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Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose
The processive cycle of the bacterial cellulose synthase (Bcs) includes the addition of a single glucose moiety to the end of a growing cellulose chain followed by the translocation of the nascent chain across the plasma membrane. The mechanism of this translocation and its precise location within the processive cycle are not well understood. In particular, the molecular details of how a polymer (cellulose) whose basic structural unit is a dimer (cellobiose) can be constructed by adding one monomer (glucose) at a time are yet to be elucidated. Here, we have utilized molecular dynamics simulations and free energy calculations to the shed light on these questions. We find that translocation forward by one glucose unit is quite favorable energetically, giving a free energy stabilization of greater than 10 kcal mol-1. In addition, there is only a small barrier to translocation, implying that translocation is not rate limiting within the Bcs processive cycle (given experimental rates for cellulose synthesis in vitro). Perhaps most significantly, our results also indicate that steric constraints at the transmembrane tunnel entrance regulate the dimeric structure of cellulose. Namely, when a glucose molecule is added to the cellulose chain in the same orientation as the acceptor glucose, the terminal glucose freely rotates upon forward motion, thus suggesting a regulatory mechanism for the dimeric structure of cellulose. We characterize both the conserved and non-conserved enzyme-polysaccharide interactions that drive translocation, and find that 20 of the 25 residues that strongly interact with the translocating cellulose chain in the simulations are well conserved, mostly with polar or aromatic side chains. Our results also allow for a dynamical analysis of the role of the so-called 'finger helix' in cellulose translocation that has been observed structurally. Taken together, these findings aid in the elucidation of the translocation steps of the Bcs processive cycle and may be widely relevant to polysaccharide synthesizing or degrading enzymes that couple catalysis with chain translocation.
Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin]
Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction, respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.
Structural characterization of framework–gas interactions in the metal–organic framework Co 2 (dobdc) by in situ single-crystal X-ray diffraction
The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4 , N 2 , O 2 , Ar, and P 4 adsorption in Co2(dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(II) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(II) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH 4 and Co–Ar interactions observed in Co 2 (dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH 4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(II) sites in Co 2 (dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol –1 (for Ar). Moreover, the structures of Co 2 (dobdc)·3.8N 2 , Co 2 (dobdc)·5.9O 2 , and Co 2 (dobdc)·2.0Ar reveal the location of secondary (N 2 , O 2 , and Ar) and tertiary (O 2 ) binding sites in Co 2 (dobdc), while high-pressure CO 2 , CO, CH 4 , N 2 , and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.
Pressure-induced structural transformations and new polymorphs in BiVO[subscript 4]
Abstract not provided
Synthesis and structural characterization of the new Zintl phases Eu 10 Mn 6 Bi 12 and Yb 10 Zn 6 Sb 12
Two new ternary compounds, Eu 10 Mn 6 Bi 12 and Yb 10 Zn 6 Sb 12 , were synthesized and structurally characterized. The synthesis was achieved either through reactions in sealed niobium tubes or in alumina crucibles by combining the elements in excess molten Sb. Their structures were elucidated using single-crystal X-ray diffraction, and they were determined to crystallize in the orthorhombic space group Cmmm (no. 65) with the Eu 10 Cd 6 Bi 12 structure type. Akin to the archetype phase, both Mn and Zn sites contain about 25% of vacancies. Furthermore, the anionic substructure of the title phases can be described as [M 6 Pn 12 ] (M = Zn, Mn; Pn = Sb, Bi) double layers composed of the corner and edge-sharing [MPn 4 ] tetrahedra, linked by [Pn 2 ] 4– dumbbells. Eu 2+ /Yb 2+ cations fill the space between the layers, with the valence electron counts adhering closely to the Zintl–Klemm rules, i.e., both Eu 10 Mn 6 Bi 12 and Yb 10 Zn 6 Sb 12 are expected to be valence-precise compounds. Analysis of the electronic structure and transport properties of Yb 10 Zn 6 Sb 12 indicate semimetallic behavior with relatively low Seebeck coefficient and resistivity that slightly decreases as a function of temperature.
Toward epitaxially grown two-dimensional crystal hetero-structures: Single and double MoS{sub 2}/graphene hetero-structures by chemical vapor depositions
Uniform large-size MoS{sub 2}/graphene hetero-structures fabricated directly on sapphire substrates are demonstrated with layer-number controllability by chemical vapor deposition (CVD). The cross-sectional high-resolution transmission electron microscopy (HRTEM) images provide the direct evidences of layer numbers of MoS{sub 2}/graphene hetero-structures. Photo-excited electron induced Fermi level shift of the graphene channel are observed on the single MoS{sub 2}/graphene hetero-structure transistors. Furthermore, double hetero-structures of graphene/MoS{sub 2}/graphene are achieved by CVD fabrication of graphene layers on top of the MoS{sub 2}, as confirmed by the cross-sectional HRTEM. These results have paved the possibility of epitaxially grown multi-hetero-structures for practical applications.
Structural transitions of 4:1 methanol–ethanol mixture and silicone oil under high pressure
A 4:1 (volume ratio) methanol–ethanol (ME) mixture and silicone oil are two of the most widely used liquid pressure-transmitting media (PTM) in high-pressure studies. Their hydrostatic limits have been extensively studied using various methods; however, the evolution of the atomic structures associated with their emerging nonhydrostaticity remains unclear. Here, we monitor their structures as functions of pressure up to ∼30 GPa at room temperature using in situ high-pressure synchrotron x-ray diffraction (XRD), optical micro-Raman spectroscopy, and ruby fluorescence spectroscopy in a diamond anvil cell. No crystallization is observed for either PTM. The pressure dependence of the principal diffraction peak position and width indicates the existence of a glass transition in the 4:1 ME mixture at ∼12 GPa and in the silicone oil at ∼3 GPa, beyond which a pressure gradient emerges and grows quickly with pressure. There may be another liquid-to-liquid transition in the 4:1 ME mixture at ∼5 GPa and two more glass-to-glass transitions in the silicone oil at ∼10 GPa and ∼16 GPa. By contrast, Raman signals only show peak weakening and broadening for typical structural disordering, and Raman spectroscopy seems to be less sensitive than XRD in catching these structural transitions related to hydrostaticity variations in both PTM. These results uncover rich pressure-induced transitions in the two PTM and clarify their effects on hydrostaticity with direct structural evidence. The high-pressure XRD and Raman data on the two PTM obtained in this work could also be helpful in distinguishing between signals from samples and those from PTM in future high-pressure experiments.
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription
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Effects of fluorinated solvents on electrolyte solvation structures and electrode/electrolyte interphases for lithium metal batteries
Electrolyte is very critical to the performance of the high-voltage lithium (Li) metal battery (LMB), which is one of the most attractive candidates for the next generation high-density energy storage systems. Electrolyte formulation and structure determine the physical properties of the electrolytes and their interfacial chemistries on the electrode surfaces. Localized high-concentration electrolytes (LHCEs) outperform state-of-the-art carbonate electrolytes in many aspects in LMBs due to their unique solvation structure. Types of fluorinated co-solvents used in LHCEs are investigated here in searching for the most suitable diluent for high concentration electrolytes (HCEs). Non-solvating solvents (including fluorinated ethers, fluorinated borate and fluorinated orthoformate) added in HCEs enable the formation of LHCEs with high-concentration solvation structures. However, low solvating fluorinated carbonate will coordinate with Li+ ions and form a second solvation shell or a pseudo-LHCE which diminishes the benefits of LHCE. In addition, it is evident that the diluent has significant influence on the electrode/electrolyte interphases (EEIs) beyond retaining the high-concentration solvation structures. Diluent molecules surrounding the high-concentration clusters could accelerate or decelerate the anion decomposition through co-participation of diluent decomposition in the EEI formation. The varied interphase features lead to significantly different battery-performance. This study points out the importance of diluents and their synergetic effects with the conductive salt and the solvating solvent in designing LHCEs. These systematic comparisons and fundamental insights into LHCEs using different types of fluorinated solvents can guide further development of advanced electrolytes for high-voltage LMBs.
The myosin II coiled-coil domain atomic structure in its native environment
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High pressure structural phase transitions in Dysprosium to 202 GPa
High pressure structural phase transitions in heavy lanthanide metal Dysprosium (Dy) have been studied to 202 GPa (Volume Compression V/V 0 = 0.36) in a diamond anvil cell employing copper as an internal x-ray pressure standard. The previously assigned monoclinic (C2/m) phase above 72 GPa has been reexamined and assigned to an orthorhombic phase with sixteen atoms per cell (oF16) based on structural refinements. The equation of state is presented to 202 GPa and indicates a volume change of 2.3% during the structural phase transition from distorted face-centered cubic (hR24) phase to oF16 phase at 72 GPa. The oF16 phase can be regarded as a pseudo-orthorhombic eight-layered structure with (b/c) ratio decreasing from an ideal value of $\sqrt{3}$ with increasing pressure to 202 GPa. The ultrahigh pressure structural phases of Dy are compared with other members of the lanthanide series.
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.
Configuration-specific electronic structure of strongly interacting interfaces: TiOPc on Cu(110)
Not Available
In situ analysis of the structural transformation of glassy carbon under compression at room temperature
Room temperature compression of graphitic materials leads to interesting superhard sp 3 rich phases which are sometimes transparent. In the case of graphite itself, the sp 3 rich phase is proposed to be monoclinic M-carbon; however, for disordered materials such as glassy carbon the nature of the transformation is unknown. We compress glassy carbon at room temperature in a diamond anvil cell, examine the structure in situ using x-ray diffraction, and interpret the findings with molecular dynamics modeling. Experiment and modeling both predict a two-stage transformation. First, the isotropic glassy carbon undergoes a reversible transformation to an oriented compressed graphitic structure. This is followed by a phase transformation at ~35 GPa to an unstable, disordered sp 3 rich structure that reverts on decompression to an oriented graphitic structure. Analysis of the simulated sp 3 rich material formed at high pressure reveals a noncrystalline structure with two different sp 3 bond lengths.
Disentangling transient charge order from structural dynamics contributions during coherent atomic motion studied by ultrafast resonant x-ray diffraction [Disentangling charge and structural contributions during coherent atomic motions studied by ultrafast resonant x-ray diffraction]
We report on the ultrafast dynamics of charge order and structural response during the photoinduced suppression of charge and orbital order in a mixed-valence manganite. Employing femtosecond time-resolved resonant x-ray diffraction below and at the Mn K absorption edge, we present a method to disentangle the transient charge order and structural dynamics in thin films of Pr 0.5 Ca 0.5 MnO 3 . Based on the static resonant scattering spectra, we extract the dispersion correction of charge-ordered Mn 3+ and Mn 4+ ions, allowing us to separate the transient contributions of purely charge order from structural contributions to the scattering amplitude after optical excitation. Furthermore, our finding of a coherent structural mode at around 2.3THz, which primarily modulates the lattice but does not strongly affect the charge order, supports the picture of the charge order being the driving force of the combined charge, orbital, and structural transition.
Measurements of d 2 n and A 1 n : Probing the neutron spin structure
We report on the results of the E06-014 experiment performed at Jefferson Lab in Hall A, where a precision measurement of the twist-3 matrix element $d_2$ of the neutron ($d_{2}^{n}$) was conducted. This quantity represents the average color Lorentz force a struck quark experiences in a deep inelastic electron scattering event off a neutron due to its interaction with the hadronizing remnants. This color force was determined from a linear combination of the third moments of the spin structure functions $g_1$ and $g_2$ on $^{3}$He after nuclear corrections had been applied to these moments. The kinematics included two average $Q^{2}$ bins of $3.2$ GeV$^{2}$ and $4.3$ GeV$^{2}$, and Bjorken-$x$ $0.25 \leq x \leq 0.90$ covering the DIS and resonance regions. We found $d_2^n$ to be small and negative for $ = 3.2$ GeV$^{2}$, and smaller for $ = 4.3$ GeV$^{2}$, consistent with a lattice QCD calculation. The twist-4 matrix element $f_{2}^{n}$ was extracted by combining our $d_{2}^{n}$ with the world data on $\Gamma_{1}^{n} = \int_{0}^{1} g_{1}^{n} dx$. We found $f_{2}^{n}$ to be roughly an order of magnitude larger than $d_{2}^{n}$. Utilizing the extracted $d_{2}^{n}$ and $f_{2}^{n}$ data, we separated the color force into its electric and magnetic components, $F_{E}^{y,n}$ and $F_{B}^{y,n}$, and found them to be equal and opposite in magnitude, in agreement with instanton model predictions but not with those from QCD sum rules. Additionally, we have extracted the neutron virtual photon-nucleon asymmetry $A_{1}^{n}$, the structure function ratio $g_{1}^{n}/F_{1}^{n}$, and the quark ratios $(\Delta u + \Delta \bar{u})/(u + \bar{u})$ and $(\Delta d + \Delta \bar{d})/(d + \bar{d})$. Lastly, these results were found to be consistent with DIS world data and with the prediction of the constituent quark model but at odds with those of perturbative QCD at large $x$.
Observation of Wakefield Suppression in a Photonic-Band-Gap Accelerator Structure
We report experimental observation of higher order mode (HOM) wakefield suppression in a room-temperature traveling-wave photonic band gap (PBG) accelerating structure at 11.700 GHz. It has been long recognized that PBG structures have potential for reducing long-range wakefields in accelerators. The first ever demonstration of acceleration in a room-temperature PBG structure was conducted in 2005. Since then, the importance of PBG accelerator research has been recognized by many institutions. However, the full experimental characterization of the wakefield spectrum and demonstration of wakefield suppression when the accelerating structure is excited by an electron beam has not been performed to date. We conducted an experiment at the Argonne Wakefield Accelerator (AWA) test facility and observed wakefields excited by a single high charge electron bunch when it passes through a PBG accelerator structure. Lastly, excellent HOM suppression properties of the PBG accelerator were demonstrated in the beam test.