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Structure of active methyl-CoM reductase, Earth’s main methane producer
Summary Our work reveals the structure of the active state of Methyl-Coenzyme M Reductase (MCR), the key and rate-limiting enzyme in biological methane formation. We find large differences between the active Ni(I) and inactive Ni(II) proteins and provide insight into how nature makes and breaks the C-H bond of methane. The Ni(II)-F430 center in inactive MCR contains four planar nitrogen ligands, a lower axial glutamine oxo, and an upper axial thiolate. The Ni(I)-enzyme replaces the axial ligands with a single water. The one-electron redox change results in movement of the Ni ion and upward swing of the β-lactam ring in the tetrapyrrole coupled to a domino-like protein quake through second sphere residues, inter-subunit interactions, a substrate tunnel, affecting even the dimensions of the unit cell. These structural changes lead Ni(I)-MCR to release a charge clamp that, in the Ni(II) state, locks down substrate Coenzyme B. Determining the Ni(I)-MCR structure required development of rigorous anaerobic crystallographic techniques. Validation of the MCR redox state was accomplished by in-line and parallel spectroscopic and unit cell analyses. This structure has large implications for developing technologies to limit methane emissions and efficiently produce biofuels. Methodology described here will enhance structural biology for other oxygen-sensitive enzymes.
Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates
X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.
Exploring the impact of nucleotide length on lipid nanoparticle structure and properties
Lipid nanoparticles (LNPs) are versatile carriers for nucleic acid (NA) therapeutics, including ASOs, siRNA, mRNA, and poly-IC. While lipid composition is known to influence LNP properties, the impact of NA length on morphology and internal structure is less understood, particularly during the stages of carrier–cargo assembly. Here, we examine NA length and lipid composition immediately after mixing using high-throughput SAXS, dynamic light scattering, and cryogenic electron microscopy. All LNPs form ordered NA/lipid compartments, with longer NAs promoting inverse hexagonal (H II ) phases and larger intercompartment distances. In contrast, short NAs, especially in formulations with SM102 ionizable lipid, favor lamellar phases. SAXS peak deconvolution quantifies ordered versus disordered phases via a Robustness of Ordered Phase factor, which correlates with particle size and encapsulation efficiency. Formulations with MC3 ionizable and DOPE helper lipids exhibit the most stable H II -phase packing, highlighting the role of helper-lipid curvature in compartment stabilization. Variations in NA compartmentalization indicate differences in payload capacity, offering a framework for rational LNP design across diverse nucleic acid cargos.
Solvent-Mediated Control of Nanocellulose Dispersion: An Integrated Computational and Experimental Investigation
Fibrillated cellulose derived from forestry feedstocks represents a renewable and high-strength materials platform for circular bioeconomies. However, its practical implementation is hindered by the irreversible aggregation of nanocellulose architectures, including cellulose nanofibers (CNFs). Solvent-based dispersion offers a simple and practical route to prevent CNF aggregation. Here, in this work, we integrate classical and enhanced sampling molecular dynamics (MD) simulations with experimental suspension rheology and atomic force microscopy (AFM) to elucidate how solvent environments tune CNF–CNF interactions and dispersion stability. CNF–CNF contact free energies computed from MD simulations reveal reduced aggregation in acetone/water, γ-valerolactone (GVL)/water, and tetrahydrofuran (THF)/water and pure acetone compared with pure water, reflecting stronger CNF-solvent relative to inter-CNF interactions. Correspondingly, CNF-solvent suspensions in these solvent systems exhibit stronger inter-fibril network structures and enhanced recovery compared to water, indicating improved CNF-solvent affinity. Liquid cell AFM imaging in acetone–water mixtures and in pure acetone further confirm the presence of well-dispersed CNFs. By combining multiscale computation with targeted experiments, this study establishes a rational framework for solvent design to achieve stable nanocellulose dispersions for high-strength biobased materials and efficient bioenergy conversion.
Enabling simultaneous photoluminescence spectroscopy and X-ray footprinting mass spectrometry to study protein conformation and interactions
A novel integrated hybrid spectroscopy and X-ray footprinting mass spectrometry system designed to study both global and local protein conformation and interactions simultaneously.
Additive Manufacturing with Cellulose-Based Composites: Materials, Modeling, and Applications
Recent advances in large-scale additive manufacturing (AM) with polymer-based composites have enabled efficient production of high-performance materials. Cellulose nanomaterials (CNMs) have emerged as bio-based feedstocks due to their exceptional strength and sustainability. However, challenges such as hornification and poor dispersion in polymer matrices still limit large-scale CNM–polymer composite manufacturing, requiring novel strategies. Here, this review outlines an approach starting with atomic-level simulations to link molecular composition to key parameters like bulk density, viscosity, and modulus. These simulations provide data for finite element analysis (FEA), which informs large-scale experiments and reduces the need for extensive trials. The strategy explores how atomic interactions impact the morphology, adhesion, and mechanical properties of CNM-based composites in AM processes. The review also discusses current developments in AM, along with predictions of mechanical and thermal properties for structural applications, packaging, flexible electronics, and hydrogel scaffolds. By integrating experimental findings with molecular dynamics (MD) simulations and finite element modeling (FEM), valuable insights for material design, process optimization, and performance enhancement in CNM-based AM are provided to address ongoing challenges.
Exploration of Nirmatrelvir Derivatives as Optimized SARS‐CoV‐2 Antivirals
Nirmatrelvir (NMV) is a SARS‐CoV‐2 antiviral component of the approved COVID‐19 therapeutic Paxlovid. It is a reversible covalent inhibitor of SARS‐CoV‐2 main protease (M Pro ) that is effluxed from human cells by P‐glycoprotein (P‐gp). To identify NMV analogs with improved potency and reduced P‐gp efflux, a structure–activity relationship campaign was conducted. Warheads alternative to nitrile for engaging the active site cysteine were tested showing aldehyde and dichloroacetamide with better enzyme inhibition potency. Crystal structure of MPI‐136−M Pro shows its aldehyde warhead forming a thiohemiacetal with active Cys145 of M Pro . Several S4 binders were explored revealing that an O‐to‐S shift at the N ‐terminal amide leads to better enzyme inhibition. By exploring different combinations of S2, S3, and S4 binders, two inhibitors with better enzyme inhibition potency than NMV were found. Crystal structure of MPI‐148, with ( S )‐2‐azaspiro[4,5]decane‐3‐carboxylate as an alternative S2 binder, shows extensive hydrogen‐bond networks for locking the inhibitor in active site, explaining high affinity of NMV analogs. Further characterization of cellular M Pro engagement and antiviral potency against SARS‐CoV‐2 revealed four inhibitors with greater potency than NMV in P‐gp‐expressing cells. Studies with the P‐gp inhibitor CP‐100356 showed that these compounds were less sensitive to P‐gp inhibition than NMV, consistent with reduced P‐gp‐mediated efflux.
Artificial intelligence tools for enzyme engineering and metabolic engineering
Enzyme engineering and metabolic engineering drive innovation in energy biotechnology. In recent years, artificial intelligence (AI) has supported successful applications in designing effective enzymes and productive microbial cell factories. This review summarizes recent advances in enzyme redesign using protein language models, de novo enzyme design with generative models, and AI tools for engineering metabolism and related cellular phenotypes. Across these areas, AI models are shifting from single modality inputs to integrated representations of protein function, metabolic pathways, and cell states. We emphasize that unifying the diverse data representations across scales will be necessary for advancements in energy biotechnology.
The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior
Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial in both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used to study membrane phenomena but has faced limitations, particularly in capturing realistic lipid phase behavior. Here, we present refined Martini 3 lipid models with a mapping scheme that distinguishes lipid tails that differ by just two carbon atoms, enhancing the structural resolution and thermodynamic accuracy of model membrane systems including ternary mixtures. The expanded Martini lipid library includes thousands of models, enabling simulations of complex and biologically relevant systems. These advancements establish Martini as a robust platform for lipid-based simulations across diverse fields.
Naturally ornate RNA-only complexes revealed by cryo-EM
The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, each empty except for a disordered loop. Extensive intramolecular and intermolecular A-minor interactions, kissing loops, an unusual A–A helix and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.
Hub stability in the calcium calmodulin-dependent protein kinase II
The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.
Phytosulfokine downregulates defense‐related WRKY transcription factors and attenuates pathogen‐associated molecular pattern‐triggered immunity
SUMMARY Phytosulfokine (PSK) is a plant growth‐promoting peptide hormone that is perceived by its cell surface receptors PSKR1 and PSKR2 in Arabidopsis. Plants lacking the PSK receptors show phenotypes consistent with PSK signaling repressing some plant defenses. To gain further insight into the PSK signaling mechanism, comprehensive transcriptional profiling of Arabidopsis treated with PSK was performed, and the effects of PSK treatment on plant defense readouts were monitored. Our study indicates that PSK's major effect is to downregulate defense‐related genes; it has a more modest effect on the induction of growth‐related genes. WRKY transcription factors (TFs) emerged as key regulators of PSK‐responsive genes, sharing commonality with a pathogen‐associated molecular pattern (PAMP) responses, flagellin 22 (flg22), but exhibiting opposite regulatory directions. These PSK‐induced transcriptional changes were accompanied by biochemical and physiological changes that reduced PAMP responses, notably mitogen‐activated protein kinase (MPK) phosphorylation (previously implicated in WRKY activation) and the cell wall modification of callose deposition. Comparison with previous studies using other growth stimuli (the sulfated plant peptide containing sulfated tyrosine [PSY] and Pseudomonas simiae strain WCS417) also reveals WRKY TFs' overrepresentations in these pathways, suggesting a possible shared mechanism involving WRKY TFs for plant growth–defense trade‐off.
Data for The Stem Cell-Type Transcriptome of Bioenergy Sorghum Reveals the Spatial Regulation of Secondary Cell Wall Networks
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.
Sorghum bicolor TX08001 Compendium Set2 Gene Expression Profiling
Bioenergy Sorghum RNA-seq Compendium, plant transcriptome
Small signaling peptides, phylogenetic analysis
ML Phylogenetic analysis of small signaling peptides in Arabidopsis, Sorghum bicolor, Rice, Wheat, Maize, and Brachypodium. Sorghum only phylogenetic trees were used to name genes. All trees but RALF tree are rooted at midpoint.
Archaeal protein containing domain of unknown function 2193 undergoes oligomeric reconfiguration upon iron–sulfur cluster binding
Methanogenic archaea are particularly rich in iron–sulfur proteins, yet their roles remain largely enigmatic. Here, we characterized aMethanococcus voltae(Mvo) protein from the domain of unknown function (DUF) 2193 family, a group of proteins present primarily in archaea and characterized by a conserved cysteine‐rich C‐terminal motif.MvoDUF2193 was heterologously expressed and characterized by a range of spectroscopic and analytical methods. The results demonstrate thatMvoDUF2193 binds a single [4Fe–4S] cluster per subunit and that cluster occupancy regulates the transition from an apo tetramer to a [4Fe–4S] monomeric form. We hypothesize thatMvoDUF2193 serves a regulatory role in the cell, mediated by [Fe–S] cluster binding and changes in oligomeric state.
The Pseudoenzyme β‐Amylase9 From Arabidopsis Activates α‐Amylase3: A Possible Mechanism to Promote Stress‐Induced Starch Degradation
ABSTRACT Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ‐ and β‐amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their functional roles are unclear. Moreover, the presence of catalytically inactive amylases that show starch excess phenotypes when deleted presents questions on how starch degradation is regulated. Plants lacking one of these catalytically inactive β‐amylases, BAM9, have enhanced starch accumulation when combined with mutations in BAM1 and BAM3, the primary starch degrading BAMs in response to stress and at night, respectively. BAM9 has been reported to be transcriptionally induced by stress although the mechanism for BAM9 function is unclear. From yeast two‐hybrid experiments, we identified the plastid‐localized AMY3 as a potential interaction partner for BAM9. We found that BAM9 interacted with AMY3 in vitro and that BAM9 enhances AMY3 activity about three‐fold. Modeling of the AMY3‐BAM9 complex predicted a previously undescribed alpha–alpha hairpin in AMY3 that could serve as a potential interaction site. Additionally, AMY3 lacking the alpha–alpha hairpin is unaffected by BAM9. Structural analysis of AMY3 showed that it can form a homodimer in solution and that BAM9 appears to replace one of the AMY3 monomers to form a heterodimer. The presence of both BAM9 and AMY3 in many vascular plant lineages, along with model‐based evidence that they heterodimerize, suggests that the interaction is conserved. Collectively these data suggest that BAM9 is a pseudoamylase that activates AMY3 in response to cellular stress, possibly facilitating stress recovery.