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At least 775 records · Page 43

Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature

Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable metering, without the need for any fluidic or pump connections. Our approach requires only the simple steps of pipetting the crystallization reagents into the device followed by either spinning or shaking to set up counter-diffusive protein crystallization trials. The use of thin, UV-curable polymers with a high level of X-ray transparency allows for in situ X-ray crystallography, eliminating the manual handling of fragile protein crystals and streamlining the process of protein structure analysis. We demonstrate the utility of our device using hen egg white lysozyme as a model system, followed by the crystallization and in situ, room temperature structural analysis of the hub domain of calcium–calmodulin dependent kinase II (CaMKIIβ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of phospholipase Cε reveals an integrated RA1 domain and previously unidentified regulatory elements

Phospholipase Cε (PLCε) generates lipid-derived second messengers at the plasma and perinuclear membranes in the cardiovascular system. It is activated in response to a wide variety of signals, such as those conveyed by Rap1A and Ras, through a mechanism that involves its C-terminal Ras association (RA) domains (RA1 and RA2). However, the complexity and size of PLCε has hindered its structural and functional analysis. Herein, we report the 2.7 Å crystal structure of the minimal fragment of PLCε that retains basal activity. This structure includes the RA1 domain, which forms extensive interactions with other core domains. A conserved amphipathic helix in the autoregulatory X–Y linker of PLCε is also revealed, which we show modulates activity in vitro and in cells. The studies provide the structural framework for the core of this critical cardiovascular enzyme that will allow for a better understanding of its regulation and roles in disease.

59 BASIC BIOLOGICAL SCIENCES↗

Simulation of convective transport during frequency chirping of a TAE using the MEGA code

Here, we present a procedure to examine energetic particle phase-space during long range frequency chirping phenomena in tokamak plasmas. To apply the proposed method, we have performed self-consistent simulations using the MEGA code and analyzed the simulation data. We demonstrate a traveling wave in phase-space and that there exist specific slices of phase-space on which the resonant particles lie throughout the wave evolution. For non-linear evolution of an n = 6 toroidicity-induced Alfvén eigenmode (TAE), our results reveal the formation of coherent phase-space structures (holes/clumps) after coarse-graining of the distribution function. These structures cause a convective transport in phase-space which implies a radial drift of the resonant particles. We also demonstrate that the rate of frequency chirping increases with the TAE damping rate. Our observations of the TAE behavior and the corresponding phase-space dynamics are consistent with the Berk–Breizman theory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is present in several MLOs, undergoes LLPS, and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some ALS-associated mutations in TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes upon dimerization of TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix–helix interaction, which are removed in part by variants at these positions, including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase-separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a minigene assay. Therefore, the TDP-43 helical region serves as a short but uniquely tunable module where application of biophysical principles can precisely control assembly and function in cellular and synthetic biology applications of LLPS.

60 APPLIED LIFE SCIENCES↗

Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties

Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180°C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be β-ether > phenylcoumaran (β−5′) > resinol (β−β′) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150°C temperature reaction, CELF lignin had higher molecular weight and retained more β-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.

59 BASIC BIOLOGICAL SCIENCES↗

Representing plant diversity in land models: An evolutionary approach to make “Functional Types” more functional

Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. Here we review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimensional hard X-ray ptychographic reflectometry imaging on extended mesoscopic surface structures

Many nanodevices and quantum devices, with their sizes often spanning from millimeters down to sub-nanometer, have intricate low-dimensional, non-uniform, or hierarchical structures on surfaces and interfaces. Since their functionalities are dependent on these structures, high-resolution surface-sensitive characterization becomes imperative to gain a comprehensive understanding of the function–structure relationship. We thus developed hard x-ray ptychographic reflectometry imaging, a new technique that merges the high-resolution two-dimensional imaging capabilities of hard x-ray ptychography for extended objects, with the high-resolution depth profiling capabilities of x-ray reflectivity for layered structures. The synergy of these two methods fully leverages both amplitude and phase information from ptychography reconstruction to not only reveal surface topography and localized structures, such as shapes and electron densities, but also yields statistical details, such as interfacial roughness that is not readily accessible through coherent imaging solely. The hard x-ray ptychographic reflectometry imaging is well-suited for three-dimensional imaging of mesoscopic samples, particularly those comprising planar or layered nanostructures on opaque supports, and could also offer a high-resolution surface metrology and defect analysis on semiconductor devices, such as integrated nanocircuits and lithographic photomasks for microchip fabrications.

47 OTHER INSTRUMENTATION↗

Protocols for isolating and characterizing polysaccharides from plant cell walls: a case study using rhamnogalacturonan-II

Abstract Background In plants, a large diversity of polysaccharides comprise the cell wall. Each major type of plant cell wall polysaccharide, including cellulose, hemicellulose, and pectin, has distinct structures and functions that contribute to wall mechanics and influence plant morphogenesis. In recent years, pectin valorization has attracted much attention due to its expanding roles in biomass deconstruction, food and material science, and environmental remediation. However, pectin utilization has been limited by our incomplete knowledge of its structure. Herein, we present a workflow of principles relevant for the characterization of polysaccharide primary structure using nature’s most complex polysaccharide, rhamnogalacturonan-II (RG-II), as a model. Results We outline how to isolate RG-II from celery and duckweed cell walls and from red wine using chemical or enzymatic treatments coupled with size-exclusion chromatography. From there, we applied mass spectrometry (MS)-based techniques to determine the glycosyl residue and linkage compositions of the intact RG-II and derived oligosaccharides including special considerations for labile monosaccharides. In doing so, we demonstrated that in the duckweed Wolffiella repanda the arabinopyranosyl (Ara p ) residue of side chain B is substituted at O- 2 with rhamnose. We used electrospray-MS techniques to identify non-glycosyl modifications including methyl-ethers, methyl-esters, and acetyl-esters on RG-II-derived oligosaccharides. We then showed the utility of proton nuclear magnetic resonance spectroscopy ( 1 H-NMR) to investigate the structure of intact RG-II and to complement the RG-II dimerization studies performed using size-exclusion chromatography. Conclusions The complexity of pectic polysaccharide structures has hampered efforts aimed at their valorization. In this work, we used RG-II as a model to demonstrate the steps necessary to isolate and characterize polysaccharides using chromatographic, MS, and NMR techniques. The principles can be applied to the characterization of other saccharide structures and will help inform researchers on how saccharide structure relates to functional properties in the future.

09 BIOMASS FUELS↗

Node Distortion as a Tunable Mechanism for Negative Thermal Expansion in Metal–Organic Frameworks

Chemically functionalized series of metal–organic frameworks (MOFs), with subtle differences in local structure but divergent properties, provide a valuable opportunity to explore how local chemistry can be coupled to long-range structure and functionality. Using in situ synchrotron X-ray total scattering, with powder diffraction and pair distribution function (PDF) analysis, we investigate the temperature dependence of the local- and long-range structure of MOFs based on NU-1000, in which Zr 6 O 8 nodes are coordinated by different capping ligands (H 2 O/OH, Cl – ions, formate, acetylacetonate, and hexafluoroacetylacetonate). We show that the local distortion of the Zr 6 nodes depends on the lability of the ligand and contributes to a negative thermal expansion (NTE) of the extended framework. Using multivariate data analyses, involving non-negative matrix factorization (NMF), we demonstrate a new mechanism for NTE: progressive increase in the population of a smaller, distorted node state with increasing temperature leads to global contraction of the framework. The transformation between discrete node states is noncooperative and not ordered within the lattice, i.e., a solid solution of regular and distorted nodes. Density functional theory calculations show that removal of ligands from the node can lead to distortions consistent with the Zr···Zr distances observed in the experiment PDF data. Control of the node distortion imparted by the nonlinker ligand in turn controls the NTE behavior. Furthermore, these results reveal a mechanism to control the dynamic structure of MOFs based on local chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: insights into enzyme mechanism and drug design

The emergence of the novel coronavirus SARS-CoV-2 has resulted in a worldwide pandemic not seen in generations. Creating treatments and vaccines to battle COVID-19, the disease caused by the virus, is of paramount importance in order to stop its spread and save lives. The viral main protease, 3CL M pro , is indispensable for the replication of SARS-CoV-2 and is therefore an important target for the design of specific protease inhibitors. Detailed knowledge of the structure and function of 3CL M pro is crucial to guide structure-aided and computational drug-design efforts. Here, the oxidation and reactivity of the cysteine residues of the protease are reported using room-temperature X-ray crystallography, revealing that the catalytic Cys145 can be trapped in the peroxysulfenic acid oxidation state at physiological pH, while the other surface cysteines remain reduced. Only Cys145 and Cys156 react with the alkylating agent N -ethylmaleimide. It is suggested that the zwitterionic Cys145–His45 catalytic dyad is the reactive species that initiates catalysis, rather than Cys145-to-His41 proton transfer via the general acid–base mechanism upon substrate binding. The structures also provide insight into the design of improved 3CL M pro inhibitors.

3CL Mpro↗

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.

Biochemistry & Molecular Biology↗

Stressors Reveal Ecosystems' Hidden Characteristics

Abstract Vegetation responds dynamically to local microclimates at both short and long time scales via mechanisms ranging from physiological behaviors, such as stomatal closure, to acclimation and adaptation. These responses influence the carbon, water, and energy cycles directly and are therefore crucial to understanding and predicting Earth system responses to a changing climate. Several recent studies have demonstrated that differences in microclimate can induce structural and functional acclimations, and potentially adaptations, within the same ecosystem. Such microclimate divergence can be caused by variability in slopes, disturbance history, or even localized resource availability. Ecosystem stressors such as low soil water availability, limited photoperiod, or high vapor pressure deficit have been shown to reveal the large impact of the subtle differences within these systems such as the number of sun versus shade leaves or differences in whole‐plant water acquisition and use. These findings highlight the linkages between plant canopy structure and ecosystem function, alongside the need for comprehensive analyses of vegetation within the broader context of its environment. This commentary addresses some of the key implications of ecosystem stress responses and accompanying acclimations across three ecosystem types for ecosystem ecology, plant physiology, ecohydrology and trait‐based modeling of vegetation‐climate dynamics.

Matheny, Ashley M.↗

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↗

Toughening by Nanodroplets: Polymer–Droplet Biocomposite with Anomalous Toughness

The development of new polymer composites is highly dependent on the design of novel fillers that can bring more benefits in the design and control of structure–property–function than conventional solid particles. Here, inspired by the unique coupling structures of tough mussel byssus, we employ nanodroplets of high-boiling-point oligomers as the liquid filler to fabricate a new class of polymer–droplet composites (PDCs). The combination of nanodroplets and chain end/tail modifier in PDCs finally generates soft-coupling structures with chain ends coupled by the nanodroplets. With this strategy, brittle poly(lactic acid) is successfully transformed into a tough bioplastic with toughness improved by over 2000% via a minimal amount of the modifiers (1.5 wt %). Moreover, the composites show unexpected speed-enhanced energy absorption capability. A soft-coupling toughening mechanism is further proposed for the first time to understand the PDCs’ mechanical properties. This work also indicates the potential of nanodroplets as a new tool for tuning the mechanical properties and even functions of polymer composites.

36 MATERIALS SCIENCE↗

Bridging length scales in organic mixed ionic–electronic conductors through internal strain and mesoscale dynamics

Understanding the structural and dynamic properties of disordered systems at the mesoscale is crucial. This is particularly important in organic mixed ionic-electronic conductors (OMIECs), which undergo significant and complex structural changes when operated in an electrolyte. Here, in this study, we investigate the mesoscale strain, reversibility and dynamics of a model OMIEC material under external electrochemical potential using operando X-ray photon correlation spectroscopy. Our results reveal that strain and structural hysteresis depend on the sample's cycling history, establishing a comprehensive kinetic sequence bridging the macroscopic and microscopic behaviours of OMIECs. Furthermore, we uncover the equilibrium and non-equilibrium dynamics of charge carriers and material-doping states, highlighting the unexpected coupling between charge carrier dynamics and mesoscale order. These findings advance our understanding of the structure-dynamics-function relationships in OMIECs, opening pathways for designing and engineering materials with improved performance and functionality in non-equilibrium states during device operation. Understanding mesoscale structure and dynamics in organic mixed ionic-electronic conductors is crucial. Mesoscale strain kinetics and structural hysteresis have been studied, and they uncover the coupling between charge carrier dynamics and mesoscale order in organic mixed ionic-electronic conductors.

36 MATERIALS SCIENCE↗

Algorithm-Driven Advances for Scientific CT Instruments: From model-based to deep learning-based approaches

Multiscale 3D characterization is widely used by materials scientists to further their understanding of the relationships between microscopic structure and macroscopic function. Scientific computed tomography (SCT) instruments are one of the most popular choices for 3D nondestructive characterization of materials at length scales ranging from the angstrom scale to the micron scale. These instruments typically have a source of radiation (such as electrons, X-rays, or neutrons) that interacts with the sample to be studied and a detector assembly to capture the result of this interaction (see Figure 1 ). A collection of such high-resolution measurements is made by reorienting the sample, which is mounted on a specially designed stage/holder after which reconstruction algorithms are used to produce the final 3D volume of interest. The specific choice of which instrument to use depends on the desired resolution and properties of the materials being imaged. Additionally, the end goal of SCT scans includes determining the morphology, chemical composition, or dynamic behavior of materials when subjected to external stimuli. In summary, SCT instruments are powerful tools that enable 3D characterization across multiple length scales and play a critical role in furthering the understanding of the structure–function relationships of different materials.

42 ENGINEERING↗

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

Structure–Activity Relationships in Ether-Functionalized Solid-State Metal–Organic Framework Electrolytes

The structure–property relationships of metal–organic framework (MOF)-based solid-state electrolytes are not well understood. Herein, a systematic investigation of 12 Zr(IV)-based UiO-66 MOFs with varying ether-chain functional groups was carried out to elucidate the critical microscopic interactions that facilitate improved solid-state electrolyte performance. Enhanced sampling molecular dynamics (MD) simulations were employed and revealed a three-tier ion hopping mechanism: linker–linker hopping, linker-counterion hopping, and counterion-counterion hopping. Detailed structural analysis of the MD trajectories revealed that the chemistry and morphology of the linker groups affect the relative stability and population distribution of the electrolyte components, such that crown-ether-based linker groups enhance the probability of extended, low-barrier ion percolation pathways. As a result, we were able to tune the ionic conductivities by rationally manipulating the counterion distributions, linker binding strengths, and the configurational entropy (multivariability of the linkers). The resulting performance of these MOF-based solid-state electrolytes was significantly enhanced, with a methoxy-functionalized framework (UiO-66-L1 100 ) achieving high ionic conductivities of 2.32 × 10 –4 S/cm and 2.07 × 10 –3 S/cm at 30 °C and 90 °C, respectively, an order of magnitude greater than other all-solid-state MOF electrolyte systems. The electrolyte stability was evaluated with LiIn|LPSCl|MOF:LiTFSI|LPSCl|LiIn symmetric cells, showing excellent Li plating/stripping processes for over 2 months.

36 MATERIALS SCIENCE↗