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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 OSTI2017

A retractable lid in lecithin:cholesterol acyltransferase provides a structural mechanism for activation by apolipoprotein A-I

Lecithin:cholesterol acyltransferase (LCAT) plays a key role in reverse cholesterol transport by transferring an acyl group from phosphatidylcholine to cholesterol, promoting the maturation of high-density lipoproteins (HDL) from discoidal to spherical particles. LCAT is activated through an unknown mechanism by apolipoprotein A-I (apoA-I) and other mimetic peptides that form a belt around HDL. Here, we report the crystal structure of LCAT with an extended lid that blocks access to the active site, consistent with an inactive conformation. Residues Thr-123 and Phe-382 in the catalytic domain form a latch-like interaction with hydrophobic residues in the lid. Because these residues are mutated in genetic disease, lid displacement was hypothesized to be an important feature of apoA-I activation. Functional studies of site-directed mutants revealed that loss of latch interactions or the entire lid enhanced activity against soluble ester substrates, and hydrogen–deuterium exchange (HDX) mass spectrometry revealed that the LCAT lid is extremely dynamic in solution. Upon addition of a covalent inhibitor that mimics one of the reaction intermediates, there is an overall decrease in HDX in the lid and adjacent regions of the protein, consistent with ordering. As a result, these data suggest a model wherein the active site of LCAT is shielded from soluble substrates by a dynamic lid until it interacts with HDL to allow transesterification to proceed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6

Significance The loading of the core Mcm2-7 helicase onto origin DNA is essential for the formation of replication forks and genomic stability. Here, we report two cryo-electron microscopy (cryo-EM) structures that capture helicase loader–helicase complexes just prior to DNA insertion. These pre-loading structures, combined with a computational simulation of the dynamic transition from the pre-loading state to the loaded state, provide crucial insights into the mechanism required for topologically linking the helicase to DNA. The helicase loading system is highly conserved from yeast to human, which means that the molecular principles described here for the yeast system are likely applicable to the human system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Synthesis, growth, structure, mechanical and optical properties of a new semi-organic 2-methyl imidazolium dihydrogen phosphate single crystal

Highlights: • 2MIDP crystals were grown by slow evaporation solution growth technique. • Single crystal XRD revealed self-assembled supramolecular framework. • Z scan technique is employed for third order nonlinear optical susceptibility. • Structure-property correlation is established. - Abstract: A new semi-organic compound, 2-methyl imidazolium dihydrogen phosphate (2MIDP), was prepared and good quality single crystals of 2MIDP were grown by slow evaporation solution growth technique. Crystal structure elucidated using Single crystal XRD showed that 2MIDP crystallizes in monoclinic system with P2{sub 1}/c space group. FT-IR, UV-Vis-NIR, Fluorescence and FT-NMR spectra confirm the molecular structure of 2MIDP. The UV-Vis-NIR spectra established the suitability of the compound for NLO applications. TG-DSC showed that 2MIDP is thermally stable up to 200 °C. Mechanical characteristics like hardness number (H{sub v}), stiffness constant (C{sub 11}), yield strength (σ{sub v}), fracture toughness (K{sub c}) and brittleness index (B{sub i}) were assessed using Vicker’s microhardness tester. Third order nonlinear optical properties determined from Z-scan measurement using femto and picosecond lasers showed two photon reverse saturable absorption. The enhancement of nonlinear optical properties in femto second laser, revealed the suitability of 2MIDP for optical limiting applications.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Technical Spotlight: NEAMS Structural Mechanics with Diablo

The Diablo code being developed at Lawrence Livermore National Laboratory (LLNL) uses implicit, Lagrangian finite element methods for the simulation of solid mechanics and multi-physics events over moderate to long time frames. A recent effort examined technologies needed to extend Diablo for use in seismic response incorporating soil-structure interaction (SSI). Our SSI study was intended to illustrate how advanced time-domain simulation approaches compare with and complement the standard frequency-domain approach for SSI.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS1989

The 3-D inelastic analyses for computational structural mechanics

The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

Hopkins, D. A.↗
NASA NTRS1984

Secular rotational motions and the mechanical structure of a dynamical viscoelastic earth

A survey is presented of analytical methods for computing the linear responses of the rotational axis of a layered viscoelastic earth to surface loading. Theoretical research in this area is first summarized, and the differences between the mechanical boundary conditions to be applied at the interface separating the upper and lower mantles for an adiabatically and chemically stratified mantle are discussed. Some examples of polar wander and secular variation of the spin rate from glacial excitation are presented for various types of chemical and viscosity stratifications. The effects of an artificial density jump at the base of the lithosphere in models are examined, and certain issues concerning the fluid tidal Love number for different types of density stratification are addressed. The meaning of effective plate thickness over geological time scales for rotational dynamics is discussed.

Yuen, D. A.↗
NASA NTRS1998

Manuel Stein's Five Decades of Structural Mechanics Contributions (1944-1988)

Manuel Stein went to work for NACA (National Advisory Committee for Aeronautics) in 1944 and left in 1988. His research contributions spanned five decades of extremely defining times for the aerospace industry. Problems arising from the analysis and design of efficient thin plate and shell aerospace structures have stimulated research over the past half century. The primary structural technology drivers during Dr. Stein's career included 1940's aluminum aircraft, 1950's jet aircraft, 1960's launch vehicles and advanced spacecraft, 1970's reusable launch vehicles and commercial aircraft, and 1980's composite aircraft. Dr. Stein's research was driven by these areas and he made lasting contributions for each. Dr. Stein's research can be characterized by a judicious mixture of physical insight into the problem, understanding of the basic mechanisms, mathematical modeling of the observed phenomena, and extraordinary analytical and numerical solution methodologies of the resulting mathematical models. This paper summarizes Dr. Stein's life and his contributions to the technical community.

Mikulas, Martin M.↗
DOE OSTI2023

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization

Abstract HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CA NTD -CA NTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45A a α9-helices compared to WT, E45A/R132T, WT PF74 , WT Nup153 , and WT CPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Structural mechanism of ligand activation in human calcium-sensing receptor

Human calcium-sensing receptor (CaSR) is a G-protein-coupled receptor (GPCR) that maintains extracellular Ca 2+ homeostasis through the regulation of parathyroid hormone secretion. It functions as a disulfide-tethered homodimer composed of three main domains, the Venus Flytrap module, cysteine-rich domain, and seven-helix transmembrane region. Here, we present the crystal structures of the entire extracellular domain of CaSR in the resting and active conformations. We provide direct evidence that L-amino acids are agonists of the receptor. In the active structure, L-Trp occupies the orthosteric agonist-binding site at the interdomain cleft and is primarily responsible for inducing extracellular domain closure to initiate receptor activation. Our structures reveal multiple binding sites for Ca 2+ and PO 4 3- ions. Both ions are crucial for structural integrity of the receptor. While Ca 2+ ions stabilize the active state, PO 4 3- ions reinforce the inactive conformation. The activation mechanism of CaSR involves the formation of a novel dimer interface between subunits.

Geng, Yong↗
DOE OSTI2018

Electronic Structure, Mechanical and Dynamical Stability of Hexagonal Subcarbides M{sub 2}C (M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt): Ab Initio Calculations

Ab initio calculations were used to study the properties of a series of hexagonal (Fe{sub 2}N-like) subcarbides M{sub 2}C, where M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt, and to calculate their equilibrium structural parameters, electronic properties, phase stability, elastic constants, compression modulus, shear modulus, Young’s modulus, compressibility, Pugh’s indicator, Poisson ratio, elastic anisotropy indices, and also hardness, Debye temperature, sound velocity, and low-temperature heat capacity. It is found based on these results that all the subcarbides are mechanically stable; however, their formation energies E{sub form} are positive with respect to a mixture of d-metal and graphite. In addition, the calculation of the phonon spectra of these subcarbides shows the existence of negative modes, which indicates their dynamical instability. Thus, a successful synthesis of these subcarbides at normal conditions is highly improbable.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Alanine 501 Mutations in Penicillin-Binding Protein 2 from Neisseria gonorrhoeae : Structure, Mechanism, and Effects on Cephalosporin Resistance and Biological Fitness

Resistance of Neisseria gonorrhoeae to expanded-spectrum cephalosporins such as ceftriaxone and cefixime has increased markedly in the past decade. The primary cephalosporin resistance determinant is a mutated penA gene, which encodes the essential peptidoglycan transpeptidase, penicillin-binding protein 2 (PBP2). Decreased susceptibility and resistance can be conferred by mosaic penA alleles containing upward of 60 amino acid changes relative to wild-type PBP2, or by nonmosaic alleles with relatively few mutations, the most important of which occurs at Ala501 located near the active site of PBP2. Recently, fully cefixime- and ceftriaxone-resistant clinical isolates that harbored a mosaic penA allele with an A501P mutation were identified. To examine the potential of mutations at Ala501 to increase resistance to expanded-spectrum cephalosporins, we randomized codon 501 in a mosaic penA allele and transformed N. gonorrhoeae to increased cefixime resistance. Interestingly, only five substitutions of Ala501 (A501V, A501T, A501P, A501R, and A501S) that increased resistance and preserved essential transpeptidase function were isolated. To understand their structural implications, these mutations were introduced into the nonmosaic PBP2-6140CT, which contains four C-terminal mutations present in PBP2 from the penicillin-resistant strain FA6140. The crystal structure of PBP2-6140CT-A501T was determined and revealed ordering of a loop near the active site and a new hydrogen bond involving Thr501 that connects the loop and the SxxK conserved active site motif. The structure suggests that increased rigidity in the active site region is a mechanism for cephalosporin resistance mediated by Ala501 mutations in PBP2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Dna2 nuclease-helicase structure, mechanism and regulation by Rpa

The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5’ end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5’ but not 3’ end, explaining how Rpa regulates cleavage polarity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR

The multidrug efflux pump MepA is a major contributor to multidrug resistance in Staphylococcus aureus. MepR, a member of the multiple antibiotic resistance regulator (MarR) family, represses mepA and its own gene. Here, we report the structure of a MepR–mepR operator complex. Structural comparison of DNA-bound MepR with ‘induced’ apoMepR reveals the large conformational changes needed to allow the DNA-binding winged helix-turn-helix motifs to interact with the consecutive major and minor grooves of the GTTAG signature sequence. Intriguingly, MepR makes no hydrogen bonds to major groove nucleobases. Rather, recognition-helix residues Thr60, Gly61, Pro62 and Thr63 make sequence-specifying van der Waals contacts with the TTAG bases. Removing these contacts dramatically affects MepR–DNA binding activity. The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp85, interacts with the O2 of T 4 and O4' ribosyl oxygens of A 23 and T 4 . Mutating Asp85 and Arg87, both conserved throughout the MarR family, markedly affects MepR repressor activity. The His14':Arg59 and Arg10':His35:Phe108 interaction networks stabilize the DNA-binding conformation of MepR thereby contributing significantly to its high affinity binding. A structure-guided model of the MepR–mepA operator complex suggests that MepR dimers do not interact directly and cooperative binding is likely achieved by DNA-mediated allosteric effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Atomic structural mechanism for ferroelectric-antiferroelectric transformation in perovskite NaNbO 3

Sodium niobate (NaNbO 3 or NN) is described as “the most complex perovskite system,” which exhibits transitions between, as well as coexistence of, several ferroelectrics (FE) and antiferroelectric (AFE) phases at different temperatures. Recently, solid solutions of NN with stabilized AFE phases(s) have gained attention for energy-related applications, such as high-density energy storage and electrocaloric cooling. A better understanding of the atomic mechanisms responsible for AFE/FE phase transitions in NaNbO 3 can enable a more rational design of its solid-solution systems with tunable functional properties. In this work, we have investigated changes in the average and local atomic structure of NN using a combination of x-ray/neutron diffraction and neutron pair-distribution function (PDF) analyses. The Rietveld refinement of the x-ray/neutron-diffraction patterns indicates a coexistence of the FE Q (P2 1 ma) and AFE P (Pbma) phases in the temperature range of 300 K ≤ T ≤ 615K, while PDF analysis indicated that the local structure (r < 8Å) is better described by a P2 1 ma symmetry. Above 615 K, the average structure transitions to an AFE R phase (Pmmn or Pnma), while PDF analysis shows an increased disordering of the octahedral distortions and Na displacements at the local scale. These results indicate that the average P/Q/R phase transitions in NN can be described as a result of complex ordering of distorted octahedral tilts at the nanoscale and off-centered displacements of the Na atoms.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural mechanism of Myb–MuvB assembly

The MuvB transcriptional regulatory complex, which controls cell-cycle-dependent gene expression, cooperates with B-Myb to activate genes required for the G2 and M phases of the cell cycle. We have identified the domain in B-Myb that is essential for the assembly of the Myb–MuvB (MMB) complex. We determined a crystal structure that reveals how this B-Myb domain binds MuvB through the adaptor protein LIN52 and the scaffold protein LIN9. Here, the structure and biochemical analysis provide an understanding of how oncogenic B-Myb is recruited to regulate genes required for cell-cycle progression, and the MMB interface presents a potential therapeutic target to inhibit cancer cell proliferation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure-mechanical properties correlation in bulk LiPON glass produced by nitridation of metaphosphate melts

The glassy solid electrolyte Lithium phosphorous oxynitride (LiPON) has been widely researched in thin film solid state battery format due to its outstanding stability when cycled against lithium. In addition, recent reports show thin film LiPON having interesting mechanical behaviors, especially its ability to resist micro-scale cracking via densification and shear flow. Here, in the present study, we have produced bulk LiPON glasses with varying nitrogen contents by ammonolysis of LiPO 3 melts. The resulting compositions were determined to be LiPO 3-3z/2 N z , where 0 ≤ z ≤ 0.75, and the z value of 0.75 is among the highest ever reported for this series of LiPON glasses. The short-range order structures of the different resulting compositions were characterized by infrared, Raman, 31 P magic angle spinning nuclear magnetic resonance, and X-ray photoelectron spectroscopies. Instrumented nano-indentation was used to measure mechanical properties. It was observed that similar to previous studies, both trigonally coordinated (N t ) and doubly bonded (N d ) N co-exist in the glasses in about the same amounts for z ≤ 0.36, the limit of N content in most previous studies. For glasses with z > 0.36, it was found that the fraction of the N t increased significantly while the fraction of N d correspondingly decreased. The incorporation of nitrogen increased both the elastic modulus and hardness of the glass by approximately a factor of 1.5 when N/P ratio reaches 0.75. At the same time, an apparent embrittlement of the glass was observed due to nitridation, which was revealed by nanoindentation with an extra sharp nanoindenter tip.

25 ENERGY STORAGE↗
DOE OSTI2023

Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin

The calcium-selective oncochannel TRPV6 is an important driver of cell proliferation in human cancers. Despite increasing interest of pharmacological research in developing synthetic inhibitors of TRPV6, natural compounds acting at this channel have been largely neglected. On the other hand, pharmacokinetics of natural small-molecule antagonists optimized by nature throughout evolution endows these compounds with a medicinal potential to serve as potent and safe next-generation anti-cancer drugs. Here we report the structure of human TRPV6 in complex with tetrahydrocannabivarin (THCV), a natural cannabinoid inhibitor extracted from Cannabis sativa . We use cryo-electron microscopy combined with electrophysiology, calcium imaging, mutagenesis, and molecular dynamics simulations to identify THCV binding sites in the portals that connect the membrane environment surrounding the protein to the central cavity of the channel pore and to characterize the allosteric mechanism of TRPV6 inhibition. We also propose the molecular pathway taken by THCV to reach its binding site. Our study provides a foundation for the development of new TRPV6-targeting drugs.

59 BASIC BIOLOGICAL SCIENCES↗