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At least 55 records · Page 3

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.

59 BASIC BIOLOGICAL SCIENCES↗

Space Product Development of Commercial NLO Materials

Growth on selected substrates under various processing conditions have been useful for preparing highly oriented and otherwise promising films of organic compounds for optical thin films and waveguides. The significance of processing conditions to uniformity in thickness, degree of orientation, film quality, and optical properties for a specific processing technique is the general focus of work in this area. A study on the effect of processing conditions relevant to thin-film deposition by various techniques is particularly difficult because of the possibility that convection may play a major role in some cases. It is a goal of some researchers to produce good quality anisotropic films, therefore, an important, yet understudied, requirement should be to assess the role of gravity during certain processing methods. This may be particularly true for the vapor deposition of diacetylenes where subsequent polymerization in the crystal is topochemical and occurs readily only when neighboring monomer molecules are sufficiently close and suitably oriented. Likewise, this requirement is equally viable for the vapor deposition of certain materials such as Pcs in view of the results of microgravity experiments by 3M Corporation involving the preparation of thin films of copper Pc (CuPc). Microgravity-grown CuPc had several desirable features which indicate that the vapor growth of organic films in low-g may result in better quality films for optical and electrical applications. Indeed, other materials vapor deposited onto specific substrates in microgravity produce films potentially beneficial for electro-optic applications. A novel technique, recently discovered, for growing polydiacetylene thin films involves exposing a transparent substrate, in contact with diacetylene monomer solution, to ultraviolet (LTV) light. A polymer film deposits on the side of the substrate in contact with monomer in solution, and there are distinct gravitational effects, which influence film quality. Good quality thin films elude growth from solutions absent of uniform flow fields and homogeneous temperature distributions near the substrate surfaces. The flow fields and temperature distributions during the polymerization process by exposure to UV light details the nature of gravitational influences on this process.

Frazier, Donald O.↗

Engineering modular enzyme assembly: synthetic interface strategies for natural products biosynthesis applications

Covering: 2020 to 2025Natural products remain indispensable sources of therapeutic and bioactive compounds, yet traditional discovery strategies are constrained by compound rediscovery. Modular biosynthetic enzymes, such as type I polyketide synthases (PKSs) and type A non-ribosomal peptide synthetases (NRPSs), offer promising platforms for combinatorial biosynthesis owing to their programmable architectures. However, practical implementation is frequently limited by inter-modular incompatibility and domain-specific interactions. This review highlights recent advances in modular enzyme assembly enabled by synthetic interfaces-including cognate docking domains, synthetic coiled-coils, SpyTag/SpyCatcher, and split inteins-which function as orthogonal, standardized connectors to facilitate post-translational complex formation. These interfaces support rational investigations into substrate specificity, module compatibility, and pathway derivatization as well as general enzyme clustering applications beyond PKS and NRPS systems. Synthetic interfaces can be integrated with computational tools to support a more systematic and scalable framework for modular enzyme engineering by providing predictive insights into domain compatibility and interface design. These approaches within iterative design-build-test-learn workflows can accelerate the programmable assembly of biosynthetic systems and expand the accessible chemical space for natural products.

Kim, Gahyeon↗

Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase

The biphasic assembly of Gram-positive pili begins with the covalent polymerization of distinct pilins catalyzed by a pilus-specific sortase, followed by the cell wall anchoring of the resulting polymers mediated by the housekeeping sortase. In Actinomyces oris, the pilus-specific sortase SrtC2 not only polymerizes FimA pilins to assemble type 2 fimbriae with CafA at the tip, but it can also act as the anchoring sortase, linking both FimA polymers and SrtC1-catalyzed FimP polymers (type 1 fimbriae) to peptidoglycan when the housekeeping sortase SrtA is inactive. To date, the structure-function determinants governing the unique substrate specificity and dual enzymatic activity of SrtC2 have not been illuminated. Here, we present the crystal structure of SrtC2 solved to 2.10-Å resolution. SrtC2 harbors a canonical sortase fold and a lid typical for class C sortases and additional features specific to SrtC2. Structural, biochemical, and mutational analyses of SrtC2 reveal that the extended lid of SrtC2 modulates its dual activity. Specifically, we demonstrate that the polymerizing activity of SrtC2 is still maintained by alanine-substitution, partial deletion, and replacement of the SrtC2 lid with the SrtC1 lid. Strikingly, pilus incorporation of CafA is significantly reduced by these mutations, leading to compromised polymicrobial interactions mediated by CafA. In a srtA mutant, the partial deletion of the SrtC2 lid reduces surface anchoring of FimP polymers, and the lid-swapping mutation enhances this process, while both mutations diminish surface anchoring of FimA pili. Evidently, the extended lid of SrtC2 enables the enzyme the cell wall-anchoring activity in a substrate-selective fashion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self‐Propelling Macroscale Sheets Powered by Enzyme Pumps

Nanoscale enzymes anchored to surfaces act as chemical pumps by converting chemical energy released from enzymatic reactions into spontaneous fluid flow that propels entrained nano‐ and microparticles. Enzymatic pumps are biocompatible, highly selective, and display unique substrate specificity. Utilizing these pumps to trigger self‐propelled motion on the macroscale has, however, constituted a significant challenge and thus prevented their adaptation in macroscopic fluidic devices and soft robotics. Using experiments and simulations, we herein show that enzymatic pumps can drive centimeter‐scale polymer sheets along directed linear paths and rotational trajectories. In these studies, the sheets are confined to the air/water interface. With the addition of appropriate substrate, the asymmetric enzymatic coating on the sheets induces chemically driven, buoyancy flows that controllably propel the sheet's motion on the air/water interface. The directionality and speed of the motion can be tailored by changing the pattern of the enzymatic coating, type of enzyme, and nature and concentration of the substrate. This work highlights the utility of biocompatible enzymes for generating motion in macroscale fluidic devices and robotics and indicates their potential utility for in vivo applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the Structural, Biochemical, and Functional Diversity of Glycoside Hydrolase Family 12 from Penicillium subrubescens

Glycoside hydrolases (GHs) play an essential role in plant biomass degradation and modification for the sustainable production of biochemicals. The filamentous Ascomycete fungus Penicillium subrubescens contains a higher number of GH12 candidates compared to related species. Therefore, we aimed to compare P. subrubescens GH12s for their ability and substrate specificity for plant cell wall polysaccharide degradation and species’ potential as a source of novel enzymes for plant biomass valorization. Our re-evaluated phylogenetic analysis of fungal GH12 members showed that the P. subrubescens GH12s were located in different (new) clades. Biochemical characterization marked PsEglA as an endoglucanase and four other P. subrubescens GH12s (i.e., PsXegA–D) as xyloglucanases. Interestingly, structural features of PsXegD and PsXegE were more comparable to those of Basidiomycete GH12 xyloglucanases with a unique open substrate-binding cleft. PsUegA displayed dual xyloglucanase and endoglucanase activity and also showed distinct structural features. Comparative transcriptome analysis supported the functional diversity of P. subrubescens GH12s in plant biomass degradation. The gene encoding PsUegA was expressed under diverse conditions, suggesting a scouting role for this enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1

Abstract Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) has been challenging because of the enzyme shallow catalytic pocket and non-specific substrate binding interactions. Recently, we discovered a quinolone-binding hot spot in TDP1’s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1 ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting and adds to the chemical biology resource toolbox for studying TDP1.

Chemistry↗

Circularity in Sequence-Controlled Copolyamides Enabled by Regioselective Enzymatic Hydrolysis

Sequence-controlled polymers enable precise control over macromolecular structures and function, but both their synthesis and end-of-life management remain fundamental challenges. Achieving high sequence fidelity is synthetically demanding, and conventional depolymerization methods lack regioselectivity, leading to irreversible loss of encoded molecular information and limiting polymer circularity. Enzymatic catalysis offers a potential solution by combining substrate specificity with selective bond cleavage. Here, we report the synthesis, characterization, and regioselective enzymatic depolymerization of poly- (X,AMA), a sequence-controlled copolyamide composed of alternating hexamethylenediamine−adipic acid (MA) and pxylylenediamine− adipic acid (XA) repeat units. Poly(X,AMA) was synthesized via solid-state polycondensation (SSP) of sequence-defined oligomers, enabling precise control over repeat-unit order. Polymer microstructure and sequence fidelity were confirmed by 13 C NMR spectroscopy and MALDI−TOF mass spectrometry. Comparison with a statistical copolymer analogue and Nylon-66 demonstrated pronounced differences in crystallinity, morphology, and thermal behavior arising from sequence control. Screening of 96 Nylon hydrolase homologues against poly(X,AMA) revealed strongly enzyme-dependent depolymerization profiles. While tetrad formation was generally favored, enzymes displayed pronounced sequence selectivity, preferentially releasing distinct sequence-defined tetrads XAMA or MAXA. SSP of sequence-defined tetrad MAXA produced a copolyamide with near identical monomer ordering as poly(X,AMA). Computational modeling of enzyme−substrate complexes identified structural features consistent with the observed regioselectivity. Together, these results establish selective enzymatic depolymerization as a viable strategy for the circular recycling of sequence-controlled polymers and provide a foundation for the rational engineering of enzymes for programmable polymer deconstruction.

Amides↗

Alloying of Mn with Bi‐Rich Surfaces of Bi 2 Te 3 by Topotactic Reaction

Interfacing topological insulators (TI) with magnetic materials enables accessing quantum effects for advanced devices. The synthesis of such heterostructures faces challenges due to interlaying mixing and the often-complex multicomponent materials required to combine the desired properties. An alternative synthesis to direct growth is the modification of 2D materials by topotactic reactions to introduce new functionalities into pre-formed single or few-component 2D sheets. Here, the self-formation of bismuthene (a bilayer of Bi; Bi 2 ) is utilized by thermal decomposition of Bi 2 Te 3 as a platform to create novel 2D overlayers on the TI- substrate. Specifically, the Bi 2 layer is modified by reacting it with vapor deposited Mn in an attempt to induce magnetic properties. Scanning tunneling microscopy indicates that the Mn modified surface remains in a planar 2D layer, indicating the formation of an ordered Mn-rich surface layer. Density functional theory (DFT) is used to develop models of both the Bi-rich Bi 2 Te 3 surface as well as their subsequent Mn-modified structure. The DFT models indicate the possibility of magnetic ordering of the high spin Mn 2+ ions. The successful synthesis of planar MnBi alloys on a van der Waals material illustrates topotactic reactions as an alternative for creating novel layered heterostructures.

2D materials↗

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Divergent viral phosphodiesterases for immune signaling evasion

Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase (PDE)-mediated oligonucleotide cleavage for immune evasion, a strategy whose diversity has not yet been explored. Here, we use a canonical 2H PDE (2H PDE) structure-based search of prokaryotic and eukaryotic viral sequences to identify an exceptional diversity of 2H PDEs across the virome, including enzymes not detectable with sequence search methods alone. Despite active site conservation, biochemical experiments reveal remarkable substrate specificity of these PDEs that corresponds to variations in the core 2H fold. This nuanced specificity allows 2H PDEs to selectively degrade oligonucleotide messengers to avoid interfering with host nucleotide signaling. Together, these findings nominate viral 2H PDEs as key regulators of CDN signaling across the tree of life.

CBASS↗

Enzyme property prediction using artificial intelligence

Artificial intelligence (AI)-driven enzyme property prediction enables rapid discovery and engineering of enzymes for a wide range of biotechnological and therapeutic applications. Here, we first introduce the key components in AI model development, including enzyme datasets, protein representation methods, and model architectures. We then highlight a variety of AI tools developed for the prediction of enzyme properties and functional annotations, including enzyme structure, kinetic parameters, substrate specificity, thermostability, solubility, Enzyme Commission number, and Gene Ontology term. Moreover, we describe representative downstream applications enabled by these AI tools. Finally, we discuss some challenges and opportunities as well as future prospects.

Yuan, Le [University of Illinois at Urbana-Champai↗

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗

Synergistic cellulase–xylanase formulations for enhanced dewatering and fiber bonding toward energy-efficient and sustainable paper and packaging production

A mechanistic understanding of the synergistic effects of enzymes on cellulosic fibers dewatering and fiber bonding is essential for advancing energy-efficiency and lightweight production of paper and packaging materials. This study investigates the impact of varying cellulase and xylanase formulations on equilibrium moisture content (EMC) after pressing and tensile strength of cellulosic fiber webs using a factorial experimental design. Nine custom enzyme formulations were evaluated at controlled dosages ranging from ∼20 to 76 FPU/mL cellulase and ∼500–1130 IU/mL xylanase. Response surface modeling revealed a significant synergy, particularly at 20–40 FPU/mL cellulase combined with ≥ 1000 IU/mL xylanase. Under these conditions, EMC decreased by up to 3.6% compared with the untreated refined control, while tensile index gains of up to 16% were statistically significant for optimized blends (p < 0.05). The interaction between cellulase and xylanase was also significant for the tensile response (p = 0.010). Protein efficiency analysis showed that optimized formulations containing 30–40% less protein outperformed the commercial benchmark. The nonlinear synergy between cellulase and xylanase is attributed to their complementary substrate specificities. Endoglucanase- and β‑glucosidase‑rich cellulases hydrolyze internal β‑1,4‑glycosidic bonds in amorphous cellulose, loosening fiber walls and increasing flexibility, while xylanases target hemicellulose, primarily xylan-rich domains, enhancing porosity and improve cellulase accessibility. Tailoring enzyme formulations at low loadings overcomes traditional trade-offs between strength and dewatering, enabling cost-effective, energy-efficient, low-carbon solutions for sustainable packaging and hygiene products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural Analysis of 23S rRNA Methylating Enzyme Cfr Reveals RNA-Binding Determinants for Methylation Regiospecificity and Antibiotic Resistance

The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus, Clostridium difficile, Escherichia coli, and Klebsiella pneumoniae, confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr’s dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr’s Q329 residue is important for C8- specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.

AlphaFold↗

Structural basis of divergent substrate recognition and inhibition of human neurolysin

A zinc metallopeptidase neurolysin (Nln) processes diverse bioactive peptides to regulate signaling in the mammalian nervous system. To understand how Nln interacts with various peptides with dissimilar sequences, we determined crystal structures of Nln in complex with diverse peptides including dynorphins, angiotensin, neurotensin, and bradykinin. The structures show that Nln binds these peptides in a large dumbbell-shaped interior cavity constricted at the active site, making minimal structural changes to accommodate different peptide sequences. The structures also show that Nln readily binds similar peptides with distinct registers, which can determine whether the peptide serves as a substrate or a competitive inhibitor. We analyzed the activities and binding of Nln toward various forms of dynorphin A peptides, which highlights the promiscuous nature of peptide binding and shows how dynorphin A (1–13) potently inhibits the Nln activity while dynorphin A (1–8) is efficiently cleaved. Our work provides insights into the broad substrate specificity of Nln and may aid in the future design of small molecule modulators for Nln.

59 BASIC BIOLOGICAL SCIENCES↗

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures

Abstract Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3′-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.

Biochemistry & Molecular Biology↗

Controlling magnetism and transport at perovskite cobaltite interfaces via strain-tuned oxygen vacancy ordering

Complex oxides such as perovskite cobaltites exhibit rich phenomena at interfaces due to the complex interplay between their structural, defect, electronic, and magnetic degrees of freedom. Here, we study this interplay here in the ferromagnetic metallic cobaltite La 1−𝑥 ⁢Sr 𝑥⁢ CoO 3−𝛿 , using specific substrates to vary both the heteroepitaxial strain (compressive vs tensile) and growth orientation ((001) vs (110)). Transmission electron microscopy, electron energy-loss spectroscopy, high-resolution X-ray diffraction, magnetometry, polarized neutron reflectometry, and electronic magnetotransport measurements are applied. Lattice mismatch and growth orientation are found to enable the precise control of interfacial oxygen vacancy ordering in La 1−𝑥⁢ Sr 𝑥 ⁢CoO 3−𝛿 , thus dictating strain relaxation and oxygen vacancy depth profiles, in turn controlling thickness-dependent magnetic and electronic properties. In particular, compressive strain and (110) orientations minimize deleterious magnetic/electronic dead layer effects, leading to the optimization of interfacial magnetism and transport. Strain and orientation tuning of oxygen vacancy ordering are thus established as powerful means to control physical properties at cobaltite-based interfaces, relevant to several fields.

36 MATERIALS SCIENCE↗