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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Nitrogen in black phosphorus structure

Group V elements in crystal structure isostructural to black phosphorus with unique puckered two-dimensional layers exhibit exciting physical and chemical phenomena. However, as the first element of group V, nitrogen has never been found in the black phosphorus structure. Here, we report the synthesis of the black phosphorus–structured nitrogen at 146 GPa and 2200 K. Metastable black phosphorus–structured nitrogen was retained after quenching it to room temperature under compression and characterized in situ during decompression to 48 GPa, using synchrotron x-ray diffraction and Raman spectroscopy. We show that the original molecular nitrogen is transformed into extended single-bonded structure through gauche and trans conformations. Raman spectroscopy shows that black phosphorus–structured nitrogen is strongly anisotropic and exhibits high Raman intensities in two A g normal modes. Synthesis of black phosphorus–structured nitrogen provides a firm base for exploring new type of high-energy-density nitrogen and a new direction of two-dimensional nitrogen.

58 GEOSCIENCES↗
DOE OSTI2020

Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch

Post-translational control of PERIOD stability by Casein Kinase 1δ and ε (CK1) plays a key regulatory role in metazoan circadian rhythms. Despite the deep evolutionary conservation of CK1 in eukaryotes, little is known about its regulation and the factors that influence substrate selectivity on functionally antagonistic sites in PERIOD that directly control circadian period. Here we describe a molecular switch involving a highly conserved anion binding site in CK1. This switch controls conformation of the kinase activation loop and determines which sites on mammalian PER2 are preferentially phosphorylated, thereby directly regulating PER2 stability. Integrated experimental and computational studies shed light on the allosteric linkage between two anion binding sites that dynamically regulate kinase activity. We show that period-altering kinase mutations from humans to Drosophila differentially modulate this activation loop switch to elicit predictable changes in PER2 stability, providing a foundation to understand and further manipulate CK1 regulation of circadian rhythms.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

A low molecular weight artificial RNA of unique size with multiple probe target regions

Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

Non-NASA Center↗
NASA NTRS2002

Predicting functional divergence in protein evolution by site-specific rate shifts

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

Review↗
DOE OSTI2024

Distinct binding conformations of epinephrine with α- and β-adrenergic receptors

Abstract Agonists targeting α 2 -adrenergic receptors (ARs) are used to treat diverse conditions, including hypertension, attention-deficit/hyperactivity disorder, pain, panic disorders, opioid and alcohol withdrawal symptoms, and cigarette cravings. These receptors transduce signals through heterotrimeric Gi proteins. Here, we elucidated cryo-EM structures that depict α 2A -AR in complex with Gi proteins, along with the endogenous agonist epinephrine or the synthetic agonist dexmedetomidine. Molecular dynamics simulations and functional studies reinforce the results of the structural revelations. Our investigation revealed that epinephrine exhibits different conformations when engaging with α-ARs and β-ARs. Furthermore, α 2A -AR and β 1 -AR (primarily coupled to Gs, with secondary associations to Gi) were compared and found to exhibit different interactions with Gi proteins. Notably, the stability of the epinephrine–α 2A -AR–Gi complex is greater than that of the dexmedetomidine–α 2A -AR–Gi complex. These findings substantiate and improve our knowledge on the intricate signaling mechanisms orchestrated by ARs and concurrently shed light on the regulation of α-ARs and β-ARs by epinephrine.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Assembly of polyelectrolyte star block copolymers at the oil–water interface

To understand and resolve adsorption, reconfiguration, and equilibrium conformations of charged star copolymers, we carried out an integrated experimental and coarse-grained molecular dynamics simulation study of the assembly process at the oil–water interface. This is important to guide development of novel surfactants or amphiphiles for chemical transformations and separations. The star block copolymer consisted of arms that are comprised of hydrophilic–hydrophobic block copolymers that are covalently tethered via the hydrophobic blocks to one point. The hydrophobic core represents polystyrene (PS) chains, while the hydrophilic corona represents quaternized poly(2-vinylpyridine) (P2VP) chains. The P2VP is modeled to become protonated when in contact with an acidic aqueous phase, thereby massively increasing the hydrophilicity of this block, and changing the nature of the star at the oil–water interface. This results in a configurational change whereby the chains comprising the hydrophilic corona are significantly stretched into the aqueous phase, while the hydrophobic core remains solubilized in the oil phase. In the simulations, we followed the kinetics of the anchoring and assembly of the star block copolymer at the interface, monitoring the lateral assembly, and the subsequent reconfiguration of the star via changes in the interfacial tension that varies as the degree-of-protonation increases. At low fractions of protonation, the arm cannot fully partition into the aqueous side of the interface and instead interacts with other arms in the oil phase forming a network near the interface. These insights were used to interpret the non-monotonic dependence of pH with the asymptotic interfacial tension from pendant drop tensiometry experiments and spectral signatures of aromatic stretches seen in vibrational sum frequency generation (SFG) spectroscopy. We describe the relationship of interfacial tension to the star assembly via the Frumkin isotherm, which phenomenologically describes anti-cooperativity in adsorbing stars to the interface due to crowding. Although our model explicitly considers long-range electrostatics, the contribution of electrostatics to interfacial tension is small and brought about by strong counterion condensation at the interface. Finally, these results provide key insights into resolving the adsorption, reconfiguration, and equilibrium conformations of charged star block copolymers as surfactants.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Nucleotide- and metalloid-driven conformational changes in the arsenite efflux ATPase ArsA

Arsenite (As III ) is toxic to all organisms due to its ability to tightly bind exposed thiols within cells. An important As III resistance mechanism in prokaryotes involves proteins encoded by thearsoperon. A central component of thearsoperon in many bacteria is the cytoplasmic ATPase, ArsA, which orchestrates a series of nucleotide-dependent handoffs, starting with the capture of As III by the ArsD metallochaperone and culminating in its removal from the cell by the ArsB efflux pump. Although the mechanism of ArsA has been widely studied, the molecular details of how nucleotide hydrolysis modulates these events remain unclear. ArsA is an archetypal member of the intradimeric Walker A (IWA) family of ATPases, implicated in a diversity of complex biological functions. Conformational changes typical of IWA ATPases have been postulated to drive these molecular events but have not been demonstrated. We report cryogenic electron microscopy (cryo-EM) structures of ArsA in MgADP-bound and MgATP-boundopenstates, as well as a distinctclosedMgATP-bound state liganded to As III . X-ray absorption spectroscopy (XAS) confirmed three-coordinate binding of As III to the conserved cysteines at the metalloid-binding site of the closed state. Coupled with biochemical characterization, our cryo-EM structures reveal key conformational changes in the ArsA catalytic cycle consistent with other IWA ATPases and provide the structural basis for allosteric activation of nucleotide hydrolysis by As III . This work establishes how the nucleotide state of ArsA transiently creates a high-affinity binding site that can sequester metalloid within the cell, followed by a nucleotide-driven handoff to ArsB for efflux.

Science & Technology - Other Topics↗
DOE OSTI2020

Lipid membrane templated misfolding and self-assembly of intrinsically disordered tau protein

The aggregation of the intrinsically disordered tau protein into highly ordered β-sheet-rich fibrils is implicated in the pathogenesis of a range of neurodegenerative disorders. The mechanism of tau fibrillogenesis remains unresolved, particularly early events that trigger the misfolding and assembly of the otherwise soluble and stable tau. We investigated the role the lipid membrane plays in modulating the aggregation of three tau variants, the largest isoform hTau40, the truncated construct K18, and a hyperphosphorylation-mimicking mutant hTau40/3Epi. Despite being charged and soluble, the tau proteins were also highly surface active and favorably interacted with anionic lipid monolayers at the air/water interface. Membrane binding of tau also led to the formation of a macroscopic, gelatinous layer at the air/water interface, possibly related to tau phase separation. At the molecular level, tau assembled into oligomers composed of ~ 40 proteins misfolded in a β-sheet conformation at the membrane surface, as detected by in situ synchrotron grazing-incidence X-ray diffraction. Concomitantly, membrane morphology and lipid packing became disrupted. Our findings support a general tau aggregation mechanism wherein tau’s inherent surface activity and favorable interactions with anionic lipids drive tau-membrane association, inducing misfolding and self-assembly of the disordered tau into β-sheet-rich oligomers that subsequently seed fibrillation and deposition into diseased tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids

The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. We report experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.

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

Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis

Abstract High‐energy X‐ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long‐range order, but is underutilized for molecular complexes in solution. We demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal⋅⋅⋅metal distances separated by over 12 Å. The metal⋅⋅⋅metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub‐Ångström conformational differences by direct comparison of solution phase and solid‐state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.

Xie, Zhu‐Lin↗
DOE OSTI2025

Ion Transport in Carbon Nanotube Porins with a pH-Switchable Entrance Gate

Molecular transport in nanofluidic channels often differs drastically from conventional bulk transport. Strong confinement in those channels amplifies the roles of surface transport, surface defects, and molecular gates. Here, in this study, we introduce a chemical functionality at the nanotube rim that acts as a pH-triggered molecular gate by forming a movable lid that blocks the pore entrance. We use ion and proton transport measurements to show that these sub-1 nm diameter fluorescent ultrashort carbon nanotube porins (FUNPs) modulate ion transport by switching between the “open” and “closed” conformations of this gate. Specifically, at neutral pH the channel lid is open, allowing unimpeded ion transport through the gate, whereas at acidic pH values the lid forms a “closed” conformation that blocks transport through the nanotube. We also report first-principles MD simulations that confirm this gating mechanism and reveal molecular details of the ion and proton transport processes in these functional nanopores.

Carbon nanotubes↗
DOE OSTI2020

Over 15% Efficiency Polymer Solar Cells Enabled by Conformation Tuning of Newly Designed Asymmetric Small‐Molecule Acceptors

Abstract The prosperous period of polymer solar cells (PSCs) has witnessed great progress in molecule design methods to promote power conversion efficiency (PCE). Designing asymmetric structures has been proved effective in tuning energy level and morphology, which has drawn strong attention from the PSC community. Two hepta‐ring and octa‐ring asymmetric small molecular acceptors (SMAs) (IDTP‐4F and IDTTP‐4F) with S‐shape and C‐shape confirmations are developed to study the relationship between conformation shapes and PSC efficiencies. The similarity of absorption and energy levels between two SMAs makes the conformation a single variable. Additionally, three wide‐bandgap polymer donors (PM6, S1, and PM7) are chosen to prove the universality of the relationship between conformation and photovoltaic performance. Consequently, the champion PCE afforded by PM7: IDTP‐4F is as high as 15.2% while that of PM7: IDTTP‐4F is 13.8%. Moreover, the S‐shape IDTP‐4F performs obviously better than their IDTTP‐4F counterparts in PSCs regardless of the polymer donors, which confirms that S‐shape conformation performs better than the C‐shape one. This work provides an insight into how conformations of asymmetric SMAs affect PCEs, specific functions of utilizing different polymer donors to finely tune the active‐layer morphology and another possibility to reach an excellent PCE over 15%.

Guo, Qing↗
DOE OSTI2021

X-ray spectroscopic identification of strain and structure-based resonances in a series of saturated carbon-cage molecules: Adamantane, twistane, octahedrane, and cubane

Novel nanocarbons such as fullerenes, nanotubes, graphene, and nanodiamond reside at the cutting edge of nanoscience and technology. Along with chemical functionalization, geometric constraints (such as extreme curvature in nanotubes or defects within or at the surfaces of diamond nanoparticles) significantly alter the electronic states of the nanocarbon material. Understanding the effects of steric strain on the electronic structure is critical to developing nanoelectronic applications based on these materials. This paper presents a fundamental study of how strain affects the electronic structure in a benchmark series of some fundamental saturated carbon cage compounds. Adamantane, C10H16, the smallest diamondoid and arguably the smallest nanodiamond crystallite, has carbon atoms essentially commensurate with diamond lattice positions and possesses by far the least molecular strain of this series. Twistane also is a C10H16 isomer but the fixed cyclohexane twist conformation of the central ring introduces additional strain into the cage. Octahedrane [(CH)12] and cubane [(CH)8] are considerably more strained, culminating in cubane where carbon–carbon bonds lie either parallel or orthogonal to one another. Using gas-phase near-edge x-ray absorption fine structure spectroscopy to probe the unoccupied electronic states, we observe two major progressions across this series. First, a broad C–C σ* resonance in the absorption splits into two more narrow and intense resonances with increasing strain. Second, the first manifold of states previously associated with tertiary C–H σ* in the diamondoid series appears to broaden and shift to lower energy. This feature is more than twice as intense in cubane than in octahedrane, even though these two molecules have only tertiary carbons, with the chemical formula (CH)x. The spectral differences are entirely due to the shape of the molecules; in particular, in cubane, the features arise from a high degree of p-p interaction between parallel C–C bonds. In contrast to the conventional wisdom that near-edge x-ray absorption is primarily an atomically localized spectroscopy, molecular shape and associated strain lead to the dominant features in spectra acquired from this fundamental series of carbon cage structures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural mechanisms of TRPV6 inhibition by ruthenium red and econazole

TRPV6 is a calcium-selective ion channel implicated in epithelial Ca 2+ uptake. TRPV6 inhibitors are needed for the treatment of a broad range of diseases associated with disturbed calcium homeostasis, including cancers. Here we combine cryo-EM, calcium imaging, and mutagenesis to explore molecular bases of human TRPV6 inhibition by the antifungal drug econazole and the universal ion channel blocker ruthenium red (RR). Econazole binds to an allosteric site at the channel’s periphery, where it replaces a lipid. In contrast, RR inhibits TRPV6 by binding in the middle of the ion channel’s selectivity filter and plugging its pore like a bottle cork. Despite different binding site locations, both inhibitors induce similar conformational changes in the channel resulting in closure of the gate formed by S6 helices bundle crossing. The uncovered molecular mechanisms of TRPV6 inhibition can guide the design of a new generation of clinically useful inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why

A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation–dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. Here, we also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗