace physics studies are discussed on the basis of a survey of time decay studies of immobile plasmas. Some of the problems analyzed and discussed are: the relative importance of the various recombination mechanisms, catalytic deionization by electro- negative particles, delayed ionization produced by metastable action, and heating of the flow by deionization reactions.
Barger, Raymond L.↗
Supporting technology for the development of Controlled Ecological Life Support Systems (CELSS)
To support the development of Controlled Ecological Life Support Systems (CELSS) in the space program, a metabolic simulator has been selected for use in a closed chamber to test functions of the CELSS. This metabolic simulator is a catalytic reactor which oxidizes the methyl acetate to produce carbon dioxide and water vapor. In this project, kinetic studies of catalytic oxidation of methyl acetate were conducted using monolithic and pellet catalysts with 0.5% (by weight) platinum (Pt) on aluminum oxide (Al2O3). The reaction was studied at a pressure of one atmosphere and at temperatures varying from 160 C to 420 C. By-products were identified at the exit of the preheater and reactor. For the kinetic study with the monolithic catalyst, a linear regression method was used to correlate the kinetic data with zero-order, first-order and Langmuir-Hinshelwood models. Results indicate that the first-order model represents the data adequately at low concentrations of methyl acetate. For higher concentrations of methyl acetate, the Langmuir-Hinshelwood model best represents the kinetic data. Both rate constant and adsorption equilibrium constants were estimated from the regression. A Taguchi orthogonal array (L(sub 9)) was used to investigate the effects of temperature, flow rate, and concentration on the catalytic oxidation of methyl acetate. For the monolithic catalyst, temperature exerts the most significant effect, followed by concentration of methyl acetate. For the pellet catalyst, reaction temperature is the most significant factor, followed by gas flow rate and methyl acetate concentration. Concentrations of either carbon dioxide or oxygen were seen to have insignificant effect on the methyl acetate conversion process. Experimental results indicate that the preheater with glass beads can accomplish thermal cracking and catalytic reaction of methyl acetate to produce acetic acid, methanol, methyl formate, and 1-propanol. The concentration of all by-products was measured in ppmv (parts per million by volume). At higher temperatures, greater amounts of these products are produced, as expected. In all cases, methanol was the predominant concentration detected, followed by methyl formate. At temperatures lower than 320 C for the P-type monolithic catalyst, methanol, acetic acid, and acetone were detected, whereas, for the E-type monolithic catalyst, only methanol was detected at 160 C. Both P and E types of the monolithic catalyst were specified with the same substrates (ceramic), washcoat (Al2O3), and promoter (Pt). However, the manufacturing and treatment procedures were quite different. It was therefore concluded that the performance of the E-type monolithic catalyst is superior to that of the P-type for oxidation of methyl acetate. At higher reaction temperatures, e.g., above 420 C, all reactants and byproducts were completely oxidized using these two types of monolithic catalyst to produce carbon dioxide and water vapor. A complex heterogenous catalytic reaction mechanism was proposed to explain the formation of the byproducts (methanol, acetic acid, and methyl formate) as the methyl acetate traveled through the preheater packed with glass beads. The by-product, 1-propanol, may be formed only through a homogeneous reaction, since it is difficult to develop a reasonable sequence of heterogeneous reaction steps to explain its formation. The homogeneous thermal decomposition of methyl acetate to form free radicals was proposed to explain the formation of 1-propanol, and also methanol, in the preheater. A dual-site catalytic reaction mechanism was proposed for the oxidation of methyl acetate over Pt/Al2O3 monolithic catalyst. The dual-site mechanism describes the chemisorption of oxygen molecules as well as a physical adsorption of methyl acetate on the active sites. On the active sites, methyl acetate is oxidized rapidly to form carbon dioxide and water vapor. A rate equation derived from this mechanism gives the Langmuir-Hinshelwood rate formula which has been observed from the experimental data obtained in this project for high methyl acetate concentration (greater than 1000 ppmv) over a monolithic catalyst. If the oxygen concentration is very high and methyl acetate concentration is very low, the reaction rate equation is then reduced to a first-order with respect to methyl acetate concentration. The first-order model has also been observed from the experimental data obtained in this project for low methyl acetate concentration (less than 1000 ppmv).
Li, Ku-Yen↗
Mechanism of the atmospheric oxidation of sulfur dioxide - Catalysis by hydroxyl radicals
A flash photolysis/resonance fluorescence technique was used to investigate the decay of OH due to the reaction OH + SO2 (+M) to HOSO2 (+M). In the presence of small amounts of NO (10 to the 14th per cu cm), the decays deviated from the normal semilogarithmic linearity due to reformation of OH. On the basis of computer simulations of the decay curves, it is suggested that the reactions HOSO2 + O2 to HO2 + SO3 (k3), and HO2 + HO to OH + NO2 are the likely subsequent steps in SO2 oxidation. The upper limit for the binding energy of HOSO2 relative to OH + SO2 is estimated to be 32 kcal/mol. The atmospheric implications of a catalytic oxidation mechanism are briefly discussed.
Margitan, J. J.↗
Water Filtration Products
American Water Corporation manufactures water filtration products which incorporate technology originally developed for manned space operations. The formula involves granular activated charcoal and other ingredients, and removes substances by catalytic reactions, mechanical filtration, and absorption. Details are proprietary. A NASA literature search contributed to development of the compound. The technology is being extended to a deodorizing compound called Biofresh which traps gas and moisture inside the unit. Further applications are anticipated.
Source record↗
Development of a modulator to measure water vapor selectively in a gaseous mixture
Selective thermal modulation (STM) is a technique which produces a concentration-dependent pulse by selectively modulating a sample in a gas stream. Several types of modulation techniques, both chemical and physical, using adsorption, decomposition, and catalytic and mechanical methods have been developed for use with multiplex gas chromatography. Two of these applications involve selective modulation of the components present in the sample gas stream. The selective modulation of the concentration of specific sample molecules or classes of molecules provides additional analytical selectivity which can lead to selective detection. For some specific applications, the column may even be eliminated. Chemical modulation by absorption of a substance from the sample stream by a stationary phase will also produce a change in the signal intensity. Removal of a substance from the sample stream results in a signal containing a vacancy peak. In the work reported here, a selective thermal modulation technique has been developed as a method for determination of water vapor for possible use in Mars' atmosphere.
NASA Center ARC↗
An interfaced system for production of methane in a spacecraft
The formose reaction, the homogeneously catalyzed condensation of formaldehyde to sugars, proceeds simultaneously with Cannizzaro and crossed Cannizzaro reactions. Reaction studies in a continuous stirred tank reactor have shown that rate instabilities are exhibited. There are temperature instabilities as well as concentration instabilities in calcium hydroxide catalyst, formaldehyde reactant, and hydroxyl ion. It is postulated that Ca(OH)+ is the actual catalytic species for the formose system. A unifying mechanism is developed that postulates that reactions proceed from a common intermediate complexed species, and that the selectivity for each reaction depends on the nature of the catalyst forming the carbohydrate complex. The catalytic mechanism explains the Lobry de Bruyn-van Eckenstein aldose ketose rearrangements and mutarotations of sugars that also proceed in the system.
Weiss, A. H.↗