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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles

The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.

Chemistry↗
NASA NTRS2000

Co-conservation of rRNA tetraloop sequences and helix length suggests involvement of the tetraloops in higher-order interactions

Terminal loops containing four nucleotides (tetraloops) are common in structural RNAs, and they frequently conform to one of three sequence motifs, GNRA, UNCG, or CUUG. Here we compare available sequences and secondary structures for rRNAs from bacteria, and we show that helices capped by phylogenetically conserved GNRA loops display a strong tendency to be of conserved length. The simplest interpretation of this correlation is that the conserved GNRA loops are involved in higher-order interactions, intramolecular or intermolecular, resulting in a selective pressure for maintaining the lengths of these helices. A small number of conserved UNCG loops were also found to be associated with conserved length helices, consistent with the possibility that this type of tetraloop also takes part in higher-order interactions.

Non-NASA Center↗
NASA NTRS2018

Development and Qualification of the Primary Structure of the Orion European Service Module

This paper presents an overview of the development and qualification test campaign for the primary structure of the European Service Module of ORION, the NASA spacecraft which will serve the future human exploration missions to the Moon, Mars and beyond. Under an agreement between NASA and ESA, the ORION will be powered by a European Service Module (ESM), providing also water and oxygen for astronauts' life sustainability. The development and qualification of the European Service Module (ESM) is under ESA responsibility with Airbus Defense and Space as the prime contractor. Thales Alenia Space Italia is responsible for design development, manufacturing, assembly and qualification of the Structure subsystem. The European Service Module, installed onto the launch adapter, shall support the crew module with its adapter and a launch abort system. It shall sustain: - A combination of global and local launch loads during lift off and ascent phases, - On orbit loads induced by engine firing for orbital transfers and attitude control. The ESM structure is based on a core made of Composite Fiber Reinforced Polymer (CFRP) sandwich panels complemented by aluminum alloy platforms, longerons and secondary structures. A development campaign has been implemented in order to define and validate composite parts' strength allowable values for design: coupon tests at material level, test at component level up to breadboards tests performed on main structural components (composite to metallic joints, and at panels' discontinuities). An incremental approach as defined in [1] has been followed. A qualification static test campaign at primary structure assembly level has been implemented in order to validate the design against static stiffness and ultimate strength as well as to correlate the structural Finite Element Model (FEM) used for sizing and confirm the margins of safety. The tests have been performed successfully by Thales Alenia Space Italia (TAS-I) on two flight representative structural models (STA1, STA2), in Turin facilities (Italy) between August 2015 and March 2017, with engineering support of technical representatives from Airbus, ESA, NASA and LMCO. The main development and qualification test activities and associated results are presented and discussed in the paper

Structural Testing↗
DOE OSTI2024

Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator

Campylobacter jejuni is a foodborne pathogen commonly found in the intestinal tracts of animals. This pathogen is a leading cause of gastroenteritis in humans. Besides its highly infectious nature, C. jejuni is increasingly resistant to a number of clinically administrated antibiotics. As a consequence, the Centers for Disease Control and Prevention has designated antibiotic-resistant Campylobacter as a serious antibiotic resistance threat in the United States. The C. jejuni CosR regulator is essential to the viability of this bacterium and is responsible for regulating the expression of a number of oxidative stress defense enzymes. Importantly, it also modulates the expression of the CmeABC multidrug efflux system, the most predominant and clinically important system in C. jejuni that mediates resistance to multiple antimicrobials. Here, we report structures of apo-CosR and CosR bound with a 21 bp DNA sequence located at the cmeABC promotor region using both single-particle cryo-electron microscopy and X-ray crystallography. These structures allow us to propose a novel mechanism for CosR regulation that involves a long-distance conformational coupling and rearrangement of the secondary structural elements of the regulator to bind target DNA.

CosR-DNA complex↗
DOE OSTI2024

Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ

Abstract The mitochondrial single-stranded DNA (ssDNA) binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.

Biochemistry & Molecular Biology↗
NASA NTRS2007

Structural Feasibility Analysis of a Robotically Assembled Very Large Aperture Optical Space Telescope

This paper presents a feasibility study of robotically constructing a very large aperture optical space telescope on-orbit. Since the largest engineering challenges are likely to reside in the design and assembly of the 150-m diameter primary reflector, this preliminary study focuses on this component. The same technology developed for construction of the primary would then be readily used for the smaller optical structures (secondary, tertiary, etc.). A reasonable set of ground and on-orbit loading scenarios are compiled from the literature and used to define the structural performance requirements and size the primary reflector. A surface precision analysis shows that active adjustment of the primary structure is required in order to meet stringent optical surface requirements. Two potential actuation strategies are discussed along with potential actuation devices at the current state of the art. The finding of this research effort indicate that successful technology development combined with further analysis will likely enable such a telescope to be built in the future.

space telescopes↗
DOE OSTI2025

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗
DOE OSTI2022

Structure of the Core Postfusion Porcine Endogenous Retrovirus Fusion Protein

Retroviral elements from endogenous retroviruses have functions in mammalian physiology. The best-known examples are the envelope proteins that function in placenta development and immune suppression. Porcine endogenous retroviruses (PERVs) are an understudied class of endogenous retroviruses that infect cultured human cells, raising concern regarding porcine xenografts. The PERV envelope glycoprotein has also been proposed as a possible swine syncytin with a role in placental development. Despite the growing interest in PERVs, their envelope glycoproteins remain poorly characterized. Here, we successfully determined the postfusion crystal structure of the PERV core fusion ectodomain. The PERV fusion protein structure reveals a conserved class I viral fusion protein six-helix bundle. Biophysical experiments demonstrated that the thermodynamic stability of the PERV fusion protein secondary structure was the same at physiological and acidic pHs. A conserved surface analysis highlights the high degree of sequence conservation among retroviral fusogens in the chain reversal region that facilitates the large-scale conformational change required for membrane fusion. Further structural alignment of class I viral fusogens revealed a phylogenetic clustering that shows evolution into various lineages that correlate with virus mechanisms of cell entry. Our work indicates that structural dendrograms can be used to qualitatively infer insights into the fusion mechanisms of newly discovered class I viral fusogen structures.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2007

On the Use of 3dB Qualification Margin for Structural Parts on Expendable Launch Vehicles

The standard random vibration qualification test used for Expendable Launch Vehicle components is Maximum Predicted Environment (MPE) + 6dB for a duration of 4 times the service life of the part. This can be a severe qualification test for these fatigue-sensitive structures. This paper uses flight data from several launch vehicles to establish that reducing the qualification approach to MPE+3dB for the duration of the peak environment (1x life) is valid for fatigue-sensitive structural components. Items that can be classified as fatigue-sensitive are probes, ducts, tubing, bellows, hoses, and any non-functional structure. Non-functional structure may be flight critical or carry fluid, but it cannot include any moving parts or electronics. This reduced qualification approach does not include primary or secondary structure which would be exclusively designed by peak loads, either transient or quasi-static, that are so large and of so few cycles as to make fatigue a moot point.

Yunis, Isam↗
NASA NTRS1973

Approximations for neutron emission spectra from proton collisions between 20 and 500 MeV on nuclei of A greater than or equal to 12

When high energy protons from solar proton events or trapped radiation belts impinge on spacecraft structures, secondary particles are emitted. The most pernicious secondaries, from either a biological or physical standpoint, are the cascade and evaporation neutrons because of their reaction with matter leading to radioactive materials in the spacecraft structures. Empirically determined cascade and evaporation neutron emission spectra for protons of energy between 20 and 500 MeV incident on all materials at or above carbon in mass number are presented.

Burrell, M. O.↗
DOE OSTI2024

Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non‐natural substrate specificity

Abstract Isopentenyl phosphate kinases (IPKs) have recently garnered attention for their central role in biocatalytic “isoprenol pathways,” which seek to reduce the synthesis of the isoprenoid precursors to two enzymatic steps. Furthermore, the natural promiscuity of IPKs toward non‐natural alkyl‐monophosphates (alkyl‐Ps) as substrates has hinted at the isoprenol pathways' potential to access novel isoprenoids with potentially useful activities. However, only a handful of IPK crystal structures have been solved to date, and even fewer of these contain non‐natural substrates bound in the active site. The current study sought to elucidate additional ternary complexes bound to non‐natural substrates using the IPK homolog fromThermococcus paralvinellae(TcpIPK). Four such structures were solved, each bound to a different non‐natural alkyl‐P and the phosphoryl donor substrate/product adenosine triphosphate (ATP)/adenosine diphosphate (ADP). As expected, the quaternary, tertiary, and secondary structures ofTcpIPK closely resembled those of IPKs published previously, and kinetic analysis of a novel alkyl‐P substrate highlighted the potentially dramatic effects of altering the core scaffold of the natural substrate. Even more interesting, though, was the discovery of a trend correlating the position of two α helices in the active site with the magnitude of an IPK homolog's reaction rate for the natural reaction. Overall, the current structures ofTcpIPK highlight the importance of continued structural analysis of the IPKs to better understand and optimize their activity with both natural and non‐natural substrates.

Biochemistry & Molecular Biology↗
NASA NTRS1982

Polymer materials research at NASA Ames Research Center

Polymers that provide significant improvements in both efficiency and safety for civilian transport aircraft and military combat aircraft were developed. High strength to weight structures such as carbon fiber composites with long term durability are requirements common to both classes of aircraft. Aircraft safety improvements in fire resistance and crashworthiness of primary and secondary structures are long term objectives for transport aircraft. Void filler ballistic foams, intumescent coatings, and radiation-resistant transparent plastics contribute to vulnerability reduction in combat military aircraft. Low and high velocity impact tolerance, fire resistance, thermal stability, and long term durability of polymers and components are emphasized.

J. A. Parker↗
NASA NTRS1992

Resin transfer molding of textile preforms for aircraft structural applications

The NASA LaRC is conducting and supporting research to develop cost-effective fabrication methods that are applicable to primary composite aircraft structures. One of the most promising fabrication methods that has evolved is resin transfer molding (RTM) of dry textile material forms. RTM has been used for many years for secondary structures, but has received increased emphasis because it is an excellent method for applying resin to damage-tolerant textile preforms at low cost. Textile preforms based on processes such as weaving, braiding, knitting, stitching, and combinations of these have been shown to offer significant improvements in damage tolerance compared to laminated tape composites. The use of low-cost resins combined with textile preforms could provide a major breakthrough in achieving cost-effective composite aircraft structures. RTM uses resin in its lowest cost form, and storage and spoilage costs are minimal. Near net shape textile preforms are expected to be cost-effective because automated machines can be used to produce the preforms, post-cure operations such as machining and fastening are minimized, and material scrap rate may be reduced in comparison with traditional prepreg molding. The purpose of this paper is to discuss experimental and analytical techniques that are under development at NASA Langley to aid the engineer in developing RTM processes for airframe structural elements. Included are experimental techniques to characterize preform and resin behavior and analytical methods that were developed to predict resin flow and cure kinetics.

Hasko, Gregory H.↗
NASA NTRSDate not supplied

Extending ISS Life Beyond 2030

The United States On-orbit Segment (USOS) of the International Space Station (ISS) was designed to meet a 15-year on-orbit life. Since the first hardware was launched in late 1998, the ISS would have reached its end of life in 2013. With the realization that the ISS would be needed well into the next decade, and beyond, a multi-disciplinary effort was undertaken to extend the ISS’ life through 2028 and to show that further extension to 2040 and beyond is not only feasible but achievable. Currently, NASA and the ISS international partners have agreed to extend its operations through 2030. This collaborative effort ensures that the ISS will continue to serve as a hub for scientific research, international cooperation, and educational endeavors for the next decade. Maintaining a continuous human presence in Low Earth Orbit (LEO) is desirable for testing new LEO, lunar, and deep-space technologies; conducting scientific research in micro-gravity for the benefit of life on Earth; and enabling a seamless transition of capabilities to one or more commercially owned and operated destinations. This paper provides an overview of the ISS life extension project with a particular focus on the analytical approach used to assess the primary structure. This analytical approach includes future operations planning, critical location screening, on-orbit dynamic load simulation, on-orbit optical property degradation studies, on-orbit thermal analyses, spectra generation, crack model idealization, fracture analyses, and post processing. Structural life results and identification of the most critical on-orbit events are presented. Also addressed are life extension approaches for other affected sub-systems, including: 1. Secondary Structure. 2. Materials. Evaluations consider environmental exposure to atomic oxygen, ionizing and gamma radiation, fluids, etc. Life limited materials, wear, and usage effects are also considered. 3. Environmental Control and Life Support Systems, including oxygen supply and generation, water recovery and management, and regenerative hardware. Evaluations are performed to determine which hardware can be run to failure and which are assessed for life extension. 4. Electrical power system. ISS is powered by eight channels of solar arrays and an electrical energy storage system providing 357 kWh power. Power generation and balance analyses are performed considering hardware degradation and increasing power demand. 5. Logistics and maintenance. Analyses are performed to determine critical spares required to maintain functionality. Consideration is given to supply chain health, obsolescence issues, onboard stowage availability, and up-mass capability. The successful life extension results have built confidence to safely operate, maintain and enhance the ISS well beyond the current decade. Extending the operational life of the ISS maintains an international presence in LEO and serves to avoid a gap in capability necessary to fulfill the exploration and research needs of NASA, international partners, and industry without interruption until a commercial space station is operational.

design life↗
DOE OSTI2020

Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion

NMR relaxation dispersion measurements report on conformational changes occurring on the μs-ms timescale. Chemical shift information derived from relaxation dispersion can be used to generate structural models of weakly populated alternative conformational states. Current methods to obtain such models rely on determining the signs of chemical shift changes between the conformational states, which are difficult to obtain in many situations. Here, we use a “sample and select” method to generate relevant structural models of alternative conformations of the C-terminal-associated region of Escherichia coli dihydrofolate reductase (DHFR), using only unsigned chemical shift changes for backbone amides and carbonyls ( 1 H, 15 N, and 13 C'). We find that CS-Rosetta sampling with unsigned chemical shift changes generates a diversity of structures that are sufficient to characterize a minor conformational state of the C-terminal region of DHFR. The excited state differs from the ground state by a change in secondary structure, consistent with previous predictions from chemical shift hypersurfaces and validated by the x-ray structure of a partially humanized mutant of E. coli DHFR (N23PP/G51PEKN). The results demonstrate that the combination of fragment modeling with sparse chemical shift data can determine the structure of an alternative conformation of DHFR sampled on the μs-ms timescale. Such methods will be useful for characterizing alternative states, which can potentially be used for in silico drug screening, as well as contributing to understanding the role of minor states in biology and molecular evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Reduced Internal Friction by Osmolyte Interaction in Intrinsically Disordered Myelin Basic Protein

Urea is a strong denaturing osmolyte that disrupts noncovalent bonds in proteins. Here, we present a small-angle neutron scattering (SANS) and neutron spin–echo spectroscopy (NSE) study on the structure and dynamics of the intrinsically disordered myelin basic protein (MBP) denatured by urea. SANS results show that urea-denatured MBP is more compact than ideal polymers, while its secondary structure content is entirely lost. Additionally, NSE experiments reveal concomitantly an increase of the relaxation time and of the amplitude of internal motions in urea-denatured MBP as compared to native MBP. If interpreted in terms of the Zimm model including internal friction (ZIF), the internal friction parameter decreased by a factor of 6.5. Urea seems to not only smooth local energy barriers, reducing internal friction on a local scale, but also significantly reduces the overall depth of the global energy landscape. This leads to a nearly complete loss of restoring forces beyond entropic forces and in turn allows for larger motional amplitudes. Obviously, the noncovalent H-bonds are largely eliminated, driving the unfolded protein to be more similar to a synthetic polymer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

How Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets

The emergence and rapid worldwide spread of the novel coronavirus disease, COVID-19, has prompted concerted efforts to find successful treatments. The causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its spike (S) protein to gain entry into host cells. Therefore, the S protein presents a viable target to develop a directed therapy. Here, we deployed an integrated artificial intelligence with all-atom molecular dynamics simulation approach to provide new details of the S protein structure. Based on a comprehensive structural analysis of S proteins from SARS-CoV-2 and previous human coronaviruses, we found that the protomer state of S proteins is structurally flexible. Without the presence of a stabilizing beta sheet from another protomer chain, two regions in the S2 domain and the hinge connecting the S1 and S2 subunits lose their secondary structures. Interestingly, the region in the S2 domain was previously identified as an immunodominant site in the SARS-CoV-1 S protein. We anticipate that the molecular details elucidated here will assist in effective therapeutic development for COVID-19.

Chen, Serena↗
DOE OSTI2024

Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation

Phytohormone levels are regulated through specialized enzymes, participating not only in their biosynthesis but also in post-signaling processes for signal inactivation and cue depletion. Arabidopsis thaliana (At) carboxylesterase 15 (CXE15) and carboxylesterase 20 (CXE20) have been shown to deplete strigolactones (SLs) that coordinate various growth and developmental processes and function as signaling molecules in the rhizosphere. Here, we elucidate the X-ray crystal structures of AtCXE15 (both apo and SL intermediate bound) and AtCXE20, revealing insights into the mechanisms of SL binding and catabolism. The N-terminal regions of CXE15 and CXE20 exhibit distinct secondary structures, with CXE15 characterized by an alpha helix and CXE20 by an alpha/beta fold. These structural differences play pivotal roles in regulating variable SL hydrolysis rates. Our findings, both in vitro and in planta, indicate that a transition of the N-terminal helix domain of CXE15 between open and closed forms facilitates robust SL hydrolysis. The results not only illuminate the distinctive process of phytohormone breakdown but also uncover a molecular architecture and mode of plasticity within a specific class of carboxylesterases.

59 BASIC BIOLOGICAL SCIENCES↗