Microbial density and substrate identity interact to determine the efficiency of mineral-associated organic matter formation
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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↗
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↗
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↗
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↗
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↗
Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase)
The structures of Aspergillus oryzae α-amylase were determined in a tetragonal crystal, having one molecule as asymmetric unit, and a monoclinic crystal with two molecules as asymmetric unit. Both crystal forms were obtained from trace contaminants of an old commercial lipase preparation. Structures were determined and refined to 1.65 Å and 1.43 Å resolution respectively. The latter crystal has a non-crystallographic (NCS) twofold axis within the asymmetric unit. Glycosylation at Asn197 is evident, and in the tetragonal crystal can be seen to include three, partially disordered sugar residues following the initial N-acetyl glucosamine (NAG). Superposition of the tetragonal crystal model on the α-amylases from Bacillus subtilis (PDB:1BAG), pig pancreas (PDB:3L2L), and barley (PDB:1AMY), show a high degree of coincidence, particularly for the (β/α)8-barrel domains, and especially within the active site. Using this structural agreement between amylases, we extrapolated the binding model of a six residue, limit dextrin found in pig pancreas α-amylase to the A. oryzae enzyme model, which predicts substrate interacting amino acid residues.
59 BASIC BIOLOGICAL SCIENCES↗
Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Formation and surface melting of nanoparticle superlattices in a solution
The wisdom in the saying of “There are no two snowflakes alike” lies in the importance of history or kinetic pathways in the phase transitions of solids. Likewise, “artificial solids,” namely superlattices consisting of functional nanoparticles, have lattice size, surface morphology, crystallinity, symmetry, and structural reconfiguration (for example, transition into a disordered state) highly dependent on the kinetic pathways as the nanoparticles interact with each other in solution [1]. Great progresses have been made in understanding the formation pathways of superlattices using liquid-phase transmission electron microscopy (TEM) [2-4]. For example, by tracking single nanoparticle’s trajectories, especially aided by U-net neural network-based machine learning, previous studies mapped the fundamental nanoparticle interactions at nanometer resolution [5]. Nonclassical, two-step nucleation pathway has also been elucidated in the system of nanoprisms, by optimizing protocols such as loading nanoparticle suspensions over the supersaturation threshold and minimizing particle‒substrate interaction [2]. Surface morphologies or exposed facets of superlattices have been shown to follow the principles of Wulff construction rule, where the facet-dependent surface energy can be measured based on the capillary wave theory [4]. However, the reverse process of crystallization of superlattices, the conversion from crystalline to disordered state, has been much less explored. On one hand, the melting of nanoparticle superlattices can provide a preferred pathway to induce structural reorganization or shuffling of building blocks for them to transform into different types of crystal structures. On the other hand, understanding nanoscale superlattice melting and comparing such behaviors with the prevailing surface melting theories developed for atomic/molecular solids can provide a potent way to engineer phase transitions of supra- and hierarchical structures constructed from nanoscale entities (e.g., DNA-coated nanoparticles, proteins), for their applications in reprogrammable and switchable materials with multifunctional properties [6, 7]. The experimental challenges to observe melting of superlattices are twofold. Practically it is difficult to load the initial superlattice form, in an intact manner, into the highly confined liquid-phase TEM chamber for in-situ observation. Here, the triggering of melting also needs meticulous manipulation of nanoparticle concentration, interparticle interaction, and solution environment.
Kim, Ahyoung↗
Emergent Epitaxial Configuration of Pr 3 IrO 7 Domains via YSZ (111) Substrate
The 5d rare Earth iridate is an intriguing material with exhibiting exotic electronic and magnetic phases due to spin-orbit coupled states. Ternary iridium oxides Ln 3 IrO 7 contain an unusual Ir 5+ (5d 4 ) system, which remain a subject of active research. Fabricating epitaxial Ln 3 IrO 7 films is challenging due to substrate compatibility, but it offers a valuable platform to explore electronic and magnetic behaviors under reduced dimensionality and substrate interactions, revealing novel phenomena based on Ir 5+ (5d 4 ). In this regard, this demonstrates that Pr 3 IrO 7 with its highly anisotropic orthorhombic structure can be epitaxially grown on a cubic (111)-oriented yttrium-stabilized ZrO 2 (YSZ) substrate. Pr 3 IrO 7 film exhibits six epitaxial domains, where the (220) and (202) planes aligning epitaxially to YSZ (111) with the threefold symmetry. This diverse domain configuration in Pr 3 IrO 7 film leads to unique magnetic properties, exhibiting spin-glass-like behavior. Pr 3 IrO 7 thin film offers a platform for exploring unconventional magnetic states, and their successful heteroepitaxy on YSZ substrates opens new avenues for discovering novel physical phenomena.
36 MATERIALS SCIENCE↗
Quasiperiodic potassium adlayer on decagonal Al–Ni–Co quasicrystal
Quasiperiodicity in free-electron-like metals is a subject of significant interest within the scientific community. In this work, utilizing scanning tunneling microscopy (STM), low energy electron diffraction (LEED), and density functional theory (DFT), we demonstrate the formation of a quasiperiodic potassium monolayer on the tenfold surface of decagonal Al–Ni–Co quasicrystal. A dispersed growth comprising of isolated K adatoms is observed at sub-monolayer coverage, which coalesce with increasing coverage and forms pentagonal and decagonal quasiperiodic motifs. LEED demonstrates distinct rings of spots displaying decagonal symmetry. Furthermore, our DFT calculation using the W-approximant surface that closely resembles d-Al–Ni–Co shows that sizable adsorbate-substrate interaction makes the potassium adatoms bind to the quasiperiodically dispersed favorable adsorption sites resulting in the formation of quasiperiodic potassium monolayer. Notably, the experimental motifs obtained from STM measurements align remarkably well with the DFT predictions, underscoring the intricate relationship between the electronic structure of the substrate that drives the quasiperiodic growth of the potassium adlayer.
alkali metal↗
Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases
Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair’s identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps.
59 BASIC BIOLOGICAL SCIENCES↗