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The cis- form of diaminodibenzocyclooctane (DADBCO, C 16 H 18 N 2 ) is of interest as a negative coefficient of thermal expansion (CTE) material. The crystal structure was determined through single-crystal X-ray diffraction at 100 K and is presented herein.
Abstract Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 to promote viral entry and modulate host immunity. Antibodies against RSV G are a known correlate of protection. Previously, several broadly reactive, high-affinity anti-RSV G human monoclonal antibodies were isolated from RSV-exposed individuals and were shown to be protective in vitro and in vivo. Here, we determined the structures of three of these antibodies in complex with RSV G and defined distinct conformational epitopes comprised of highly conserved RSV G residues. Binding competition and structural studies demonstrated that this highly conserved region displays two non-overlapping antigenic sites. Analyses of anti-RSV G antibody sequences reveal that antigenic site flexibility may promote the elicitation of diverse antibody germlines. Together, these findings provide a foundation for next-generation RSV prophylactics, and they expand concepts in vaccine design for the elicitation of germline lineage-diverse, broadly reactive, high-affinity antibodies.
Alkali-activated slag (AAS) is a promising low-CO 2 alternative cement consisting of several disordered phases of similar composition. Although their local atomic arrangements are known to influence macroscopic behavior, determination of structural changes in response to external stimuli remains a challenge. Here, X-ray diffraction-computed tomography (XRD-CT), pair distribution function-CT (PDF-CT), and nanoprobe X-ray fluorescence (nano-XRF) have been used to uncover how an increase of magnesium in AAS affects the atomic structure and spatial arrangement of phases after aggressive carbonation (100% dry CO 2 ), conditions experienced in applications such as oil and gas wells and geological storage of CO 2 . From PDF-CT it is found that a higher magnesium content decreases the average nanoscale crystallite size of disordered calcium carbonate. At the same time, higher magnesium content is correlated with a less decalcified C-(N)-A-S-H gel, as determined via analysis of Ca-Si atom-atom correlations from PDF-CT and Ca/Si ratios from nano-XRF. Finally, nano-XRF reveals that the disordered (i.e., amorphous) calcium carbonate is stabilized by the presence of silicates.
Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.
Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.
In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.
Significant progress has been made in describing the structure of hadrons in terms of Quantum ChromoDynamics (QCD) degrees of freedom. The recently developed framework of Generalized Parton Distribtions (GPDs) may provide the path towards three-dimensional imaging of the hadronic structure. Integrating the GPDs over the fractional momentum (x), the form factors are obtained which are integrally related to understanding the emergent hadron mass-generating mechanism (EHM) embedded in QCD and the mass-scale that characterizes the proton [Roberts (2016)]. The Sullivan process, in which one scatters electrons off the proton?s virtual meson cloud and thus creates a meson target, is used to probe this structure. Studies of kaon electroproduction offer unique opportunities in this. The last two decades saw a dramatic improvement in the precision of charged meson form factor data, and new results have become available on the transition form factor. The KaonLT experiment (E12-09-011) carried out in Hall C at Jefferson Lab (Jlab) was designed to measure longitudinal/transverse (L/T) separated kaon cross sections required to access form factors and GPDs [Bosted et al. (2008)]. KaonLT aimed to confirm the exclusive kaon electroproduction mechanism, which is essential for determining the kaon form factor and investigating GPDs. The results obtained from this experiment have provided the highest Q2 for L-T separated kaon electroproduction cross section, and it is the first time that a separated kaon cross-section measurement has been carried out above W = 2:2GeV.
The conventional approach to elucidate the atomic structure of liquid and glass is to start with local structural units made of several atoms, and to use them as building blocks to form a global structure, the bottom-up approach. We propose to add an alternative top-down approach in which we start with a global high-temperature gas state and then apply interatomic potentials to all atoms at once. This causes collective density wave instability in all directions with the same wavelength. These two driving forces, local and global, are in competition and are mutually frustrated. The final structure is determined through the compromise of frustration between these two, which creates the medium-range-order. This even-handed approach on global and local potential energy landscapes explains the distinct natures of short-range order and medium-range order, and strong temperature dependence of various properties of liquid.
Covalent triazine frameworks (CTFs) represent one of the most extensively studied organic networks characterized by graphitic π-conjugated structures linked by aza-fused rings, possessing unique features such as compositions of light elements (e.g., C, H, and N), porous architectures abundant heteroatom involvement, and extensively conjugated structures. In addition, the textural and chemical structures of CTFs could be engineered via synthesis control to accommodate diverse applications. CTF materials with notable characteristics, including plentiful (ultra-)micropores, high surface areas, and the presence of CO 2 -philic functional groups involving nitrogen (N), oxygen (O), and fluorine (F), hold great promise as potential candidates for anthropogenic CO 2 capture and sequestration (CCS) applications. However, the conventional high-temperature involved ionothermal procedures and the solution-based coupling pathway only afforded CTF materials in powder form, which is difficult to be processed toward membrane formation. Successful fabrication of CTF-derived membranes will rely on the development of alternative polymerization approaches as well as structural engineering to afford membrane architectures with controllable porosity distribution and active interaction sites with CO 2 benefiting the CO 2 separation procedure. In this Account, a demonstration of the latest progress in the development of CTF-derived membranes was provided. The CTF membranes were mainly synthesized via a superacid (e.g., CF 3 SO 3 H)-promoted sol–gel approach involving the polymerization of aromatic nitrile monomers. The formation of the triazine unit through the trimerization of cyano groups served as the cross-linkers, resulting in the creation of π-conjugated networks alongside the arenes present in the starting materials. The aromatic nitrile monomers with rigid and sterically hindered structures were required to afford CTF membranes with nanoporous architectures. The acidity of the superacid and reactivity of the aromatic monomers played critical roles in the polymerization efficiency. The monomer diversity and synthesis tunability endowed the introduction of CO 2 -philic functionalities (e.g., pyrazole and fluorine) within the CTF skeletons, and integration of ionic moieties was achieved by adopting FSO 3 H with stronger acidity as the catalyst and aromatic nitrile monomers with pyrazine structures. To ensure the successful construction of fluorinated CTF membranes, it is important to avoid any fluorines on the ortho-position of the cyano groups on the benzene ring. Through control over the monomers and reaction conditions, flexible, transparent, and insoluble CTF membranes could be fabricated. The sol–gel method could be further expanded to membrane fabrication through acetyl-to-benzene transformation through synthesis control. The mild oxidation-exfoliation-filtration method was also demonstrated to fabricate substrate-supported CTF membranes. The as-afforded membranes are well characterized to determine the structural features and provide information to study the structure-performance relationship. Here, the application of CTF membranes in CO 2 separation was summarized, focusing on the approaches being developed to enhance CO 2 uptake and separation performance. In addition to utilizing the pristine CTF membranes for gas separation, functionalized carbon molecular sieve membranes could be obtained from the pyrolysis of thermally stable CTF membrane precursors toward efficient CO 2 separation, benefiting from the abundant ultramicropores being created during the pyrolysis/decomposition procedure and involvement of CO 2 -philic functionalities such as fluorine and nitrogen-containing moieties. Based on these achievements, unsolved issues in CTF membrane-related fabrication and applications, including the potential solution approaches, have been proposed to advance the application of CTF membranes.
Block copolymers exhibiting an enhanced segregation strength due to an underlying high Flory–Huggins interaction parameter (high χ) have attracted considerable attention because of their potential of forming microphase-separated domains with very small feature sizes (<10 nm) useful for next-generation lithography. Here, we report the synthesis, characterization, and self-assembly of poly(styrene)- block -poly(2-vinylpyridine N -oxide) (PS- b -P2VPNO) and poly(styrene)- block -poly(4-vinylpyridine N -oxide) (PS- b -P4VPNO) block copolymers. These PS- b -PVPNOs were obtained from the oxidation of their precursors, poly(styrene)- block -poly(2-vinylpyridine) (PS- b -P2VP) and poly(styrene)- block -poly(4-vinylpyridine) (PS- b -P4VP), respectively. The PS- b -PVPNOs exhibit an enhanced segregation as revealed by ordered cylindrical and lamellar structures in the sub-10 nm scale from copolymers with relatively low molecular weight. The morphologies and periodicities of the ordered structures were determined by small-angle X-ray scattering, while atomic-force microscopy was used to image the self-assembly in thin films. Estimates of the changes in disorder–order transition temperature and domain spacing are derived from a theory based on the effects of dipolar interactions. All the experimentally observed morphological changes resulting from the oxidation of P2VP and P4VP precursors can be qualitatively explained in terms of an increased dipole moment of vinylpyridine N -oxide segments. Therefore, our results demonstrate that PVPNO based block copolymers are versatile candidates toward nanopatterned structures with small feature sizes critical for the future microelectronics industry and beyond.
The present disclosure relates to transmission electron microscopy for evaluation of biological matter. According to an embodiment, the present disclosure further relates to an apparatus for determining the structure and/or elemental composition of a sample using 4D STEM, comprising a direct bombardment detector operating with global shutter readout, processing circuitry configured to acquire images of bright-field disks using either a contiguous array or non-contiguous array of detector pixel elements, correct distortions in the images, align each image of the images based on a centroid of the bright-field disk, calculate a radial profile of the images, normalize the radial profiles by a scaling factor, calculate the rotationally-averaged edge profile of the bright-field disk, and determine elemental composition within the specimen based on the characteristics of the edge profile of the bright-field disk corresponding to each specimen location.
Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O 2 -binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme–substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.
Heterostructures consisting of vertically stacked two-dimensional (2D) materials have recently gained large attention due to their highly controllable electronic properties and resulting quantum phases. In contrast to the mechanically stacked multilayered systems, which offer exceptional control over a stacking sequence or interlayer twist angles, the epitaxially grown 2D materials express unprecedented quality and stability over wafer-scale lengths. However, controlling the growth conditions remains a major obstacle toward the formation of complex, epitaxial heterostructures with well-defined electronic properties. Here, we synthesized a trilayer graphene heterostructure on the SiC(0001) substrate with two specific interlayer locations occupied by gadolinium. We applied multitechnique methodology based on low-temperature scanning tunneling microscopy/spectroscopy (STM/S) and angle-resolved photoelectron spectroscopy (ARPES) to determine the intercalant’s locations in the complex, epitaxial graphene heterostructure. Our approach relies on very high quality and large, micrometer-scale homogeneity of the synthesized system. The experimentally determined electronic structure is dominated by the two topmost graphene layers. Overall, our spectroscopic results show quantitative agreement between global ARPES, local STM/S, and density functional theory predictions. The characterized electronic properties primarily reflect highly anisotropic doping levels between the two corresponding graphene layers, which significantly affect the band structure topology. Two pairs of hybridized massive Dirac bands from our initial synthesis–the bilayer graphene on the SiC(0001) substrate–are transformed upon Gd intercalation into two pairs of massless Dirac bands with a new hybridization region in between. Our results open perspectives in the realization of exotic 2D quantum materials via atomically precise synthesis of epitaxial, multilayered graphene–rare earth heterostructures.
The study of the motion of atoms in molecules is important to understanding many areas of physical and life sciences. Such motion occurs on many different times scales, with electronic motion occurring on a sub-femtosecond time scale, and simple vibrational motion in tens to hundreds of femtoseconds. One way to follow such processes in real time is by the use of shortpulsed lasers, and in particular by studying time-resolved photoionization and the related process of high-harmonic generation (HHG). Thus there has been much effort to develop the tools necessary to probe molecular systems using short pulse lasers and understanding the sensitivity of the different possible probes to the time dependent geometric structure as well as the electronic structure of molecules. Our research has particularly focused on the connection between high-field processes and the more traditional weak field photoionization processes. Strong field and weak field processes can be connected through models that involve the same matrix elements. We have demonstrated in our study of HHG from SF 6 that the spectrum is sensitive to the interplay between the angular dependence of the ionization step and recombination step. In our study of rescattering spectroscopy, we have shown that with a combination of experiment and theory, we can use this high-field spectroscopy to determine molecular structure in molecules such as C 2 H 4 . We have also developed new computational tools based on overset grids to enable studies on larger molecular systems which use much more robust numerical approaches so that the resulting code can be a tool that non-specialists can use to study related systems.
Two new transition metal oxides with the nominal chemical compositions of Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6 were successfully synthesized. Both compounds crystallize in an ordered rock salt structure type in the monoclinic C2/m space group. The crystal structures were determined using both synchrotron X-ray and time-of-flight neutron, powder diffraction data. In both phases, Ni2+ ions are present while oxidation states of osmium are +6 and +5 in Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6 , respectively. Ni2+ ions in the hypothetical fully ordered phase form a honeycomb arrangement in the ab crystallographic plane and these hexagons are centered by osmium ions. Furthermore, the magnetic layers are separated along the c axis by the octahedra, which are centered by Li+ (or Li+/Ni 2+ , depending on the chemical compositions). Crystal structure refinements reveal that there is some degree of mixed occupancy in cationic positions. Temperature dependent magnetic susceptibility data for both phases show ferrimagnetic transitions with predominant antiferromagnetic (AFM) interactions among 3d electrons of nickel and Sd electrons of osmium. Iso-thermal magnetization loops as a function of the applied magnetic field below the transition temperatures confirm the ferrimagnetic nature in magnetic transitions. Temperature dependent heat capacity data, however, did not exhibit any anomaly in either phase, indicating the absence of long-range magnetic ordering. The lack of long-range order for both Os 5+ and Os 6+ -based compounds was also confirmed by low temperature neutron diffraction data down to 10 K. Temperature dependent AC magnetic susceptibility data in various frequencies for both samples indicate that Li 4 NiOsO 6 exhibits spin-glass-like behavior, while the transition temperature for Li 3 Ni 2 OsO 6 is nearly frequency independent.
The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with ~1.5–2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.
EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying selection and its fusogenic activity has been maintained for over 40 million years. We determined the structure of the RBD of human EnvP(b)1, which defines structural similarities with extant leukemia viruses, despite little sequence conservation. This structure highlights a common scaffold from which novel receptor binding specificities likely evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses.
A longstanding challenge in catalysis by noble metals has been to understand the origin of enhancements of rates of hydrogen transfer that result from bonding of oxygen near metal sites. We investigated structurally well-defined catalysts consisting of supported tetrairidium carbonyl clusters with single-atom (apical iridium) catalytic sites for ethylene hydrogenation. Reaction of the clusters with ethylene and H 2 followed by O 2 led to the onset of catalytic activity as a terminal CO ligand at each apical Ir atom was removed and bridging dioxygen ligands replaced CO ligands at neighboring (basal-plane) sites. The presence of the dioxygen ligands caused a 6-fold increase in the catalytic reaction rate, which is explained by the electron-withdrawing capability induced by the bridging dioxygen ligands, consistent with the inference that reductive elimination is rate determining. Electronic structure calculations demonstrate an additional role of the dioxygen ligands, changing the mechanism of hydrogen transfer from that involving equatorial hydride ligands to that involving bridging hydride ligands. This mechanism is made evident by an inverse kinetic isotope effect observed in ethylene hydrogenation reactions with H 2 and, alternatively, with D 2 on the cluster incorporating the dioxygen ligands, and is a consequence of quasi-equilibrated hydrogen transfer in this catalyst. The same mechanism accounts for rate enhancements induced by the bridging dioxygen ligands for the catalytic reaction of H 2 with D 2 to give HD. Here, we posit that the mechanism involving bridging hydride ligands facilitated by oxygen ligands remote from the catalytic site may have some generality in catalysis by oxide-supported noble metals.