Results for “shell protein”

NASA NTRS2005

Rate of Iron Transfer Through the Horse Spleen Ferritin Shell Determined by the Rate of Formation of Prussian Blue and Fe-desferrioxamine Within the Ferritin Cavity

Iron (2+ and 3+) is believed to transfer through the three-fold channels in the ferritin shell during iron deposition and release in animal ferritins. However, the rate of iron transit in and out through these channels has not been reported. The recent synthesis of [Fe(CN)(sub 6)](3-), Prussian Blue (PB) and desferrioxamine (DES) all trapped within the horse spleen ferritin (HoSF) interior makes these measurements feasible. We report the rate of Fe(2+) penetrating into the ferritin interior by adding external Fe(2+) to [Fe(CN)(sub 6)](3-) encapsulated in the HoSF interior and measuring the rate of formation of the resulting encapsulated PB. The rate at which Fe(2+) reacts with [Fe(CN)(sub 6)](3-) in the HoSF interior is much slower than the formation of free PB in solution and is proceeded by a lag period. We assume this lag period and the difference in rate represent the transfer of Fe(2+) through the HoSF protein shell. The calculated diffusion coefficient, D approx. 5.8 x 10(exp -20) square meters per second corresponds to the measured lag time of 10-20 s before PB forms within the HoSF interior. The activation energy for Fe(2+) transfer from the outside solution through the protein shell was determined to be 52.9 kJ/mol by conducting the reactions at 10 to approximately 40 C. The reaction of Fe(3+) with encapsulated [Fe(CN)6](4-) also readily forms PB in the HoSF interior, but the rate is faster than the corresponding Fe(2+) reaction. The rate for Fe(3+) transfer through the ferritin shell was confirmed by measuring the rate of the formation of Fe-DES inside HoSF and an activation energy of 58.4 kJ/mol was determined. An attempt was made to determine the rate of iron (2+ and 3+) transit out from the ferritin interior by adding excess bipyridine or DES to PB trapped within the HoSF interior. However, the reactions are slow and occur at almost identical rates for free and HoSF-encapsulated PB, indicating that the transfer of iron from the interior through the protein shell is faster than the rate-limiting step of PB dissociation. The method described in this work presents a novel way of determining the rate of transfer of iron and possibly other small molecules through the ferritin shell.

Zhang, Bo↗

NASA NTRS1967

Separation of proteins in mollusc shells by gel-filtration

Separation of proteins in mollusk shells by gel filtration

PROTEIN↗

NASA NTRS2009

Identifying and Inactivating Bacterial Spores

Problems associated with, and new strategies for, inactivating resistant organisms like Bacillus canaveralius (found at Kennedy Space Center during a survey of three NASA cleanrooms) have been defined. Identifying the particular component of the spore that allows its heightened resistance can guide the development of sterilization procedures that are targeted to the specific molecules responsible for resistance, while avoiding using unduly harsh methods that jeopardize equipment. The key element of spore resistance is a multilayered protein shell that encases the spore called the spore coat. The coat of the best-studied spore-forming microbe, B. subtilis, consists of at least 45 proteins, most of which are poorly characterized. Several protective roles for the coat are well characterized including resistance to desiccation, large toxic molecules, ortho-phthalaldehyde, and ultraviolet (UV) radiation. One important long-term specific goal is an improved sterilization procedure that will enable NASA to meet planetary protection requirements without a terminal heat sterilization step. This would support the implementation of planetary protection policies for life-detection missions. Typically, hospitals and government agencies use biological indicators to ensure the quality control of sterilization processes. The spores of B. canaveralius that are more resistant to osmotic stress would serve as a better biological indicator for potential survival than those in use currently.

Newcombe, David↗

NASA NTRS2004

Kinetic Studies of Iron Deposition in Horse Spleen Ferritin Using H2O2 and O2 as Oxidants

The reaction of horse spleen ferritin (HoSF) with Fe(2+) at pH 6.5 and 7.5 using O2, H2O2 and 1:1 a mixture of both showed that the iron deposition reaction using H2O2 is approx. 20- to 50-fold faster than the reaction with O2 alone. When H2O2 was added during the iron deposition reaction initiated with O2 as oxidant, Fe(2+) was preferentially oxidized by H2O2, consistent with the above kinetic measurements. Both the O2 and H202 reactions were well defined from 15 to 40 C from which activation parameters were determined. The iron deposition reaction was also studied using O2 as oxidant in the presence and absence of catalase using both stopped-flow and pumped-flow measurements. The presence of catalase decreased the rate of iron deposition by approx. 1.5-fold, and gave slightly smaller absorbance changes than in its absence. From the rate constants for the O2 (0.044 per second) and H2O2 (0.67 per second) iron-deposition reactions at pH 7.5, simulations of steady-state H2O2 concentrations were computed to be 0.45 micromolar. This low value and reported Fe2(+)/O2 values of 2.0-2.5 are consistent with H2O2 rapidly reacting by an alternate but unidentified pathway involving a system component such as the protein shell or the mineral core as previously postulated.

Lowery, Thomas J., Jr.↗

NASA NTRS2003

Perfection of Apoferritin Crystals: An Advanced X-Ray Imaging and Diffraction Study

Ferritin is a well-known iron-storage protein, and is a spherical shell that consists of 24 identical subunits packed in a 432 symmetry. The typically large protein size and its distinction from lysozyme as to chemical and physical characteristics make ferritin an attractive model protein for crystal growth and perfection investigation-as an alternative to the most widely studied lysozyme. In this contribution, the latest results obtained from coherence-based x-ray diffraction imaging and diffraction experiments will be presented on octahedral apoferritin (a demetalized form of ferritin) crystals grown from various growth conditions. Crystal specimens, which have the measured rocking-curve widths varying from a few arcseconds to several tens arcseconds (or more), are comparatively examined by intrinsically highly sensitive mapping of lattice perfection and defects. The richness of the observed defects and growth features offers insight into perfection and growth of protein crystals. Beautiful interference fringe patterns formed in diffraction images and fine oscillation structure of rocking curves observed will be discussed for understanding of physical origins and the underlying impact.

Hu, Z. W.↗

NASA NTRS1972

Calcified proteins in the sedimentary environment.

Amino acid diagenesis is considered in relatively young fossil mollusk shells which are capable of preserving some of their original organic constituents. The rate of change of amino acid content in fossils is related to time and diagenetic temperature. Thus, the amino acid content provides information relating to the approximate ages of shells. Pleistocene temperatures and sea level changes in Florida are discussed, along with stratification correlation.

Mitterer, R. M.↗

NASA NTRS2019

Local frustration around enzyme active sites

Conflicting biological goals often meet in the specification of protein sequences for structure and function. Overall, strong energetic conflicts are minimized in folded native states according to the principle of minimal frustration, so that a sequence can spontaneously fold, but local violations of this principle open up the possibility to encode the complex energy landscapes that are required for active biological functions. We survey the local energetic frustration patterns of all protein enzymes with known structures and experimentally annotated catalytic residues. In agreement with previous hypotheses, the catalytic sites themselves are often highly frustrated regardless of the protein oligomeric state, overall topology, and enzymatic class. At the same time a secondary shell of more weakly frustrated interactions surrounds the catalytic site itself. We evaluate the conservation of these energetic signatures in various family members of major enzyme classes, showing that local frustration is evolutionarily more conserved than the primary structure itself.

Maria I. Freiberger↗

NASA NTRS2014

Biomaterials Out of Thin Air: In Situ, On-Demand Printing of Advanced Biocomposites: A New Materials Design and Production Technique Using 3D-Printed Arrays of Bioengineered Cells

We have completed the proof of concept described in our Phase I proposal, a two-material array of nonstructural proteins. We created an implementation of each step in our technology concept and demonstrated its critical functionality. The biological chassis and printing hardware we created as part of this work can be re-used for future work by inserting a material coding region upstream of the fluorescent tag. Overall, we showed that our technology concept is sound. The mission benefit analyses, as described in our Phase I proposal, are complete and contained in this report. These calculations show that our technology can save hundreds of kilograms of upmass for a potential planetary human habit construction mission: the mass per habitat module can be reduced by approximately one third if the biomaterials are manufactured on Earth and included in the mission upmass, and the full 240 kg per module can be saved if the materials are derived entirely from in situ resources. Mass savings between these two extremes is expected for an actual mission, depending on the level of in situ resource extraction technology. We have shown that continued advancement of this technology concept for use in a space mission environment is justified. Our survey of future development pathways proved extremely informative in light of the lessons learned from our proof of concept work and mission scenario analyses. For example, we were able for the first time to distinguish between the levels of functionality provided by production of structural proteins, other polymers such as polysaccharides, and true organic-inorganic composites such as bone and mineralized shell. This new information represents a significant advance in formulating specific applications, and key enabling technologies, for our proposed concept. We surveyed potential collaborations with other projects and synergies with enabling technologies that are developing. We have received requests for collaboration from other institutions, including labs at Stanford University and Drexel University. We have also received visits from industry, including Organovo, a tissue engineering company, and Autodesk, a major 3D and materials design software company. Finally, we have been in touch with the team behind the 2013 NIAC Phase ll 'Super Ball Bot-Structures for Planetary Landing and Exploration' and are planning to develop our biomaterial printing technology with the goal of enabling tensegrity-based rovers such as theirs to use lighter, more robust materials. A smooth transition from TRL 2 to TRL 3 assumes that the implementations of the technology concept which demonstrate critical functionality are also pathways for future development; while this is the case for most hardware or software projects, the multidisciplinary nature of our project, particularly the biological aspect of it, means that this is not always true. For example, as part of this work we showed that although there are large number of known genetic parts that correspond to non-structural materials, this is not true for sequences for structural organic proteins, let alone biominerals. These realizations allowed us to further subdivide our concept into more detailed development areas, some of which are clearly established at TRL 3, others of which were newly identified sub-technologies moved from TRL 1 to TRL 2. Similarly, although a single feasibility /benefit analysis is sufficient for advancement from TRL 2 to TRL 3, not all potential benefits to a technology concept as broad in scope as ours are apparent at TRL 2. Both our future pathways survey and our proof of concept work highlighted that the true mass savings potential of our technology concept cannot be quantified without modification of existing materials modelling tools to take into account the possibility of positional materials properties customization. Therefore, we have simultaneously both advanced one potential set of applications of our technology concept from TRL 2 to TRL 3 and also identified a previously unknown set of applications and advanced it from TRL 1 to TRL 2. Overall, we have moved the original formulation of our concept forward from TRL 2 to TRL 3, and the expanded formulation of it presented in this document has been advanced from a combination of TRL 1 and early 1RL 2 to an overall late TRL 2. We have also identified the key areas necessary for both short-term and long-term advancement, and made recommendations for specific future work in the most promising directions. With future work on a 1-2 year timeframe to continue advancement to overall TRL 3, we will be well positioned to begin work on a specific space mission technology insertion path.

Biology↗

NASA NTRS2001

A Structural and Molecular Approach for the Study Biomarkers

Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.

Thomas-Keprta, Kathie↗

NASA NTRS2000

Microgravity mediated changes in phytoferritin accumulation in soybean root cap cells

Phytoferritin is an iron-protein complex analogous to the ferritin found in mammalian, bacteria and fungi cells. Phytoferritin molecules are large proteins, about 10.5 nm in diameter, visualised in an electron microscope as discrete, electron dense particles with iron-containing core, where several thousand atoms of iron lie within the proteinaceous shell (apoferritin). In higher plants, a plastid stroma is the site of phytoferritin storage. Phytoferritin is seen in all types of plastids. It is considered to be a mechanism used by cells to store iron in a non-toxic form. Phytoferritin-bound iron may subsequently be used to form iron-containing components. It was shown that low levels of phytoferritin are synthesised in normal green leaves, whereas chlorotic leaves do not have a measurable amount of phytoferritin and leaves of iron-loaded seedlings contain a high level of total iron, and phytoferritin well-filled by iron. Phytoferritin accumulation was observed in photosynthetic inactivity chloroplasts during senescence and disease. In this study we analised the effects of microgravity and ethylene on production of phytoferritin in the root cap columella cells of soybean seedlings.

short duration↗

NASA NTRS2015

Biomaterials Out of Thin Air: in Situ, On-Demand Printing of Advanced Biocomposites

Upmass is the single most significant limitation of our current space mission capability. Although biomaterials and biocomposites have mass, strength, flexibility, and self-healing properties that could significantly reduce upmass, their use is limited by the following drawbacks: Expensive, specific production. Many biomaterials can only be produced as part of significant support ecosystem; Inaccessible functional customization. The grain of wood, the porosity of bone, and so on are an integral part of the materials' desired mechanical properties, but are not deterministic when the material is naturally grown; Limited compositions. Most biomaterials (unlike metal, plastic, etc.) cannot be easily combined or modified to produce new materials. This project builds on recent advances in: Synthetic biology. Libraries of standardized genetic parts which can be used for controlled cellular material production, delivery, and binding; 3D printing. Commercial off-the-shelf components which can be used to make of a pico- to nanoliter cell deposition system; Tissue engineering. Proven cell-compatible support hydrogels and scaffolds can be modified to bind the deposited biomaterials of interest. Objectives: Feasibility and benefit analysis. Two mission contexts span the concept's scope (see below); Proof-of-concept demonstration. A simple grid of two proteins, fluorescent for easy detection, to validate the core technology concept; Proposed implementations for follow-on work. Avenues for future work on each core component (host cell, production control, material delivery, material binding, etc.); Complementary studies exploration. A survey of other emerging areas (in situ resource utilization, protein engineering, etc.) with the potential to multiply our technology's impact. Potential Impacts: This application could dramatically expand manufacturing capabilities on Earth and in space: In situ resource utilization. A far greater range of materials and products will be available from the limited palette offered by in situ resource extraction techniques; Reduced equipment and material upmass for off-Earth habitats. Ready- to-use highly specialized construction materials (radiation hardened, compressive/tensile, light or dense) from an extremely low starting mass; Structured biomaterial production. New ready-to-use macro, micro, and molecular manufacturing techniques for traditional biomaterials such as wood, bone and shell; New and novel biocomposite creation. The ability to create completely novel material composites from any base material that cells can be engineered to produce. Suggested Mission Contexts: ISS part manufacturing. A 'minimal working example' making a finished biomaterial part aboard the International Space Station; A long-term Mars habitat. 'Cradle-to-grave' use at a hypothetical Mars habitat, covering everything from tools to construction materials. Alternate Abstract: Imagine being able to print anything from tools and composite building materials to food and human tissues. Imagine being on Mars with the ability to replace any broken part, whether it's a part of your spacesuit, your habitat, or your own body. We propose a technique that would allow just that. By printing 3D arrays of cells engineered to secrete the necessary materials, the abundant in situ resources of atmosphere and regolith become organic, inorganic, or organic-inorganic composite materials. Such materials include novel, biologically derived materials not previously possible to fabricate.

habitats↗

NASA NTRS2015

Biomaterials Out of Thin Air: in Situ, On-demand Printing of Advanced Biocomposites

Upmass is the single most significant limitation of our current space mission capability. Although biomaterials and biocomposites have mass, strength, flexibility, and self-healing properties that could significantly reduce upmass, their use is limited by the following drawbacks: Expensive, specific production. Many biomaterials can only be produced as part of significant support ecosystem; Inaccessible functional customization. The grain of wood, the porosity of bone, and so on are an integral part of the materials' desired mechanical properties, but are not deterministic when the material is naturally grown; Limited compositions. Most biomaterials (unlike metal, plastic, etc.) cannot be easily combined or modified to produce new materials. This project builds on recent advances in: Synthetic biology. Libraries of standardized genetic parts which can be used for controlled cellular material production, delivery, and binding; 3D printing. Commercial off-the-shelf components which can be used to make of a pico- to nanoliter cell deposition system; Tissue engineering. Proven cell-compatible support hydrogels and scaffolds can be modified to bind the deposited biomaterials of interest. Objectives: Feasibility and benefit analysis. Two mission contexts span the concept's scope (see below); Proof-of-concept demonstration. A simple grid of two proteins, fluorescent for easy detection, to validate the core technology concept; Proposed implementations for follow-on work. Avenues for future work on each core component (host cell, production control, material delivery, material binding, etc.); Complementary studies exploration. A survey of other emerging areas (in situ resource utilization, protein engineering, etc.) with the potential to multiply our technology's impact. Potential Impacts: This application could dramatically expand manufacturing capabilities on Earth and in space: In situ resource utilization. A far greater range of materials and products will be available from the limited palette offered by in situ resource extraction techniques; Reduced equipment and material upmass for off-Earth habitats. Ready- to-use highly specialized construction materials (radiation hardened, compressive/tensile, light or dense) from an extremely low starting mass; Structured biomaterial production. New ready-to-use macro, micro, and molecular manufacturing techniques for traditional biomaterials such as wood, bone and shell; New and novel biocomposite creation. The ability to create completely novel material composites from any base material that cells can be engineered to produce. Suggested Mission Contexts: ISS part manufacturing. A 'minimal working example' making a finished biomaterial part aboard the International Space Station; A long-term Mars habitat. 'Cradle-to-grave' use at a hypothetical Mars habitat, covering everything from tools to construction materials. Alternate Abstract: Imagine being able to print anything from tools and composite building materials to food and human tissues. Imagine being on Mars with the ability to replace any broken part, whether it's a part of your spacesuit, your habitat, or your own body. We propose a technique that would allow just that. By printing 3D arrays of cells engineered to secrete the necessary materials, the abundant in situ resources of atmosphere and regolith become organic, inorganic, or organic-inorganic composite materials. Such materials include novel, biologically derived materials not previously possible to fabricate.

habitats↗

NASA NTRS2019

De novo design of symmetric ferredoxins that shuttle electrons in vivo

A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from −405 to −515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway in Escherichia coli. These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality.

Andrew C. Mutter↗

NASA NTRS1977

A critical evaluation of the application of amino acid racemization to geochronology and geothermometry

Attempts have been made to determine the age of biological samples by measuring the racemization of amino acids in protein samples. The pitfalls and inherent complications in diagenetic racemization studies are reviewed, and recent advances in improving techniques are outlined. Methodological topics include isolation of amino acids from geological samples, resolution of amino acid enantiomers, and the effects of acid hydrolysis. The theory and kinetics of amino acid racemization are discussed with attention to the derivation of the rate expression for amino acid racemization, isoleucine and the equilibrium constant, the mechanism of amino acid racemization, the racemization of 'bound' versus 'free' amino acids, and factors affecting the racemization rates of free amino acids in aqueous solution. Applications of amino acid racemization kinetics to geochronology is considered with reference to shells, marine sediments, and bones. Potential complications include heating and diagenesis, diagenetic formation of amino acids, the effect of clays, species effect, and contamination.

Williams, K. M.↗

NASA NTRS2003

Near-infrared detection of potential evidence for microscopic organisms on Europa

The possibility of an ocean within the icy shell of Jupiter's moon Europa has established that world as a primary candidate in the search for extraterrestrial life within our Solar System. This paper evaluates the potential to detect evidence for microbial life by comparing laboratory studies of terrestrial microorganisms with measurements from the Galileo Near Infrared Imaging Spectrometer (NIMS). If the interior of Europa at one time harbored life, some evidence may remain in the surface materials. Examination of laboratory spectra of terrestrial extremophiles measured at cryogenic temperatures reveals distorted, asymmetric nearinfrared absorption features due to water of hydration. The band centers, widths, and shapes of these features closely match those observed in the Europa spectra. These features are strongest in reddish-brown, disrupted terrains such as linea and chaos regions. Narrow spectral features due to amide bonds in the microbe proteins provide a means of constraining the abundances of such materials using the NIMS data. The NIMS data of disrupted terrains exhibit distorted, asymmetric near-infrared absorption features consistent with the presence of water ice, sulfuric acid octahydrate, hydrated salts, and possibly as much as 0.2 mg cm(-3) of carbonaceous material that could be of biological origin. However, inherent noise in the observations and limitations of spectral sampling must be taken into account when discussing these findings.

Extraterrestrial Environment↗