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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin

Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Convergent momentum-space OPE and bootstrap equations in conformal field theory

General principles of quantum field theory imply that there exists an operator product expansion (OPE) for Wightman functions in Minkowski momentum space that converges for arbitrary kinematics. This convergence is guaranteed to hold in the sense of a distribution, meaning that it holds for correlation functions smeared by smooth test functions. The conformal blocks for this OPE are conceptually extremely simple: they are products of 3-point functions. We construct the conformal blocks in 2-dimensional conformal field theory and show that the OPE in fact converges pointwise to an ordinary function in a specific kinematic region. Using microcausality, we also formulate a bootstrap equation directly in terms of momentum space Wightman functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Global aspects of conformal symmetry and the ANEC in dS and AdS

Starting from the averaged null energy condition (ANEC) in Minkowski we show that conformal symmetry implies the ANEC for a conformal field theory (CFT) in a de Sitter and anti-de Sitter background. A similar and novel bound is also obtained for a CFT in the Lorentzian cylinder. Using monotonicity of relative entropy, we rederive these results for dS and the cylinder. As a byproduct we obtain the vacuum modular Hamiltonian and entanglement entropy associated to null deformed regions of CFTs in (A)dS and the cylinder. A third derivation of the ANEC in dS is shown to follow from bulk causality in AdS/CFT. Finally, we use the Tomita-Takesaki theory to show that Rindler positivity of Minkowski correlators generalizes to conformal theories defined in dS and the cylinder.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain

Ion-binding intrinsically disordered proteins (IDPs) recruit and bind to specific metal ions to perform critical biological functions. In proteins where ion binding and structural transitions are coupled, interactions with off-target toxic metals can dramatically disrupt protein structure and function, exemplified by lead and mercury poisoning. Understanding the complex mechanisms underlying how IDPs exclude or allow binding to different ionic species is crucial for addressing the origins of metal toxicity in biological systems. Here, we elucidate mechanisms of ion selectivity in an IDP that adopts a structure upon Ca 2+ binding. We probed ion-induced conformational changes of a repeats-in-toxin (RTX) protein domain in the presence of different ion ligands—Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ —with chemical similarities but drastically different ionic radii. RTX adopts ion-selective conformations measured by x-ray crystallography, small-angle x-ray scattering, and circular dichroism. High-resolution x-ray structures reveal that Sr 2+ induces a nearly identical RTX structure as natively binding Ca 2+ , enabled by the intrinsic flexibility and disorder of the protein. Small-angle x-ray scattering and circular dichroism indicate that smaller Mg 2+ does not induce a significant conformational change in RTX, whereas larger Ba 2+ induces a partially folded structure. These results highlight the importance of geometric constraints imposed by protein structure in determining metal ion selectivity, yielding insights into how off-target ion binding may result in protein misfolding and malfunction.

Gudinas, Alana P. [Stanford Univ., CA (United Stat↗
DOE OSTI2021

Long-term thermal aging of parylene conformal coating under high humidity and its effects on tin whisker mitigation

Usage of pure tin (Sn) or Sn-rich alloy in electronics industry is growing, which makes them more susceptible to the spontaneous growth of tin whiskers. The risk of having these whiskers can be dramatically mitigated by applying a conformal coating provided that it not only possesses excellent mechanical and adhesion properties but also maintains these properties throughout their service. Parylene C is commonly used as a conformal coating because of its favorable mechanical and physical properties, as well as superior conformal coverage. The purpose of this paper is to investigate the degradation of parylene C coating during the thermal aging in high humidity environment (85°C/85% relative humidity for up to 5000hrs) and its effect on the tin whisker mitigation capacity. It was observed that during aging at high temperature and high humidity (HTHH) environment, the oxidation occurs at early times, followed by bond scission, resulting in the loss of strength of the coating. Thinner parylene coating (12.5-μm-thick) had better coating adhesion on the silane-treated tin surface, so provided the better protection for tin whisker penetration than the thicker counterpart (25-μm-thick). After 2500hrs of aging, due to the degradation of the silane agent at the tin/parylene interface, the adhesion of the parylene coating was significantly weakened on the tin surface, which resulted in extensive corrosion of the tin solderpads. The loss of adhesion of the coating, along with the corrosion of the tin surface facilitated the tin whisker nucleation at the interface while the loss of mechanical strength and the brittleness made the coating easily penetrated by the growing whiskers. Tin whiskers with a smaller diameter were buckled and grew along the delaminated region while those with a larger diameter penetrated and continued to grow through the coating. Hence, the effectiveness of the parylene coatings on tin whisker mitigation is significantly reduced under long exposure to such high temperature and high humidity.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Dramatic Conformer-Dependent Reactivity of the Acetaldehyde Oxide Criegee Intermediate with Dimethylamine Via a 1,2-Insertion Mechanism

The reactivity of carbonyl oxides has previously been shown to exhibit strong conformer and substituent dependencies. Through a combination of synchrotron multiplexed photoionization mass spectrometry experiments (298 K, 4 Torr) and high-level theory (CCSD(T)-F12/cc-pVTZ-F12//B2PLYP-D3/cc-pVTZ with an added CCSDT(Q) correction), we explore the conformer dependence of the reaction of acetaldehyde oxide (CH 3 CHOO) with dimethyl amine (DMA). The experimental data supports the theoretically predicted 1,2-insertion mechanism and the formation of an amine-functionalized hydroperoxide reaction product. Tunable-VUV photoionization probing of anti- or anti- + syn-CH 3 CHOO reveals a strong conformer dependence of the title reaction. Here, the rate coefficient of DMA with anti-CH 3 CHOO is predicted to exceed that for the reaction with syn-CH 3 CHOO by a factor of ~34,000, which is attributed to submerged barrier (syn) vs. barrierless (anti) mechanisms for energetically downhill reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Conformer-Dependent Chemistry: Experimental Product Branching of the Vinyl Alcohol + OH + O 2 Reaction

The concentration of formic acid in Earth's tropo-sphere is underestimated by detailed chemical models compared to field observations. Phototautomerization of acetaldehyde to its less stable tautomer vinyl alcohol, followed by the OH-initiated oxidation of vinyl alcohol, has been proposed as a missing source of formic acid that improves the agreement between models and field measurements. Theoretical investigations of the OH + vinyl alcohol reaction in excess O 2 conclude that OH addition to the alpha carbon of vinyl alcohol produces formaldehyde + formic acid + OH, whereas OH addition to the β site leads to glycoaldehyde + HO 2 . Furthermore, these studies predict that the conformeric structure of vinyl alcohol controls the reaction pathway, with the anti-conformer of vinyl alcohol promoting α OH addition, whereas the syn-conformer promotes β addition. However, the two theoretical studies reach different conclusions regarding which set of products dominate. We studied this reaction using time-resolved multiplexed photoionization mass spectrometry to quantify the product branching fractions. Our results, supported by a detailed kinetic model, conclude that the glycoaldehyde product channel (arising mostly from syn-vinyl alcohol) dominates over formic acid production with a 3.6:1.0 branching ratio. Additionally, this result supports the conclusion of Lei et al. that conformer-dependent hydrogen bonding at the transition state for OH-addition controls the reaction outcome. As a result, tropospheric oxidation of vinyl alcohol creates less formic acid than recently thought, increasing again the discrepancy between models and field observations of Earth's formic acid budget.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Probing Conformational Evolution and Associated Dynamics of Mg(N(SO 2 CF 3 ) 2 ) 2 ·Dimethoxyethane Adduct Using Solid-State 19 F and 1 H NMR

Bis(trifluoromethanesulfonimide) or TFSI is widely used as a counter anion in electrolyte design due to its structural flexibility and chemical stability. Here we studied the conformational variations and associated dynamics of TFSI in adduct of Mg(TFSI) 2 with dimethoxyethane (DME), a solvate crystalline material using solid-state 1 H and 19 F NMR. TFSI molecular motion in this solvate structure falls within the timescale of the 19 F NMR experiment, yielding spectroscopic signatures for unique TFSI conformers under the coordination environment of Mg 2+ cation. Within the temperature range of -5 to 82 °C, we observe nine distinct TFSI sites in both crystalline and disordered regions using 19 F NMR, reflecting complexity of structural and dynamics of TFS1 anions within solvate structure. The four distinguishable sites in the disordered region for the two CF 3 groups of the same TFSI molecule are identified using chemical shift analysis. The exchange rate constants from site to site are calculated through variable temperature 19 F NMR and two-dimensional (2D) exchange spectroscopy (EXSY) experiments, along with respective activation enthalpies using Eyring's formulation. The flip rate of CF 3 around the S-C bond is estimated as ~ 15 s -1 at 8 °C with ΔH ≠ ~ 22 kJ/mol, but the rotation of the entire TFSI is 4.8 s -1 at 8 °C with a significantly greater ΔH ≠ = 98 ± 10 kJ/mol. Furthermore, the slow conversion of trans to cis conformers at a lower temperature (T ≤ 1 °C) in the crystalline region is monitored, with a conversion rate of ~ 2 x 10 -5 s -1 at -5 °C. Density functional theory (DFT)-based calculations were performed to support further the assignment of experimental chemical shifts, and the activation energy E a = 21.1 kJ/mol obtained for the cis to trans transition is consistent with experimental values. The combined set of 19 F and 1 H under both one-dimensional (1D) and 2D NMR methods demonstrated here can be further used for examining electrode-electrolyte interfaces to probe the motions of various constituents that can enable detailed studies of interfacial processes and dynamics. Ultimately, such studies will aid in the design and discovery of interfacial constructs in which directed defect chemistry, chemical moiety distribution, and nanostructure are employed to drive efficient charge transport.

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

Observation of Conformational Simplification upon N-methylation on Amino Acid Iodide Clusters

This work reports a surprising observation that methylation of glycine-iodide cluster leads to less conformations and spectroscopic simplicity. We used cryogenic “iodide-tagging” negative ion photoelectron spectroscopy (NIPES) to probe specific binding sites of three N-methylated glycine derivatives, i.e., N-methylglycine (sarcosine, Sar), N,N-dimethylglycine (Dmg), and N,N,N-trimethylglycine (glycine betaine, Bet). NIPES reveals a progressive spectral simplification of the iodide clusters with increasing methylation due to the presence of fewer contributing structures, a reduction in the number of NH and OH hydrogen bond donating sites, and an increase in the basicity of the amine. Low energy conformers and tautomers of each cluster are computationally identified, and those observed in the experiments are assigned based on excellent agreement between the NIPE spectra and theoretical simulations. Clusters with zwitterionic structures for Gly, Sar, and Dmg are found to be less stable than their canonical forms and do not contribute to the observed spectra. This work demonstrates the power of “iodide-tagging” NIPES in probing conformational and tautomeric structures of amino acid-iodide clusters and provides a molecular level understanding on the effect of methyl substitution on the active binding sites of amino acids.

Cao, Wenjin↗
DOE OSTI2022

Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations

Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Biased localization of actin binding proteins by actin filament conformation

The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1–CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1–CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.

42 ENGINEERING↗
DOE OSTI2021

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs

To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assay. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved longrange pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg 2+ - dependent, furthermore, the Mg 2+ -dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg 2+ to stabilize its folding, exhibits reduced conformational dynamics and strong Xrn1 resistance even at low Mg 2+ , and tolerates mutations at key tertiary motifs at high Mg 2+ , which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Active conformation of the p97-p47 unfoldase complex

The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a “hand-over-hand” mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery

Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A 2A receptor (A 2A R), a class A GPCR. Our study reveals a structurally conserved cation-π lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a “gatekeeper” for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-π lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Probing single-chain conformation and its impact on the optoelectronic properties of donor–accepter conjugated polymers

The chain conformation of donor–acceptor conjugated polymers (D–A CPs) is critical to their optical and electronic properties. However, probing the conformation of D–A CPs (e.g., persistence length and contour length) at a single-chain level is challenging due to the formation of aggregates in dilute solution, even in a good solvent. In this work, we studied the chain conformation and corresponding optical spectra for high-performance D–A CPs in the single-chain state by multimodal variable-temperature scattering and spectroscopy techniques, as well as by molecular dynamics simulations. Here we found a critical role of the side-chain length and branch point in the persistence length and optical absorption due to steric effects. Hence, it is important to consider both the chain rigidity and coplanarity of the polymer backbone to achieve desirable optoelectronic properties. Our findings bridge the fundamental knowledge gaps to design new CPs with desired optoelectronic properties via molecular engineering for next-generation electronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗