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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure of the dengue virus RNA promoter

Dengue virus, a single-stranded positive sense RNA virus, is the most prevalent mosquito-borne pathogen in the world. Like all RNA viruses, it uses conserved structural elements within its genome to control essential replicative steps. A 70 nt stem–loop RNA structure (called SLA), found at the 5'-end of the genome of all flaviviruses, functions as the promoter for viral replication. This highly conserved structure interacts with the viral polymerase NS5 to initiate RNA synthesis. Here, we report the NMR structure of a monomeric SLA from dengue virus serotype 1, assembled to high-resolution from independently folded structural elements. The DENV1 SLA has an L-shaped structure, where the top and side helices are coaxially stacked, and the bottom helix is roughly perpendicular to them. Because the sequence is highly conserved among different flavivirus genomes, it is very likely that the three-dimensional fold and local structure of SLA are also conserved among flaviviruses and required for efficient replication. This work provides structural insight into the dengue promoter and provides the foundation for the discovery of new antiviral drugs that target this essential replicative step.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

Swinglel, Mark↗
DOE OSTI2022

Experimental realization of neutron helical waves

Methods of preparation and analysis of structured waves of light, electrons, and atoms have been advancing rapidly. Despite the proven power of neutrons for material characterization and studies of fundamental physics, neutron science has not been able to fully integrate these techniques because of small transverse coherence lengths, the relatively poor resolution of spatial detectors, and low fluence rates. Here, we demonstrate methods that are practical with the existing technologies and show the experimental achievement of neutron helical wavefronts that carry well-defined orbital angular momentum values. We discuss possible applications and extensions to spin-orbit correlations and material characterization techniques.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains

Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)–to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. Furthermore, these results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Nanoscale dynamics of Dynamin 1 helices reveals squeeze-twist deformation mode critical for membrane fission

Dynamin 1 (Dyn1) GTPase, a principal driver of membrane fission during synaptic endocytosis, self-assembles into short mechanoactive helices cleaving the necks of endocytic vesicles. While structural information about Dyn1 helix is abundant, little is known about the nanoscale dynamics of the helical scaffolding at the moment of fission, complicating mechanistic understanding of Dyn1 action. To address the role of the helix dynamics in fission, we used High-Speed Atomic Force Microscopy (HS-AFM) and fluorescence microscopy to track and compare the spatiotemporal characteristics of the helices formed by wild-type Dyn1 and its K44A mutant impaired in GTP hydrolysis on minimal lipid membrane templates. In the absence of nucleotide, membrane-bound WT Dyn1 and K44A Dyn1 self-assembled into tubular protein scaffolding of similar diameter encaging the lipid bilayer. In both cases, the GTP addition caused scaffold constriction coupled with formation of 20 to 30 nm nanogaps in the protein coverage. While both proteins reached scaffold diameters characteristic for membrane superconstriction causing fission, the fission was detected only with WT Dyn1. We associated the fission activity with the dynamic evolution of the nanogaps: K44A Dyn1 gaps were static, while WT Dyn1 gaps actively evolved via repetitive nonaxisymmetric constriction-bending deformations caused by localized GTP hydrolysis. Modeling of the deformations implicated filament twist as an additional deformation mode which combines with superconstriction to facilitate membrane fission. Our results thus show that the dynamics of the Dyn1 helical scaffold goes beyond radial constriction and involves nonaxisymmetric deformations, where filament twist emerges as a critical driver of membrane fission.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

Rodriquez-Gomez, D.↗
DOE OSTI2022

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor

Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ~5-50 cm -1 . This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effect of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal/mol -1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Air-buoyant structures and vehicles

Air-buoyant structures, and vehicles incorporating air-buoyant structures, are provided. Hollow, air-buoyant structures may include a shell of ultra-low density aerogel material, foam material, or vapor-expanded material that is strong and stiff enough to withstand atmospheric pressure and lightweight enough to achieve buoyancy in air under evacuation. The shell may be reinforced with a suitable reinforcing material, such as helical nanofibers. The air-buoyant structures may also include vacuum pumps and valves operably connected to or integrated with the hollow shell. The vacuum pumps and valves may be configured to pump air out of the hollow shell and allow air back into the hollow shell to control buoyancy.

Beaux, II, Miles Frank↗
DOE OSTI2024

Understanding the Effect of Curvature on the Magnetization Reversal of Three-Dimensional Nanohelices

Comprehending the interaction between geometry and magnetism in three-dimensional (3D) nanostructures is important to understand the fundamental physics of domain wall (DW) formation and pinning. Here, we use focused-electron-beam-induced deposition to fabricate magnetic nanohelices with increasing helical curvature with height. Using electron tomography and Lorentz transmission electron microscopy, we reconstruct the 3D structure and magnetization of the nanohelices. The surface curvature, helical curvature, and torsion of the nanohelices are then quantified from the tomographic reconstructions. Furthermore, by using the experimental 3D reconstructions as inputs for micromagnetic simulations, we can reveal the influence of surface and helical curvature on the magnetic reversal mechanism. Hence, we can directly correlate the magnetic behavior of a 3D nanohelix to its experimental structure. In conclusion, these results demonstrate how the control of geometry in nanohelices can be utilized in the stabilization of DWs and control of the response of the nanostructure to applied magnetic fields.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif

Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Membrane peptides and their role in protobiological evolution

How simple membrane peptides performed such essential protocellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we explain how these peptides fold at water-membrane interfaces, insert into membranes, self-assemble into higher-order structures and acquire functions. We have investigated the interfacial behavior and folding of several peptides built of leucine and glutamine residues and have demonstrated that many of them tend to adopt ordered structures. Further, we have studied the insertion of an alpha-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)3 into a model membrane. The transmembrane state is metastable, and approximately 15 kcal mol(-1) is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)3 and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self-assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to re-engineer the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Models, Chemical↗
DOE OSTI2024

Structures of methane and ammonia monooxygenases in native membranes

Methane- and ammonia-oxidizing bacteria play key roles in the global carbon and nitrogen cycles, respectively. These bacteria use homologous copper membrane monooxygenases to accomplish the defining chemical transformations of their metabolisms: the oxidations of methane to methanol by particulate methane monooxygenase (pMMO) and ammonia to hydroxylamine by ammonia monooxygenase (AMO), enzymes of prime interest for applications in mitigating climate change. However, investigations of these enzymes have been hindered by the need for disruptive detergent solubilization prior to structure determination, confounding studies of pMMO and precluding studies of AMO. Here, we overcome these challenges by using cryoEM to visualize pMMO and AMO directly in their native membrane arrays at 2.4 to 2.8 Å resolution. These structures reveal details of the copper centers, numerous bound lipids, and previously unobserved components, including identifiable and distinct supernumerary helices interacting with pMMO and AMO, suggesting a widespread role for these helices in copper membrane monooxygenases. Comparisons between these structures, their metallocofactors, and their unexpected protein–protein interactions highlight features that may govern activity or the formation of higher-order arrays in native membranes. The ability to obtain molecular insights within the native membrane will enable further understanding of these environmentally important enzymes.

Science & Technology - Other Topics↗
NASA NTRS1999

A More Accurate and Efficient Technique Developed for Using Computational Methods to Obtain Helical Traveling-Wave Tube Interaction Impedance

The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made in the analysis were addressed and fully investigated for their accuracy by using the three-dimensional electromagnetic simulation code MAFIA (Solution of Maxwell's Equations by the Finite Integration Algorithm) (refs. 3 and 4). We found that several approximations introduced significant error (ref. 5).

Kory, Carol L.↗
DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface

General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis , an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure–activity relationship studies.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Prediction of structures and magnetic orientations in solid alpha and beta-O2

A quasi-harmonic-lattice-dynamics method coupled with a pattern-recognition optimization scheme is used to determine the minimum energy structures and magnetic orientations of solid oxygen. It is shown that the magnetic interaction is responsible for the stability of alpha-O2 with respect to beta-O2 at zero temperature and pressure. The calculated alpha-O2 lattice parameters, magnetic orientations, and sublimation energy are in good agreement with experiment. Phonon dispersion curves are calculated at vector k not equal to zero and the acoustic sound velocities are determined. The rms translational and orientational fluctuations from equilibrium are also calculated. The beta-O2 phase is described by constraining the magnetic moments so that the magnetic Hamiltonian preserves the hexagonal symmetry of the crystal. The calculated lattice parameters are in good agreement with the experiments, and a three-sublattice, quasi-helical magnetic orientation is predicted from structural and energetic considerations.

Etters, R. D.↗