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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

Structural Basis for "Flip-Flop" Action of Human Pyruvate Dehydrogenase

The derivative of vitamin B1, thiamin pyrophosphate is a cofactor of pyruvate dehydrogenase, a component enzyme of the mitochondrial pyruvate dehydrogenase multienzyme complex that plays a major role in directing energy metabolism in the cell. This cofactor is used to cleave the C(sup alpha)-C(=O) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase. In alpha(sub 2)beta(sub 2)-tetrameric human pyruvate dehydrogenase, there are two cofactor binding sites, each of them being a center of independently conducted, although highly coordinated enzymatic reactions. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites can now be understood based on the recently determined crystal structure of the holo-form of human pyruvate dehydrogenase at 1.95A resolution. The structure of pyruvate dehydrogenase was determined using a combination of MAD phasing and molecular replacement followed by rounds of torsion-angles molecular-dynamics simulated-annealing refinement. The final pyruvate dehydrogenase structure included coordinates for all protein amino acids two cofactor molecules, two magnesium and two potassium ions, and 742 water molecules. The structure was refined to R = 0.202 and R(sub free) = 0.244. Our structural analysis of the enzyme folding and domain assembly identified a simple mechanism of this protein motion required for the conduct of catalytic action.

Ciszak, Ewa↗
NASA NTRS2004

Intricate Crystal Structure of Dihydrolipoamide Dehydrogenase (E3) with its Binding Protein: Multiple Copies, Dynamic and Static Disorders

Human E3 and binding protein E3BP are two components of the pyruvate dehydrogenase complex. Crystallization of E3 with 221-amino acid fragment of E3BP (E3BPdd) led to crystals that diffracted to a resolution of 2.6 Angstroms. Structure determination involved molecular replacement using a dimer of E3 homolog as a search model and de novo building of the E3BPdd peptide. Solution was achieved by inclusion of one E3 dimer at a time, followed by refinement until five E3 dimers were located. This complete content of E3 provided electron density maps suitable for tracing nine peptide chains of E3BPdd, eight of them being identified with partial occupancies. Final content of the asymmetric unit consists of five E3 dimers, each binding one E3BPdd molecule. In four of these molecular complexes, E3BPdd is in static disorder resulting in E3BPdd binding to either one or the other monomer of the E3 dimer. However, E3BPdd of the fifth E3 dimer forms specific contacts that lock it at one monomer. In addition to this static disorder, E3BPdd reveals high mobility in the limited space of the crystal lattice. Support from NIH and NASA.

Makal, A.↗
NASA NTRS1994

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) (Muster T et al., 1993, J Virol 67:6642-6647) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class (Ji X, Zhang P, Armstrong RN, Gilliland GL, 1992, Biochemistry 31:10169-10184) was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(3)2(1)2, with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Schistosoma japonicum/enzymology/genetics/immunolo↗
NASA NTRS1983

The existence of Hadley convective regimes of atmospheric motion

The solutions of the equations describing deep global convection on a rotating planet are discussed. The existence of generalized steady axisymmetric solutions is established. It is then shown that these are classical solutions when the heat source is sufficiently smooth. The solutions are shown to be unique when the heating is sufficiently weak and asymptotically stable when the shear is sufficiently small. Finally, the application of these results to earth's atmosphere is discussed, with eddy viscosity replacing molecular viscosity.

Dutton, J. A.↗
NASA NTRS1994

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Lim, Kap↗
NASA NTRS2002

Crystallization and Preliminary X-ray Analysis of Der f 2, a Potent Allergen Derived from the House Dust Mite

Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophugoides sp.) are particularly ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis, and asthma associated with allergic reactions to these arthropods are often caused by relatively small (125-129 amino acids) mite proteins of unclear biological function. Der f 2, a major allergen from the mite Dermatophagoides farinae, has been recombinantly expressed and characterized. The Der f 2 protein has been crystallized in our laboratory and a native data set collected at a synchrotron source. The crystals belong to the orthorhombic space group I422 with unit cell parameters of a = 95.2 Angstroms, b = 95.2 Angstroms, and c = 103.3 Angstroms. An essentially complete (97.2%) data set has been collected to 2.4 Angstroms. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the available NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pterovssinus) failed to reveal a creditable solution.

Roeber, Dana↗
NASA NTRS2003

Crystallization and preliminary X-ray analysis of Der f 2, a potent allergen derived from the house dust mite (Dermatophagoides farinae)

Although a number of allergens have been identified and isolated, the underlying molecular basis for the potent immune response is poorly understood. House dust mites (Dermatophagoides sp.) are ubiquitous contributors to atopy in developed countries. The rhinitis, dermatitis and asthma associated with allergic reactions to these arthropods are frequently caused by relatively small (125-129 amino acids) mite proteins of unknown biological function. Der f 2, a major allergen from the mite D. farinae, has been recombinantly expressed, characterized and crystallized. The crystals belong to the tetragonal space group I4(1)22, with unit-cell parameters a = b = 95.2, c = 103.3 A. An essentially complete (97.2%) data set has been collected to 2.4 A at a synchrotron source. Attempts to solve the crystal structure of Der f 2 by molecular replacement using the NMR coordinates for either Der f 2 or Der p 2 (the homologous protein from D. pteronyssinus) failed, but preliminary searches using the crystalline Der p 2 atomic coordinates appear to be promising.

Pyroglyphidae/chemistry/immunology↗
NASA NTRS1994

Preliminary crystallographic studies of four crystal forms of serum albumin

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Serum Albumin/chemistry↗
NASA NTRS1989

On the Nature of Navier-stokes Turbulence

Several turbulent and nonturbulent solutions of the Navier-Stokes equations are obtained. The unaveraged equations are used numerically in conjunction with tools and concepts from nonlinear dynamics, including time series, phase portraits, Poincare sections, largest Liapunov exponents, power spectra, and strange attractors. Initially neighboring solutions for a low-Reynolds-number fully developed turbulence are compared. The solutions, separate exponentially with time, having a positive Liapunov exponent. Thus the turbulence is characterized as chaotic. In a search for solutions which contrast with the turbulent ones, the Reynolds number is reduced. Several qualitatively different flows are noted. These are, fully chaotic, complex period, weakly chaotic, simple periodic, and fixed-point. Of these, only the fully chaotic flows are classified as turbulent. Those flows have both a positive Liapunov exponent and Poincare sections without pattern. By contrast, the weakly chaotic flows have some pattern in their Poincare sections. The fixed-point and periodic flows are nonturbulent, since turbulence, is both time-dependent and aperiodic. Turbulent solutions are obtained in which energy cascades from large to small-scale motions. In general, the spectral energy transfer takes place between wavenumber bands that are considerably separated. The special transfer can occur either as a result of nonlinear turbulence self-interaction or by interaction of turbulence with mean gradients. Turbulent systems are compared with those studied in kinetic theory. The two types of systems are fundamentally different (continuous and dissipative as opposed to discrete and conservative), but there are similarities. For instance, both are nonlinear and show sensitive dependence on initial conditions. Also, the turbulent and molecular stress tensors are identical if the macroscopic velocities for the turbulent stress are replaced by molecular velocities.

Deissler, Robert G.↗
NASA NTRS1996

High Spectral Resolution Lidar Measurements of Extinction and Particle Size in Clouds

The University of Wisconsin High Spectral Resolution Lidar (HSRL) measures optical properties of the atmosphere by separating the Doppler broadened molecular backscatter return from the unbroadened aerosol return. In the past, the HSRL employed a 150 mm diameter Fabry-Perot etalon to separate the aerosol and molecular signals. The replacement of the etalon with an I2 absorption filter significantly improved the ability of the HSRL to separate weak molecular signals inside dense clouds.

Eloranta, E. W.↗
NASA NTRS2017

The HITRAN2016 Molecular Spectroscopic Database

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

HITRAN↗
NASA NTRS1966

Approximation of molecular integrals.

Approximation method for molecular integrals that depends on replacement of two-center charge distributions by single-center distributions, giving results in terms of Coulomb type integrals

COULOMB POTENTIAL↗
NASA NTRS2002

Biomaterials and scaffolds in reparative medicine

Most approaches currently pursued or contemplated within the framework of reparative medicine, including cell-based therapies, artificial organs, and engineered living tissues, are dependent on our ability to synthesize or otherwise generate novel materials, fabricate or assemble materials into appropriate 2-D and 3-D forms, and precisely tailor material-related physical and biological properties so as to achieve a desired clinical response. This paper summarizes the scientific and technological opportunities within the fields of biomaterials science and molecular engineering that will likely establish new enabling technologies for cellular and molecular therapies directed at the repair, replacement, or reconstruction of diseased or damaged organs and tissues.

Non-NASA Center↗
NASA NTRS2007

Resistively Heated SiC Nozzle for Generating Molecular Beams

An improved nozzle has been developed to replace nozzles used previously in an apparatus that generates a substantially unidirectional beam of molecules passing through a vacuum at speeds of several kilometers per second. The basic principle of operation of the apparatus is the same for both the previous and the present nozzle designs. The main working part of the nozzle is essentially a cylinder that is closed except that there is an inlet for a pressurized gas and, at one end, the cylinder is closed by a disk that contains a narrow central hole that serves as an outlet. The cylinder is heated to increase the thermal speeds of the gas molecules into the desired high-speed range. Heated, pressurized gas escapes through the outlet into a portion of the vacuum chamber that is separated, by a wall, from the rest of the vacuum chamber. In this portion of the vacuum chamber, the gas undergoes a free jet expansion. Most of the expanded gas is evacuated and thus does not become part of the molecular beam. A small fraction of the expanded beam passes through a narrow central orifice in the wall and thereby becomes a needle- thin molecular beam in the portion of the vacuum on the downstream side of the wall.

Cagiano, Steven↗
NASA NTRS1994

Solar system formation and the distribution of volatile species

To understand how the solar system formed we must understand the compositional distribution of the current system. Volatile species are particularly important in that their stability as condensed phases is limited in temperature-pressure space, and hence variations in their distribution at present potentially contain an imprint of processes by which temperature and pressure varied in the solar nebula. In this talk we restrict ourselves to species more volatile than water ice, and address issues related to processes in the outer solar system and the formation of bodies there; others in this conference will cover volatile species relevant to inner solar system processes. Study of the outer solar system is relevant both to understanding the interface between the solar nebula and the progenitor giant molecular cloud (since the chemical links to present-day observables in molecular clouds are species like methane, carbon monoxide, etc.), as well as the origin of terrestrial planet atmospheres and oceans (the latter to be covered by Owen). The wealth of compositional information on outer solar system bodies which has become available from spacecraft and ground-based observations challenges traditional simplistic views of the composition and hence dynamics of the solar nebula. The basic assumption of thermochemical equilibrium, promulgated in the 1950's, in which methane and ammonia dominate nitrogen- and carbon-bearing species, is demonstrably incorrect on both observational and theoretical grounds. However, the kinetic inhibition model which replaced it, in which carbon monoxide and molecular nitrogen dominate a nebula which is fully mixed and hence cycles outer solar system gases through a hot, chemically active zone near the disk center, is not supported either by observations. Instead, a picture of the outer solar system emerges in which the gas and grains are a mixture of relatively unaltered, or modestly altered, molecular cloud material, along with a fraction which has been chemically altered in the solar nebula itself (and perhaps giant planet nebulae).

Lunine, Jonathan I.↗
NASA NTRS2018

Characterization of Sorbents for Controlling Ammonia in Spacecraft Cabin Air

The trace contaminant control system (TCCS) utilizes packed beds of Barnebey-Sutcliffe (B-S) Type 3032 to remove ammonia from ISS (International Space Station) cabin air. BS Type 3032, an acid-impregnated activated carbon, is no longer produced and must be replaced. The adsorptive capacities of Calgon Carbon Ammonasorb II and Molecular Products Chemsorb® 1425 for ammonia were measured using moist (40% RH (Relative Humidity)) spacecraft simulated gas streams. These candidate replacement sorbents had 66% greater ammonia removal capacities at low (5 ppm) ammonia concentrations than B-S Type 3032.

Monje, Oscar↗
NASA NTRS2010

Selection of Environmentally Friendly Solvents for the Extravehicular Mobility Unit Secondary Oxygen Pack Cold Trap Testing

Freon-113(TradeMark) has been used as a chemistry lab sampling solvent at NASA/JSC for EMU (extravehicular Mobility Unit) SOP (Secondary Oxygen Pack) oxygen testing Cold Traps utilized at the USA (United Space Alliance) Houston facility. Similar testing has occurred at the HSWL (Hamilton Sundstrand Windsor Locks) facility. A NASA Executive Order bans the procurement of all ODS (ozone depleting substances), including Freon-113 by the end of 2009. In order to comply with NASA direction, HSWL began evaluating viable solvents to replace Freon-113 . The study and testing effort to find Freon-113 replacements used for Cold Trap sampling is the subject of this paper. Test results have shown HFE-7100 (a 3M fluorinated ether) to be an adequate replacement for Freon-113 as a solvent to remove and measure the non-volatile residue collected in a Cold Trap during oxygen testing. Furthermore, S-316 (a Horiba Instruments Inc. high molecular weight, non-ODS chlorofluorocarbon) was found to be an adequate replacement for Freon-113 as a solvent to reconstitute non-volatile residue removed from a Cold Trap during oxygen testing for subsequent HC (hydrocarbon) analysis via FTIR (Fourier Transform Infrared Spectroscopy).

Steele, John↗
NASA NTRS1997

Combustibility Tests of 1,1,1,2-tetrafluoroethane in a Simulated Compressor Cylinder

The advantages of high-molecular-weight gas (heavy gas) as a wind-tunnel medium have been recognized for some time. The current heavy gas of choice chlorofluorocarbon-12(CFC-12) (refrigerant R12) for the Transonic Dynamics Tunnel(TDT) must be replaced because manufacture of this gas ceased in 1995. An attractive replacement is 1,1,1,2-tetrafluoroethane (refrigerant R134a). Acceptable properties of this gas include molecular weight and speed of sound. Its vapor pressure allows simplified reclamation from mixtures with air. However, it is recognized that R134a is combustible under certain conditions of temperature, pressure, and concentration. A comprehensive study was conducted to identify those conditions and the influence of various parameters on the combustibility of the gas-air mixture.

Babcock, Dale A.↗