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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Local Chain Dynamics in Sequence-Controlled Polymers as a Tunable Handle for Rare Earth Sequestration

Chain dynamics govern the intricate behaviors of proteins, underpinning functions such as catalysis, recognition, and stimulus response, and are an increasingly appreciated aspect of structure–function relationships. Analogously, manipulating chain dynamics and structure in abiotic polymers via sequence control is an exciting, yet underexplored, strategy for improving material functions. In this work, we report a systematic study relating the sequence of polymeric sequestrants to their structure and dynamics, as well as to their binding affinity and selectivity for model substrates, rare earth elements (REEs). A series of sequence-controlled polymers with metal chelating, solubilizing, and structure forming monomers was synthesized via multiblock polymerization, yielding compositionally identical polymers with spectroscopically resolved domains and distinct morphologies. Using a combination of small-angle X-ray scattering and 19 F NMR relaxometry measurements, we connected differences in polymer structure and dynamics to polymer sequence variables such as the patchiness (density) of the structure forming monomer and the location of the chelating monomer. Furthermore, we found that, relative to calcium, all polymers in the series collapse more and have slower dynamics when binding REEs (lanthanum and lutetium) , though the extent of these effects were sequence-dependent and localized to specific domains within the polymer. Notably, sequence-controlled polymers that exhibited the largest conformational and dynamic changes upon binding REEs also bound REEs with the greatest affinity and modest selectivity. Collectively, these results correlate monomer patterning with dynamics, morphology, and REE binding performance en route to the development of efficient and selective macromolecular chelators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Evolved Gas Analysis–Mass Spectrometry Exposes Polymer Network Structures

Polymer network structures in epoxy thermosets play an important role in the final thermoset material properties. However, analytical characterization of these network structures is difficult due to their amorphous nature. In this work, the application of evolved gas analysis–mass spectrometry (EGA-MS) to characterize the polymer network structures of bisphenol A (BPA)-based thermosets is demonstrated. Analytical characterization of the polymer network structures is accomplished by monitoring the Product-Specific Kinetics (PSK) of BPA monomer formation during thermal degradation investigations. We relate observed differences in the activation energy (E a ) of BPA monomer formation to the local packing environment around the BPA monomer units within the polymer network. Variations in the local environment related to the polymer networks manifest qualitatively as broadening in the thermal profile of the BPA monomer evolution and quantitatively as changes in the activation energy (E a ). Three BPA thermoset formulations were investigated; two amine-cured thermoset with 4,4′-diaminodiphenylmethane (DDM) or poly(propylene glycol) bis(2-amino-propyl ether) (PPG400) and a homopolymerized thermoset via curing with Epikure 3253 catalyst (3253). Results revealed that the 3253 thermoset contained two distinct packing densities in the polymer network, while DDM and PPG400 thermosets had uniform distributions of packing densities. Results from the DDM thermoset revealed a gradually decreasing E a , while the apparent E a of PPG400 was consistent over the entire degradation. Furthermore, these differences in E a were concluded to stem from the flexibility of the corresponding polymer networks and the ability of the network components to rearrange and occupy formed voids. Due to the minimal sample required for analysis (100–200 μg), this EGA-MS technique has great potential for postproduction evaluation of composite parts to identify changes in the polymer networks from use and aging, which could signal compromised performance.

Degradation↗
DOE OSTI2023

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives–3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)–the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mastering the Copolymerization Behavior of Ethyl Cyanoacrylate as Gel Polymer Electrolyte for Lithium‐metal Battery Application

Polymers with strong electron-withdrawing groups (e.g., cyano-containing polymers) are attractive for a wide range of applications due to their high dielectric constant and outstanding electrochemical stability. However, the polymerization of such monomers is difficult to control with trace of water affording instant reactions, and copolymerization with other monomers without using strong acid is even more challenging. The present study demonstrates a facile approach enabling efficient and controllable copolymerization of ethyl cyanoacrylate (ECA) without adding undesired additives, achieving mechanically robust and high ion-conduction gel polymer electrolyte (GPE) for safe and long cycle-life lithium-metal batteries (LMBs). The incorporated dual-lithium salts, i.e., lithium difluoro(oxalato)borate (LiDFOB) and lithium bis(trifluoromethanesulphonyl)imide (LiTFSI) not only facilitate radical polymerization of ECA monomers by suppressing their anionic polymerization, but also promote the formation of high-ionic conducting GPE. The incorporated methyl methacrylate (MMA) monomer accelerates the radical polymerization of ECA (confirmed by DFT calculations), achieving controlled copolymerization of ECA-based copolymers. Here, the mechanically robust polymer network made by the ECA copolymer enables LMBs with both LFP cathodes and high-voltage LCO cathodes (4.5 V) operatable at different temperatures with ultra-long cycle life at 1 C (capacity retention of 81.1 % and 83.8 %, respectively, over 1000 cycles).

Min, Weixing [Nankai University, Tianjin (China)]↗
DOE OSTI2025

Zinc(II) Monomeric, Dimeric, and Trimeric Photosensitizers with Microsecond‐Lived Intra‐ligand Charge Transfer Excited States Investigated through Time‐Resolved Optical and X‐Ray Spectroscopy

Zn II photosensitizers relative to Cu I complexes have received less attention due to their energetically higher metal‐to‐ligand charge transfer states. Three Zn II complexes, namely a Monomer, a bimetallic helicate, and a trimetallic helicate, bearing phenanthroline ligands are hereby studied through time‐resolved X‐ray absorption (tr‐XAS) and femto‐microsecond optical transient absorption spectroscopy (OTA). The formation of intraligand singlet charge transfer ( I ILCT) excited states is achieved within femtoseconds, followed by intersystem crossing (ISC) in nanoseconds to generate microsecond‐lived triplet ( 3 ILCT) states. Femtosecond OTA shows that the 1 ILCT states in the Monomer, Dimer, and Trimer occur within 235 fs, 683 fs, and 730 fs, respectively, while nano‐microsecond OTA and tr‐XAS show their 3 ILCT states to decay within 1.00 µs, 1.48 µs, and 1.51 µs. The ISC from the 1 ILCT to the 3 ILCT state for the Trimer is 42.8 ns compared to the Monomer and Dimer with ISC rates of less than 13 ns. These differences arise due to the stabilization by π‐π and CH‐π noncovalent interactions of the phenanthroline ligands. The dihedral and torsional angles indicate stronger ligand strains in the excited states of the Dimer and Trimer versus the Monomer. DFT calculations for the electrochemical oxidation potentials further highlight their capability in inducing photoredox processes.

earth-abundant Zn-based photosensitizers↗
DOE OSTI2024

Reductive Depolymerization of Lignin to Aromatic Compounds over Promoted Nickel Catalysts in Sub– and Supercritical Methanol

The use of γ-Al 2 O 3 -supported Ni catalysts promoted with either Cu or Fe was investigated for the reductive catalytic fractionation (RCF) of hybrid poplar in methanol at 200 and 250 °C. The effectiveness of lignin depolymerization was quantified in terms of the lignin oil production, the quantity and distribution of identifiable monomers present in the lignin oil, and the yield of residual solids. All of the Ni-based catalysts tested provided improved yields of lignin oil and monomers, along with reduced char formation, relative to blank (sans catalyst) runs. The highest monomer yield of 51 % was obtained at 250 °C over a 20 wt.% Ni-5 wt.% Cu/Al 2 O 3 catalyst, the improved performance obtained through Cu promotion being attributed to the ability of Cu to facilitate NiO reduction, resulting in an increased amount of Ni 0 on the catalyst surface and, consequently, improved hydrogenation activity. Finally, the main monomers formed were propanol-, propyl- and propenyl-substituted guaiacol and syringol, the S/G ratio of the products corresponding closely to that in the native lignin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Investigations of Polymethacrylate Tribochemical Films Using X-Ray Spectroscopy and Optical Profilometry

This study investigates the elemental composition and surface morphology of solid tribochemical films formed on steel surfaces. The reversible addition-fragmentation chain transfer (RAFT) method was used to synthesize nine different metal-free polymers, which were blended into commercial base oils. The polymers were either homopolymers of dodecyl methacrylate and ethylhexyl methacrylate or were co-polymers of these monomers with six polar monomers. After tribological testing at 100 degrees C using the ball-on-flat geometry, the resulting tribochemical films were imaged using scanning electron microscopy (SEM) and optical microscopy. The resulting tribochemical films have thicknesses around 50-100 nm. Two of the films corresponding to small (P1-imidazole-containing copolymer) and large (P3-less polar homopolymer) wear were cross-sectioned using focused ion beam (FIB) and analyzed for elemental composition using energy-dispersive X-Ray (EDX) mapping. Oxygen and nitrogen enrichment was observed, consistent with the relative chemical composition of the precursor polymers. Transmission electron microscopy (TEM) evidence suggests that at the worn surface, some organic elements penetrate or are mixed into the steel substrate giving an interlocking appearance. The two samples examined with TEM showed that P1 tribofilm is diffused or mixed with the steel substrate more so than P3, suggesting a stronger affinity and contact during tribofilm formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An in-situ crosslinking binder for binder jet additive manufacturing

Additive Manufacturing (AM) of metals is a potentially disruptive technology that could significantly change the industrial supply chain. There are a limited number of AM methods capable of creating metal parts, and one method showing significant potential is Binder Jet AM (Binder Jetting). Binder Jetting utilizes an inkjet print head to deposit a binder fluid onto a powder bed and bind together powder particles into a desired geometry. This study investigates a new binder system consisting of a difunctional monomer, triethylene glycol dimethacrylate (TEG-DMA). TEG-DMA exhibits excellent printability with an Ohnesorge’s number of .258 making the Z number 3.876. During the thermal curing process, the difunctional monomer polymerizes and crosslinks at the onset temperature of 138 °C, becoming a solid dimethacrylate network. When the binder is utilized within the stainless-steel powder bed at 200 °C, it forms a network incorporating the stainless-steel particles, binding the powder into any specified geometry. Crosslinking the monomer within the stainless-steel 420 powder bed imparts a flexural strength of 1.0–3.3 MPa to the green part depending on the volume of monomer in the part. After sintering, the final stainless-steel parts results in a void fraction close to 60 % and carbon content below 0.4 %.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Facile polymerization in a bicellar template to produce polymer nano-rings

We report a well-defined discoidal bicelle composed of three lipids, specifically zwitterionic long-chain 1,2-dipalmitoyl phosphocholine (DPPC) and short-chain 1,2-dihexanoyl phosphocholine (DHPC) doped with anionic 1,2-dipalmitoyl phosphoglycerol (DPPG) provides a generalized template for the synthesis of hydrophobic polymer nano-rings. The lipid molar ratio of DPPC/DHPC/DPPG is 0.71/0.25/0.04. The detailed investigation and discussion were based on styrene but tested on three other vinyl monomers. The structure of nano-rings is identified through the detailed analysis of small angle X-ray/neutron scattering (SAXS and SANS) data and transmission electron micrographs (TEM), supported by the differential scanning calorimetric (DSC) data before and after polymerization. The investigation covers samples with a styrene-to-lipid ratio ranged varied from 1:50 to 1:10.The styrene monomers are initially located at both the discoidal planar (long-chain lipid rich) and rim (short-chain lipid rich) regions. During polymerization, they migrate to the more fluid rim region-section. The formation mechanism involves the interplay of hydrophobic interaction, mismatched miscibility of polystyrene between the ordered and disordered phases, and crystallinity of the long lipid acyl chains. This facile synthesis is proven applicable for several hydrophobic monomers. The well-defined nano-rings greatly enhance the interfacial area and have the potential to be the building blocks for functional materials, if monomers are incorporated with desirable functions, for future applications. Crosslinked polymer nano-rings are produced in well-defined discoidal bicelles. The enhanced immiscibility in the planar region drives the hydrophobic polymers to the fluidic rim. The platform can be generalized for synthesis of other hydrophobic polymer nano-rings.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Product-specific kinetics reveal effect of epoxy crystallization on thermoset thermal degradation

Crystallization is a common problem for epoxy resins, which are ubiquitous in industrial and commercial use. Integration of crystallized epoxy monomers into cured thermosets has been shown to alter the thermosets’ final mechanical properties. However, no studies have investigated the impact of these crystals on the thermal stability of the thermoset. Here we investigate the degradation kinetics of a bisphenol F–based epoxy thermoset with and without crystallized monomers using Product-Specific Kinetic (PSK) analysis coupled with Evolved Gas Analysis-Mass Spectrometry (EGA-MS). PSK analysis revealed significant differences in evolved product ion kinetics, suggesting changes in the degradation kinetics between thermoset configurations. Further, it was concluded that early stages of degradation are influenced most by crystal presence due to the high concentration of unreacted epoxy monomers and lower cross-linking density of the cured network. After post-cure annealing, significant changes are observed in the degradation kinetics of thermosets without crystal inclusions. Conversely, post-cure annealing procedures of crystal integrated thermosets showed little change in the thermoset degradation kinetics across all conversion extents. These findings suggest that post-cure annealing of thermosets with crystals present at the onset does not alter the cross-linking density of the polymer network enough to significantly change the degradation kinetics. We hypothesize this is because the excess monomers from the melted crystals are unable to find suitable reaction sites for complete binding into the polymer network, which has direct implications for the material properties and final thermal stability of the thermoset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Development of an Amine Oxide Polyzwitterion Brush Martini Model with Polarizable Water and Ions

Abstract In order to accurately simulate the fouling process of proteins onto polyzwitterion brushes, models that accurately capture the hydration properties and chain conformations of such brushes must first be established. We developed a Martini coarse-grained (CG) model for amine oxide polyzwitterion (PNOMA) brushes, a promising class of antifouling materials, in polarizable water and ions by fitting to all-atom bond and angle distributions, monomer hydration free energy, monomer–monomer distance potential of mean force (PMF), and monomer–salt radial distribution functions (RDFs). Martini 2.2P was selected for compatibility with the established polarizable water and ion models. For comparison with PNOMA, we also constructed models for conventional sulfobetaine (PSBMA) and phosphorylcholine (PMPC) polyzwitterions and the polycation PMETAC using established nonbonded bead types from the literature and refitting bond and angle potentials. We simulated each polymer brush chemistry for varying grafting density and chain length, validating brush height scaling relations against experimental data. The CG models captured the relative hydration strengths among different polyzwitterion chemistries, and brush heights extrapolated to higher molecular weights are in agreement with experimental ellipsometry data. We find that chain swelling of the superhydrophilic PNOMA brushes lies between that of the traditional polyzwitterions PSBMA/PMPC and the polycation PMETAC. For PNOMA brushes in NaCl solution, simulated brush height decreases with salt concentration due to the selectively strong interactions between amine oxide and sodium ions.

Walker, Christopher C. [Oak Ridge National Laborat↗
DOE OSTI2024

Recycling of Post-Consumer Waste Polystyrene Using Commercial Plastic Additives

Photothermal conversion can promote plastic depolymerization (chemical recycling to a monomer) through light-to-heat conversion. The highly localized temperature gradient near the photothermal agent surface allows selective heating with spatial control not observed with bulk pyrolysis. However, identifying and incorporating practical photothermal agents into plastics for end-of-life depolymerization have not been realized. Interestingly, plastics containing carbon black as a pigment present an ideal opportunity for photothermal conversion recycling. Herein, we use visible light to depolymerize polystyrene plastics into styrene monomers by using the dye in commercial black plastics. A model system is evaluated by synthesizing polystyrene–carbon black composites and depolymerizing under white LED light irradiation, producing styrene monomer in up to 60% yield. Excitingly, unmodified postconsumer black polystyrene samples are successfully depolymerized to a styrene monomer without adding catalysts or solvents. Using focused solar irradiation, yields up to 80% are observed in just 5 min. Furthermore, combining multiple types of polystyrene plastics with a small percentage of black polystyrene plastic enables full depolymerization of the mixture. This simple method leverages existing plastic additives to actualize a closed-loop economy of all-colored plastics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Design and Validation of a High-Throughput Reductive Catalytic Fractionation Method

Reductive catalytic fractionation (RCF) is a promising method to extract and depolymerize lignin from biomass, and bench-scale studies have enabled considerable progress in the past decade. RCF experiments are typically conducted in pressurized batch reactors with volumes ranging between 50 and 1000 mL, limiting the throughput of these experiments to one to six reactions per day for an individual researcher. Here, we report a high-throughput RCF (HTP-RCF) method in which batch RCF reactions are conducted in 1 mL wells machined directly into Hastelloy reactor plates. The plate reactors can seal high pressures produced by organic solvents by vertically stacking multiple reactor plates, leading to a compact and modular system capable of performing 240 reactions per experiment. Using this setup, we screened solvent mixtures and catalyst loadings for hydrogen-free RCF using 50 mg poplar and 0.5 mL reaction solvent. The system of 1:1 isopropanol/methanol showed optimal monomer yields and selectivity to 4-propyl substituted monomers, and validation reactions using 75 mL batch reactors produced identical monomer yields. To accommodate the low material loadings, we then developed a workup procedure for parallel filtration, washing, and drying of samples and a 1H nuclear magnetic resonance spectroscopy method to measure the RCF oil yield without performing liquid-liquid extraction. As a demonstration of this experimental pipeline, 50 unique switchgrass samples were screened in RCF reactions in the HTP-RCF system, revealing a wide range of monomer yields (21-36%), S/G ratios (0.41-0.93), and oil yields (40-75%). These results were successfully validated by repeating RCF reactions in 75 mL batch reactors for a subset of samples. We anticipate that this approach can be used to rapidly screen substrates, catalysts, and reaction conditions in high-pressure batch reactions with higher throughput than standard batch reactors.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2022

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict intra-chain residue-residue distances of monomers accurately, but few methods can accurately predict inter-chain residue-residue distances of complexes. We develop a deep learning method CDPred (i.e., Complex Distance Prediction) based on the 2D attention-powered residual network to address the gap. Tested on two homodimer datasets, CDPred achieves the precision of 60.94% and 42.93% for top L/5 inter-chain contact predictions (L: length of the monomer in homodimer), respectively, substantially higher than DeepHomo’s 37.40% and 23.08% and GLINTER’s 48.09% and 36.74%. Tested on the two heterodimer datasets, the top Ls/5 inter-chain contact prediction precision (Ls: length of the shorter monomer in heterodimer) of CDPred is 47.59% and 22.87% respectively, surpassing GLINTER’s 23.24% and 13.49%. Moreover, the prediction of CDPred is complementary with that of AlphaFold2-multimer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Controllable growth of interpenetrating or random copolymer networks

Interpenetrating and random copolymer networks are vital in a number of industrial applications, including the fabrication of automotive parts, damping materials, and tissue engineering scaffolds. We develop a theoretical model for a process that enables the controlled growth of interpenetrating network (IPNs), or a random copolymer network (RCN) of specified size and mechanical properties. In this process, a primary gel “seed” is immersed into a solution containing the secondary monomer and crosslinkers. After the latter species are absorbed into the primary network, the absorbed monomers are polymerized to form the secondary polymer chains, which then can undergo further crosslinking to form an IPN, or undergo inter-chain exchange with the existing network to form a RCN. The swelling and elastic properties of the IPN and RCN networks can be tailored by modifying the monomer and crosslinker concentrations in the surrounding solution, or by tuning the enthalpic interactions between the primary polymer, secondary monomer and solvent through a proper choice of chemistry. This process can be used repeatedly to fabricate gels with a range of mechanical properties from stiff, rigid materials to soft, flexible networks, allowing the method to meet the materials requirements of a variety of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Solvent selection for a biomass-to-bioproduct pipeline through integrated reductive catalytic fractionation and microbial funneling

The growing significance of lignin-first biorefineries, which focus on upgrading the aromatics resulting from lignin depolymerization, presents opportunities for bioproduct synthesis using microbial strains capable of funneling a diverse array of phenolics into a single commodity chemical. In this study, we evaluated a biomass-to-bioproduct pipeline involving the reductive catalytic fractionation (RCF) of poplar biomass followed by biological funneling with a Novosphingobium aromaticivorans strain that produces 2-pyrone-4,6-dicarboxylic acid (PDC), a potential bioplastic precursor. Considering the impact of solvent on RCF reactor operating pressure, and the potential inhibitory effects of solvent on downstream microbial funneling, we performed an analysis of six pure solvents, namely methanol, ethanol, isopropanol, isobutanol, 1,4-dioxane and ethylene glycol, and different variations of their aqueous mixtures comprising 5 to 50 vol% water. For each pure solvent and solvent/water system, we measured phenolic monomer yields in the RCF process and PDC yields from the phenolic monomers. We then developed correlation models that relate phenolic monomer yields from RCF-derived samples to Hansen solubility parameters to determine solvent descriptors that contribute to high yields. Furthermore, we developed an integrated biorefinery system to estimate the minimum selling price (MSP) of PDC and the associated carbon footprint to identify solvent systems with better costs and sustainability metrics. These analyses resulted in the 50 vol% methanol/water system being identified as optimal because it reduces RCF reactor pressure and is compatible with microbial funneling with N. aromaticivorans. This solvent system produced 63 g PDC per kg biomass (264 g PDC per kg lignin) from 85 g phenolic monomers per kg biomass at a reduced reactor pressure of 48 bar (reduced by 26% compared to our previous poplar-to-PDC pipeline). The MSP for this system is $\$$13.98 per kg of purified PDC (carbon footprint of 1.47 kg CO 2 e per kg), which is about 24% lower than a previously described poplar-to-PDC pipeline and 46% lower than a lignin-to-PDC pipeline that used pure methanol as the solvent. The results from this study illustrate improvements that can be made in lignocellulosic biorefineries that are compatible with the hybrid chemical and biological processes needed to gain value from lignin.

Sripada, Sarada [Great Lakes Bioenergy Research Ce↗
DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans

ABSTRACT Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the β-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans . We used genome-wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidate genes elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans . Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers vanillin and 5-formylferulate (5-FF). We also showed that the aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in the β-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans . A comparative genomic analysis predicted that the newly discovered β-5 aromatic catabolic pathway is common within the order Sphingomonadales. IMPORTANCE In the transition to a circular bioeconomy, the plant polymer lignin holds promise as a renewable source of industrially important aromatic chemicals. However, since lignin contains aromatic subunits joined by various chemical linkages, producing single chemical products from this polymer can be challenging. One strategy to overcome this challenge is using microbes to funnel a mixture of lignin-derived aromatics into target chemical products. This approach requires strategies to cleave the major inter-unit linkages of lignin to release monomers for funneling into valuable products. In this study, we report newly discovered aspects of a pathway by which the Novosphingobium aromaticivorans DSM12444 catabolizes aromatics joined by the second most common inter-unit linkage in lignin, the β-5 linkage. This work advances our knowledge of aromatic catabolic pathways, laying the groundwork for future metabolic engineering of this and other microbes for optimized conversion of lignin into products.

59 BASIC BIOLOGICAL SCIENCES↗