Intermediates in allosteric equilibria of DnaK?ATP interactions with substrate peptides
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Wang, Wei↗
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Microbial density and substrate identity interact to determine the stabilization efficiency of microbial-derived, mineral-associated organic matter
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Biological and medical sciences, Geosciences, Envi↗
Microbial density and substrate identity interact to determine the efficiency of mineral-associated organic matter formation
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Biological and medical sciences, Geosciences, Envi↗
Dynamic asymmetric strain imprinted into substrates by an oxide thin film
In film-substrate systems, the substrate role is often considered to be limited to providing static mechanical constraints. Dynamic film-substrate interactions when a structural change in the film modifies the substrate are generally disregarded. Here, using combined x-ray and electron microscopies, we observed that an electrically induced filament in a vanadium dioxide film created strong asymmetric strain in an underlying sapphire substrate. This asymmetric substrate strain fed back into the film and defined the filament expansion direction, revealing the importance of film-substrate dynamic interactions in determining film functionality. Furthermore, the strain imprint propagated at least tens of micrometers deep into the substrate, exceeding the film thickness by more than 200-fold, potentially enabling substrate functionalization as an active mechanical coupling media in three-dimensional integrated microelectronic architectures.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Superconductivity devices: Commercial use of space
High T sub C superconducting thick film were prepared by a screen printing process. Y-based (YBa2Cu3O(7-x) superconducting thick film were printed on 211/Al2O3, SNT/Al2O3, and YSZ substrates. Because of poor adhesion of the superconductor thick films to 211/Al2O3 and SNT/Al2O3 substrates, relatively low T sub C and J sub C values were obtained from the films printed on these substrates. Critical temperatures (T sub C) of YBa2Cu3O(7-x) thick films deposited on 211/Al2O3 and SNT/Al2O3 substrates were about 80 K. The critical current densities (J sub C) of these films were less than 2 A/sq cm. Higher T sub C and J sub C YBa2Cu3O(7-x) thick films were printed on YSZ substrates. A YBa2Cu3O(7-x) thick film with T sub C=86.4 and J sub C= 50.4 A/sq cm was prepared by printing the film on YSZ substrate and firing at 990 C for 10 minutes. Multiple-lead samples were also prepared on the YSZ substrates. The multiple-lead samples showed lower T sub C and/or J sub C values than those of the plain samples. The electrical properties of YBa2Cu3O(7-x) thick films were determined by the microstructures of the films. The YBa2Cu3O(7-x) thick films printed on the YSZ substrates, which had the best properties among the films printed on the three different kinds of substrates, had the highest density and the best particle interconnection. The YBa2Cu3O(7-x) thick films with preferred orientation in (001) direction were obtained on the YSZ substrates. Cracks, which retard the properties of the films, were found from the films deposited on the YSZ substrates. Currently, a MSZ (Magnesium Stabilized Zirconia) substrate, which had higher thermal expansion coefficient than the YSZ substrate, is used as substrate for the YBa2Cu3O(7-x) thick film in order to eliminate the cracks on the film. Bi-based superconductor thick films were printed on polycrystalline MgO and YSZ substrates. Interactions between BSCCO thick films and the YSZ substrates were observed. Various buffer layer materials were applied onto the substrates in order to avoid the interactions between the BSCCO thick films and the ZrO2-based substrates. So far, a BSCCO printed on MgO substrate with T Sub C=89K was obtained. The J sub C of the film was lower than 0.1 A/sq cm by reason of poor interconnectivity of the BSCCO particles.
Haertling, Gene↗
Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases
Abstract Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate’s C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10’s recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.
Science & Technology - Other Topics↗
Substrate-Driven Catalyst Reducibility for Oxygen Evolution and Its Effect on the Operation of Proton Exchange Membrane Water Electrolyzers
To increase the efficiency of hydrogen production by proton exchange membrane water electrolyzers (PEMWEs), the relationships between the specific activity and stability of the membrane–electrode assembly (MEA) must be clarified. Ir oxide electrodeposited on Ti substrate is used as an oxygen electrode, and its electronic properties and electrochemical behavior in PEMWE operation are observed. The electrode, fabricated through a facile strategy based on annealing in the air atmosphere, enhances the specific oxygen evolution reaction (OER) activity and stability in PEMWE operation. Furthermore, the electronic catalyst–substrate interactions associated with different reducibilities in the heteroatom system are studied. The morphology, electronic properties, and chemical state of the oxygen electrode are investigated through X-ray spectroscopy, microscopy techniques, and computational analyses. Thermal treatment of the catalyst-coated substrate decreases the bulk oxidation state of Ir and increases the surface oxidation state. According to the electrochemical and physical behavior analyses of PEMWEs, the oxygen content in the Ir oxide structure, which defines the OER activity and its stability, is influenced by the crystalline structure and formation of a stable interface between the catalyst and substrate. The outcomes can facilitate the development of strategies for enhancing the performance of PEMWEs and designing rational MEAs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Self‐Assembly and Oriented Growth of Conductive Ni‐CAT‐1 Metal‐Organic Framework at Solid–Liquid Interfaces
Abstract Two‐dimensional (2D) conductive metal‐organic frameworks (MOF) represent a unique class of electrode materials with high capacity and power density. Understanding molecular mechanisms and pathways for heterogeneous nucleation of 2D π‐conjugated MOFs is highly desirable for controlling the structure and properties of conductive MOFs on solid substrates. Herein, a systematic study of nucleation and growth of 2D π‐conjugated Ni‐catecholate (Ni‐CAT‐1) MOFs on highly oriented pyrolytic graphite (HOPG) and copper substrates is reported. It is discovered that the nucleation density and growth kinetics of the MOF film can be controlled by varying substrate interactions with the organic linker. Specifically, π–π interactions between the linker and the HOPG dictate lower nucleation density, whereas π–metal interactions between the linker and the copper substrate dictate faster nucleation and higher nucleation densities. These studies reveal the key mechanism for Ni‐CAT‐1 nucleation on different surfaces and provide insights into interfacial control over the growth of other 2D π‐conjugated MOF films on solid substrates to inform synthesis of functional materials.
2D materials↗
Theoretical Study of Low-Energy Electron-Molecule Collisions
Polarized studies of electron collisions with carbon tetrafluoride and beryllium carbonyl are reported. In the e-CF4 study, the resonance structure between 8-9 eV is shown to be a superposition of the T2- and A1-symmetry shape resonances. The unequivocal assignment of this feature as a double-resonance structure clarifies certain discrepancies in previous attempts to ascribe the 8-9 eV feature to a shape resonance in one or another partial channel and explains the sensitivities found in the fragment ion production in the resonance region. The Be-CO system is chosen as a prototypical example of an absorbate-substrate interaction. To understand how bonding with the substrate affects the CO resonance, electron collision with two states of BeCO are studied, one with a very weak van der Waals bond and the other, with a normal chemical bond. It is shown that the nature of the Be-CO bond has strong effects on the cross section feature.
Huo, Winfred M.↗
Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis
Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.
93 SC - Biological and Environmental Research (BER↗
Water as a matrix for life
Life is based on non-covalent interactions. They might be either specific (enzyme-substrate interactions, selective ion transport) or nonspecific (lipid-lipid and lipid-protein interactions needed for membrane integrity, fusion and division). Their strength needs to be properly tuned, and this is mediated by the solvent. If interactions are too weak, there might be undesired response to natural fluctuations of physical and chemical parameters. If they are too strong it could impede kinetics and energetics of cellular processes. Thus, the solvent must allow for balancing these interactions. Physical and chemical properties of solvent provide strong constraints for life. Water exhibits a remarkable trait that it promotes both solvophobic and solvophilic interactions. Solvophobic interactions; related to high dielectric constant of the solvent) are necessary for self-organization of matter whereas solvophilic interactions are needed to ensure solubility of polar species. Water offers a large temperature domain of stable liquid and the characteristics hydrophobic effects are a consequence of the temperature in sensitivity of essential properties of its liquid state. Water, however, is not the only liquid with these favorable properties. I will compare in detail properties of water and other pure liquids or their mixtures that have a high dielectric constant and simultaneously support self-organization. I will also discuss properties of water that are unfavorable to life (e.g. its chemical activity against polymerization reactions) and close with summarizing what are alternatives to water as a matrix of life in space.
Pohorille, Andrew↗
Focused Helium Ion Beam for Direct Patterning of Monolayer MoS 2 Nanoribbon Field Effect Devices
The helium ion microscope (HIM) focused ion beam (FIB) has emerged as a powerful tool to directly pattern nanostructures below 10 nm due to its high-resolution capabilities and the inert nature of the ion source. These attributes make HIM FIB particularly interesting for patterning 2D materials such as transition metal dichalcogenides (TMDs) to investigate transport phenomena at the nanoscale. Reported here is the fabrication of MoS 2 nanoribbon devices using HIM FIB-induced etching (FIBIE) with XeF 2 , allowing for reduced ion dose compared to direct sputtering. While patterning is efficacious, the devices exhibit performance degradation with decreasing nanoribbon width due to damage up to 150 nm beyond the patterned edge. Incorporating an hBN encapsulation improves device performance by one order of magnitude, although the lateral extent of damage remains unchanged. The spatial distribution of damage is shown to be determined by the forward- and backscattered ions and electrons, while the hBN encapsulation layer substantially reduces damage from XeF 2 interactions in unexposed regions. Raman and photoluminescence (PL) measurements corroborate these findings, while ion/solid interaction simulations further elucidate the resolution limits imposed by substrate interactions. In conclusion, this work provides critical insights and a practical pathway for utilizing HIM FIBIE in 2D TMD functional device patterning.
MoS 2↗
Nucleation and Antiphase Twin Control in Bi 2 Se 3 via Step‐Terminated Al 2 O 3 Substrates
The epitaxial synthesis of high-quality 2D layered materials is an essential driver of both fundamental physics studies and technological applications. Bi 2 Se 3 , a prototypical 2D layered topological insulator, is sensitive to defects imparted during the growth, either thermodynamically or due to the film-substrate interaction. Here, in this study, it is shown that step-terminated Al 2 O 3 substrates with a high miscut angle (3°) can effectively suppress a particular hard-to-mitigate defect, the antiphase twin. Systematic investigations across a range of growth temperatures and substrate miscut angles confirm that atomic step edges act as preferential nucleation sites, stabilizing a single twin domain. First-principles calculations suggest that there is a significant energy barrier for twin boundary formation at step edges, supporting the experimental observations. Detailed structural characterization indicates that this twin-selectivity is lost through the mechanism of the 2D layers overgrowing the step edges, leading to higher twin density as the thickness increases. These findings highlight the complex energy landscape unique to 2D materials that is driven by the interplay between substrate properties, nucleation dynamics, and defect formation, and overcoming and controlling these are critical to improve material quality for quantum and electronic applications.
36 MATERIALS SCIENCE↗
OH density, flux and loss probability measurements in a room temperature atmospheric pressure surface discharge by microscopic laser induced fluorescence
Many applications involving atmospheric pressure plasma-substrate interactions are enabled by the large fluxes of short-lived reactive species such as OH radicals to the substrate, nonetheless, the accurate measurement of radical densities and fluxes at substrates at atmospheric pressure has received little attention to date, particularly for surface ionization waves. We report the measurement of the OH density distribution in a surface discharge on a fused silica (quartz) substrate generated by an impinging atmospheric pressure plasma jet in dry and humid helium. The OH density is measured by microscopic laser induced fluorescence with a spatial resolution of 10 µm in the direction perpendicular to the quartz substrate. The measured OH diffusive flux varied for the investigated experimental conditions by almost three orders of magnitude and had a maximum value of 1.7 × 10 15 cm -2 s -1 . The corresponding surface loss probability of OH on the quartz surface was determined to be ~0.01. The high spatial resolution was required to accurately resolve the near surface gradient of OH radicals.
plasma-surface interactions↗
Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein–carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM–substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose–CBM bond rupture forces exceeding 15 pN.
09 BIOMASS FUELS↗
Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning
Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.
59 BASIC BIOLOGICAL SCIENCES↗
Fluorescence studies of substrate and subunit interactions of the beta sub 2 protein of Escherichia coli tryptophan synthetase.
Substrate and subunit interactions influence of beta 2 protein of Escherichia coli tryptophan synthetase on fluorescence properties of pyridoxal phosphate prosthetic groups
Goldberg, M. E.↗
How Precisely Can Individual Molecules Be Analyzed? A Case Study on Locally Quantifying Forces and Energies Using Scanning Probe Microscopy
Recent advances in scanning probe microscopy methodology have enabled the measurement of tip-sample interactions with picometer accuracy in all three spatial dimensions, thereby providing a detailed site-specific and distance-dependent picture of the related properties. This paper explores the degree of detail and accuracy that can be achieved in locally quantifying probe-molecule interaction forces and energies for adsorbed molecules. Toward this end, cobalt phthalocyanine (CoPc), a promising CO 2 reduction catalyst, was studied on Ag(111) as a model system using low-temperature, ultrahigh vacuum noncontact atomic force microscopy. Data were recorded as a function of distance from the surface, from which detailed three-dimensional maps of the molecule's interaction with the tip for normal and lateral forces as well as the tip-molecule interaction potential were constructed. The data were collected with a CO molecule at the tip apex, which enabled a detailed visualization of the atomic structure. Determination of the tip-substrate interaction as a function of distance allowed isolation of the molecule-tip interactions; when analyzing these in terms of a Lennard-Jones-type potential, the atomically resolved equilibrium interaction energies between the CO tethered to the tip and the CoPc molecule could be recovered. Interaction energies peaked at less than 160 meV, indicating a physisorption interaction. As expected, the interaction was weakest at the aromatic hydrogens around the periphery of the molecule and strongest surrounding the metal center. In conclusion, the interaction, however, did not peak directly above the Co atom but rather in pockets surrounding it.
36 MATERIALS SCIENCE↗