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NASA NTRS2014

Proteins with Novel Structure, Function and Dynamics

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828‐831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81‐83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha‐helix or beta‐sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Proteins↗

NASA NTRS2017

Flexible Proteins at the Origin of Life

Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.

Flexible protein↗

NASA NTRS1997

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↗

NASA NTRS1990

Cooling system and insulation concept for a Mach 5 turbo-ramjet aircraft

A cooling system and insulation concept for a Mach 5 cruise aircraft, using non-cryogenic fuel is presented. Catalytic endothermic reaction of petroleum fuel is used as the heat sink for engine cooling. A secondary closed-loop coolant circuit removes heat from the engine and transfers this heat to the catalytic reactor. Insulation on the engine flow path surfaces reduces the cooling requirements. A high temperature insulation system, which is capable of a surface temperature of 4,000 F, is used for the combustor and nozzle. A complete closed-loop cooling system design is shown in detail. Main features of this system include a fuel preheater, a catalytic fuel reactor, and engine wall cooling panels. A silicone-based liquid polymer, designed for extended use at 750 F, is used as the coolant. The preheater and reactor design are based on the results of recent experimental work. The cooling panels are designed using a thermal fluid analysis computer program, which was originally developed for the National Aero-Space Plane (NASP). Major components are analyzed structurally as well as thermally and weights are presented.

Jones, S. C.↗

NASA NTRS1995

Closed-Loop System Removes Contaminants From Inert Gas

Concentration of oxygen in this closed-loop system kept low by use of heated catalytic sorbent bed in cartridge. Proposed to keep concentration of water vapor low by use of predried zeolite sorbent bed in another cartridge, and to remove particles smaller than 0.1 micrometer by use of porous metal filters. In specific application, chamber is one in which semiconducting materials processed. By virtue of closed-loop operation, limited supply of inert gas adequate to provide atmosphere for industrial processing of semiconductors.

Sharma, Pramod K.↗

NASA NTRS2003

Regenerable Incinerator Exhaust Purification and Trace Contaminant Control System

In this novel approach to air purification, contaminants removed from a process air stream by a high-capacity adsorbent are displaced periodically by a warm, high-humidity, reverse-flow air stream. Displaced contaminants flow into a closed regeneration loop, in which organic compounds are oxidized catalytically and acid gases are removed by a gas- water contactor (which also serves as the source of the water vapor). These features are expected to result in a design that has few expendables and lower energy consumption than alternative regenerable techniques. The joint project between NASA Ames Research Center and Vanderbilt University has completed its third year. Breadboard development continues at NASA Ames, while Vanderbilt has completed most of its adsorption equilibria development. Vanderbilt has completed its fixed-bed apparatus for investigation of dynamic adsorption and desorption processes for trace organic compounds and water vapor, and is continuing its development of the mathematical model describing the column dynamics.

Finn, John E.↗

NASA NTRS2010

Advanced Catalysts for the Ambient Temperature Oxidation of Carbon Monoxide and Formaldehyde

The primary applications for ambient temperature carbon monoxide (CO) oxidation catalysts include emergency breathing masks and confined volume life support systems, such as those employed on the Shuttle. While Hopcalite is typically used in emergency breathing masks for terrestrial applications, in the 1970s, NASA selected a 2% platinum (Pt) on carbon for use on the Shuttle since it is more active and also more tolerant to water vapor. In the last 10-15 years there have been significant advances in ambient temperature CO oxidation catalysts. Langley Research Center developed a monolithic catalyst for ambient temperature CO oxidation operating under stoichiometric conditions for closed loop carbon dioxide (CO2) laser applications which is also advertised as having the potential to oxidize formaldehyde (HCHO) at ambient temperatures. In the last decade it has been discovered that appropriate sized nano-particles of gold are highly active for CO oxidation, even at sub-ambient temperatures, and as a result there has been a wealth of data reported in the literature relating to ambient/low temperature CO oxidation. In the shorter term missions where CO concentrations are typically controlled via ambient temperature oxidation catalysts, formaldehyde is also a contaminant of concern, and requires specially treated carbons such as Calgon Formasorb as untreated activated carbon has effectively no HCHO capacity. This paper examines the activity of some of the newer ambient temperature CO and formaldehyde (HCHO) oxidation catalysts, and measures the performance of the catalysts relative to the NASA baseline Ambient Temperature Catalytic Oxidizer (ATCO) catalyst at conditions of interest for closed loop trace contaminant control systems.

Nalette, Tim↗

NASA NTRS1976

A mature Bosch CO2 reduction technology

The reduction of CO2 is one of the steps in closing the oxygen loop for long-duration manned space missions. Several units utilizing the Bosch process, which catalytically reduces CO2 with hydrogen, have been built and operated during the past decade. Each contributed substantial information affecting subsequent designs. Early challenges were primarily concerned with carbon control, materials durability, and reliability of reaction initiation. These were followed by concern about power consumption, expendable weight, volume, and process rate control. Suitable materials and techniques for carbon containment and process reliability have been demonstrated. Power requirements have been reduced by almost an order of magnitude. Methods for significant reductions in expendable weight and volume have been developed. The technology is at a state of maturity directly applicable to designs for space missions.

King, C. D.↗

NASA NTRS2015

Evaluation of Volatile Species in Green Monopropellant Project

NASA is interested in green monopropellants to replace hydrazine in reaction control systems (RCSs). Some current NASA programs require reduced vapor pressure and low toxicity monopropellant (green) and superior performance (specific impulse and density) formulations. Earlier vapor phase studies of a candidate green monopropellant at the NASA White Sands Test Facility (WSTF) showed the presence of a volatile species that warranted further investigation. The purpose of this study was to further characterize the volatile species and to evaluate it. The evaluation was with respect to whether the volatile species was an impurity or how it is formed, and to use that information to examine whether its presence as an impurity can be eliminated during formulation. The evaluation also considered whether formation of the volatile impurity could be prevented while not compromising the propellant. To reduce variables associated with evaluation of the propellant formulation as a whole, a precursor to one of the individual components in the propellant formulation was subjected to a NASA Standard 6001B Flammability, Off-gassing, and Compatibility Requirements and Test Procedures "Determination of Off-gassed Products (Test 7)". Testing took place in the NASA WSTF Molecular Desorption and Analysis Laboratory. One gram of the precursor was placed in a flask within a specimen container. After thermal conditioning for 72 +/- 1 h at 50 +/- 3 deg C (122 +/- 5 deg F), the atmosphere inside the specimen container was analyzed for off-gassed compounds by cryotrap gas chromatography-mass spectrometry (GC-MS) and fixed sample loop GC-flame ionization detection (GC-FID). The specimen container used was glass to minimize potential catalytic surfaces. The identification of compounds was difficult due to the complexity of the vapor phase concentrations and overlapping chromatographic peaks and mass spectra. However, eleven compounds were specifically identified and five compounds or classes of compounds were reported as unidentified. Quantitation of most of the compounds, including unidentified compounds, was as methane. Quantitating compounds or classes of compounds that were detected but for which specific calibration is not established as methane is in accordance with the Test 7 standard protocol. The thermal decomposition temperature of the precursor was significantly higher than the test temperature. Based on thermal decomposition temperature and on an examination of the structure and chemistry of the identified volatile species, the presence of the volatile species appears to be chemically reasonable with respect to the propellant formulation and is at this time attributed to impurities. Further examination of the overall propellant formulation process (including the individual components' synthesis processes) and process quality control (including purity of reagents and possible decomposition reactions) is indicated.

Greene, Benjamin↗

NASA NTRS1972

Bosch CO2 reduction unit research and development.

Development of Bosch CO2 reduction units for manned spacecraft application has been in progress for a decade. The Bosch process catalytically reacts CO2 with H2 to produce water and carbon. The water may then be electrolyzed to close the biological oxygen and process hydrogen loops. A critical problem has been to confine the reaction so that carbon does not block flow and stop the process. Reaction isolation within a replaceable catalyst cartridge has been successfully demonstrated. Objectives of the current development program are a 25% reduction in operating power, an 80% reduction in expendable weight, and minimized resupply volume.

Holmes, R. F.↗

NASA NTRS2001

The Effect of Cytidine on the Structure and Function of an RNA Ligase Ribozyme

A cytidine-free ribozyme with RNA ligase activity was obtained by in vitro evolution, starting from a pool of random- sequence RNAs that contained only guanosine, adenosine, and uridine. This ribozyme contains 74 nt and catalyzes formation of a 3',5' -phosphodiester linkage with a catalytic rate of 0.016/min. The RNA adopts a simple secondary structure based on a three-way junction motif, with ligation occurring at the end of a stem region located several nucleotides away from the junction. Cytidine was introduced to the cytidine-free ribozyme in a combinatorial fashion and additional rounds of in vitro evolution were carried out to allow the molecule to adapt to this added component. The resulting cytidine-containing ribozyme formed a 3',5' linkage with a catalytic rate of 0.32/min. The improved rate of the cytidine-containing ribozyme was the result of 12 mutations, including seven added cytidines, that remodeled the internal bulge loops located adjacent to the three-way junction and stabilized the peripheral stem regions.

Rogers, Jeff↗

NASA NTRS1982

Low and medium heating value coal gas catalytic combustor characterization

Catalytic combustion with both low and medium heating value coal gases obtained from an operating gasifier was demonstrated. A practical operating range for efficient operation was determined, and also to identify potential problem areas were identified for consideration during stationary gas turbine engine design. The test rig consists of fuel injectors, a fuel-air premixing section, a catalytic reactor with thermocouple instrumentation and a single point, water cooled sample probe. The test rig included inlet and outlet transition pieces and was designed for installation into an existing test loop.

Schwab, J. A.↗

NASA NTRS2006

Generating Breathable Air Through Dissociation of N2O

A nitrous oxide-based oxygen-supply system (NOBOSS) is an apparatus in which a breathable mixture comprising 2/3 volume parts of N2 and 1/3 volume part of O2 is generated through dissociation of N2O. The NOBOSS concept can be adapted to a variety of applications in which there are requirements for relatively compact, lightweight systems to supply breathable air. These could include air-supply systems for firefighters, divers, astronauts, and workers who must be protected against biological and chemical hazards. A NOBOSS stands in contrast to compressed-gas and cryogenic air-supply systems. Compressed-gas systems necessarily include massive tanks that can hold only relatively small amounts of gases. Alternatively, gases can be stored compactly in greater quantities and at low pressures when they are liquefied, but then cryogenic equipment is needed to maintain them in liquid form. Overcoming the disadvantages of both compressed-gas and cryogenic systems, the NOBOSS exploits the fact that N2O can be stored in liquid form at room temperature and moderate pressure. The mass of N2O that can be stored in a tank of a given mass is about 20 times the mass of compressed air that can be stored in a tank of equal mass. In a NOBOSS, N2O is exothermically dissociated to N2 and O2 in a main catalytic reactor. In order to ensure the dissociation of N2O to the maximum possible extent, the temperature of the reactor must be kept above 400 C. At the same time, to minimize concentrations of nitrogen oxides (which are toxic), it is necessary to keep the reactor temperature at or below 540 C. To keep the temperature within the required range throughout the reactor and, in particular, to prevent the formation of hot spots that would be generated by local concentrations of the exothermic dissociation reaction, the N2O is introduced into the reactor through an injector tube that features carefully spaced holes to distribute the input flow of N2O widely throughout the reactor. A NOBOSS includes one or more "destroyer" subsystems for removing any nitrogen oxides that remain downstream of the main N2O-dissociation reactor. A destroyer includes a carbon bed in series with a catalytic reactor, and is in thermal contact with the main N2O-dissociation reactor. The gas mixture that leaves the main reactor first goes through a carbon bed, which adsorbs all of the trace NO and most of the trace NO2. The gas mixture then goes through the destroyer catalytic reactor, wherein most or all of the remaining NO2 is dissociated. A NOBOSS can be designed to regulate its reactor temperature across a range of flow rates. One such system includes three destroyer loops; these loops act, in combination with a heat sink, to remove heat from the main N2O-dissociation reactor. In this system, the N2O and product gases play an additional role as coolants; thus, as needed, the coolant flow increases in proportion to the rate of generation of heat, helping to keep the main-reactor temperature below 540 C.

Zubrin, Robert↗

NASA NTRS1983

The study of integrated coal-gasifier molten carbonate fuel cell systems

A novel integration concept for a coal-fueled coal gasifier-molten carbonate fuel cell power plant was studied. Effort focused on determining the efficiency potential of the concept, design, and development requirements of the processes in order to achieve the efficiency. The concept incorporates a methane producing catalytic gasifier of the type previously under development by Exxon Research and Development Corp., a reforming molten carbonate fuel cell power section of the type currently under development by United Technologies Corp., and a gasifier-fuel cell recycle loop. The concept utilizes the fuel cell waste heat, in the form of hydrogen and carbon monoxide, to generate additional fuel in the coal gasifier, thereby eliminating the use of both an O2 plant and a stream bottoming cycle from the power plant. The concept has the potential for achieving coal-pile-to-busbar efficiencies of 50-59%, depending on the process configuration and degree of process configuration and degree of process development requirements. This is significantly higher than any previously reported gasifier-molten carbonate fuel cell system.

Source record↗

NASA NTRS1975

Development of an advanced spacecraft water and waste materials processing system

An Integrated Waste Management-Water System (WM-WS) which uses radioisotopes for thermal energy is described and results of its trial in a 4-man, 180 day simulated space mission are presented. It collects urine, feces, trash, and wash water in zero gravity, processes the wastes to a common evaporator, distills and catalytically purifies the water, and separates and incinerates the solid residues using little oxygen and no chemical additives or expendable filters. Technical details on all subsystems are given along with performance specifications. Data on recovered water and heat loss obtained in test trials are presented. The closed loop incinerator and other projects underway to increase system efficiency and capacity are discussed.

Murray, R. W.↗

NASA NTRS1985

Space shuttle revitalization system

The Space Shuttle air revitalization system is discussed. The sequential steps in loop closure are examined and a schematic outline of the regenerative air revitalization system is presented. Carbon dioxide reduction subsystem concepts are compared. Schemes are drawn for: static feedwater electrolysis cell, solid polymer electrolyte water electrolysis cell, air revitalization system, nitrogen generation reactions, nitrogen subsystem staging, vapor compression distillation subsystem, thermoelectric integrated membrane evaporation subsystem, catalytic distillation water reclamation subsystem, and space shuttle solid waste management system.

Quattrone, P. D.↗

NASA NTRS2016

Development of a Microwave Regenerative Sorbent-Based Hydrogen Purifier

This paper describes the design and fabrication of a Microwave Regenerative Sorbent-based Hydrogen Purifier (MRSHP). This unique microwave powered technology was developed for the purification of a hydrogen stream produced by the Plasma Pyrolysis Assembly (PPA). The PPA is a hydrogen recovery (from methane) post processor for NASA's Sabatier-based carbon dioxide reduction process. Embodied in the Carbon dioxide Reduction Assembly (CRA), currently aboard the International Space Station (ISS), the Sabatier reaction employs hydrogen to catalytically recover oxygen, in the form of water, from respiratory carbon dioxide produced by the crew. This same approach is base-lined for future service in the Air Revitalization system on extended missions into deep space where resupply is not practical. Accordingly, manned exploration to Mars may only become feasible with further closure of the air loop as afforded by the greater hydrogen recovery permitted by the PPA with subsequent hydrogen purification. By utilizing the well-known high sorbate loading capacity of molecular sieve 13x, coupled with microwave dielectric heating phenomenon, MRSHP technology is employed as a regenerative filter for a contaminated hydrogen gas stream. By design, freshly regenerated molecular sieve 13x contained in the MRSHP will remove contaminants from the effluent of a 1-CM scale PPA for several hours prior to breakthrough. By reversing flow and pulling a relative vacuum the MRSHP prototype then uses 2.45 GHz microwave power, applied through a novel coaxial antenna array, to rapidly heat the sorbent bed and drive off the contaminants in a short duration vacuum/thermal contaminant desorption step. Finally, following rapid cooling via room temperature cold plates, the MRSHP is again ready to serve as a hydrogen filter.

Wheeler, Richard R., Jr.↗

NASA NTRS2011

Carbon Dioxide Reduction Technology Trade Study

For long-term human missions, a closed-loop atmosphere revitalization system (ARS) is essential to minimize consumables. A carbon dioxide (CO2) reduction technology is used to reclaim oxygen (O2) from metabolic CO2 and is vital to reduce the delivery mass of metabolic O2. A key step in closing the loop for ARS will include a proper CO2 reduction subsystem that is reliable and with low equivalent system mass (ESM). Sabatier and Bosch CO2 reduction are two traditional CO2 reduction subsystems (CRS). Although a Sabatier CRS has been delivered to International Space Station (ISS) and is an important step toward closing the ISS ARS loop, it recovers only 50% of the available O2 in CO2. A Bosch CRS is able to reclaim all O2 in CO2. However, due to continuous carbon deposition on the catalyst surface, the penalties of replacing spent catalysts and reactors and crew time in a Bosch CRS are significant. Recently, technologies have been developed for recovering hydrogen (H2) from Sabatier-product methane (CH4). These include methane pyrolysis using a microwave plasma, catalytic thermal pyrolysis of CH4 and thermal pyrolysis of CH4. Further, development in Sabatier reactor designs based on microchannel and microlith technology could open up opportunities in reducing system mass and enhancing system control. Improvements in Bosch CRS conversion have also been reported. In addition, co-electrolysis of steam and CO2 is a new technology that integrates oxygen generation and CO2 reduction functions in a single system. A co-electrolysis unit followed by either a Sabatier or a carbon formation reactor based on Bosch chemistry could improve the overall competitiveness of an integrated O2 generation and CO2 reduction subsystem. This study evaluates all these CO2 reduction technologies, conducts water mass balances for required external supply of water for 1-, 5- and 10-yr missions, evaluates mass, volume, power, cooling and resupply requirements of various technologies. A system analysis and comparison among the technologies was made based on ESM, technology readiness level and reliability. Those technologies with potential were recommended for development.

Jeng, Frank F.↗