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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Inhibition of Pyruvate Kinase From Thermoanaerobacterium saccharolyticum by IMP Is Independent of the Extra-C Domain

The pyruvate kinase (PYK) isozyme from Thermoanaerobacterium saccharolyticum (TsPYK) has previously been used in metabolic engineering for improved ethanol production. This isozyme belongs to a subclass of PYK isozymes that include an extra C-domain. Like other isozymes that include this extra C-domain, we found that TsPYK is activated by AMP and ribose-5-phosphate (R5P). Our use of sugar-phosphate analogs generated a surprising result in that IMP and GMP are allosteric inhibitors (rather than activators) of TsPYK. We believe this to be the first report of any PYK isozyme being inhibited by IMP and GMP. A truncated protein that lacks the extra C-domain is also inhibited by IMP. A screen of several other bacterial PYK enzymes (include several that have the extra-C domain) indicates that the inhibition by IMP is specific to only a subset of those isozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed

The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennes(see United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimental conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile

Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/ Q 10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity ( V max ) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. V max and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/ Q 10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Synechocystis sp. PCC 6803 Requires the Bidirectional Hydrogenase to Metabolize Glucose and Arginine Under Oxic Conditions

The cyanobacterium Synechocystis sp.PCC 6803 possesses a bidirectional NiFe-hydrogenase, HoxEFUYH. It functions to produce hydrogen under dark, fermentative conditions and photoproduces hydrogen when dark-adapted cells are illuminated. Unexpectedly, we found that the deletion of the large subunit of the hydrogenase (HoxH) in Synechocystis leads to an inability to grow on arginine and glucose under continuous light in the presence of oxygen. This is surprising, as the hydrogenase is an oxygen-sensitive enzyme. In wild-type (WT) cells, thylakoid membranes largely disappeared, cyanophycin accumulated, and the plastoquinone (PQ) pool was highly reduced, whereas ΔhoxH cells entered a dormant-like state and neither consumed glucose nor arginine at comparable rates to the WT. Hydrogen production was not traceable in the WT under these conditions. We tested and could show that the hydrogenase does not work as an oxidase on arginine and glucose but has an impact on the redox states of photosynthetic complexes in the presence of oxygen. It acts as an electron valve as an immediate response to the supply of arginine and glucose but supports the input of electrons from arginine and glucose oxidation into the photosynthetic electron chain in the long run, possibly via the NDH-1 complex. Despite the data presented in this study, the latter scenario requires further proof. The exact role of the hydrogenase in the presence of arginine and glucose remains unresolved. In addition, a unique feature of the hydrogenase is its ability to shift electrons between NAD(H), NADP(H), ferredoxin, and flavodoxin, which was recently shown in vitro and might be required for fine-tuning. Taken together, our data show that Synechocystis> depends on the hydrogenase to metabolize organic carbon and nitrogen in the presence of oxygen, which might be an explanation for its prevalence in aerobic cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism

Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H 2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD + and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP + , cofactor F 420 , formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Alteration of phycobilisome excitation energy transfer properties in response to attenuations in peripheral electron flow

In Synechocystis sp. PCC 6803 ( S . 6803), two types of phycobilisome (PBS) complexes, CpcG-PBS and CpcL-PBS, function to harvest light energy for photosynthetic reaction centers (RCs), photosystem I (PSI) and photosystem II (PSII). The compositional differences between these two forms of PBS and their specificity for RCs have led to suggestions that they may differ in function. To address this question, we examined how PBS-RC interactions, and the transfer of excitation energy from PBS to RCs, might be adjusted under conditions where electron demand and photon availability are modulated. The CpcG-PBS, CpcL-PBS, and RC complexes were isolated from a S . 6803 strain defective in expression of flavodiiron 1 (oxygen reduction reaction 1, ORR1) grown under varied light regimes. The energy transfer preference from CpcL-PBS to either PSI or PSII was investigated by in vitro crosslinking and 77 K fluorescence emission spectroscopy to assess energy transfer efficiency under photoexcitation. While the results demonstrate that the transfer of excitation energy from CpcL-PBS favors PSI over PSII in WT strains as previously shown, the preference of CpcL-PBS switches from PSI to PSII in ORR1 strains. Surprisingly, this change in preference was reproduced when ORR1 CpcL-PBS was crosslinked with WT RCs, or when WT CpcL-PBS was cross-crosslinked with ORR1 RCs, indicating there are physical modifications to both PBS and RCs that mediate the preference switch. In contrast, the analysis with ORR1 CpcG-PBS shows similar preferences to WT. Additionally, PBS populations in ORR1 shifted to a greater proportion of CpcL-PBS relative to CpcG-PBS. These results demonstrate that under conditions where electron utilization changes, there is a tuning of the excitation energy allocation from CpcL-PBS to RCs to manage the energy distribution for photosynthesis under dynamic flux conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Boron adatom adsorption on graphene: A case study in computational chemistry methods for surface interactions

Though weak surface interactions and adsorption can play an important role in plasma processing and materials science, they are not necessarily simple to model. A boron adatom adsorbed on a graphene sheet serves as a case study for how carefully one must select the correct technique from a toolbox of computational chemistry methods. Using a variety of molecular dynamics potentials and density functional theory functionals, we evaluate the adsorption energy, investigate barriers to adsorption and migration, calculate corresponding reaction rates, and show that a surprisingly high level of theory may be necessary to verify that the system is described correctly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Manhattan Project 1940s research on the prompt fission neutron spectrum

We describe how the prompt fission neutron spectrum (PFNS) was determined for the Manhattan Project at Los Alamos. Early work before World War II at American and British universities is described, together with theoretical work by Feather at Cambridge and Bethe at Los Alamos. As the Manhattan Project was being planned in 1942, two experiments on natural uranium were commissioned that proved to be influential: 1) An integral experiment at Chicago by Christy and Manley that accurately determined the average PFNS spectrum energy, 2.2 ± 0.2 MeV; 2) Bloch and Staub’s Stanford cyclotron measurement of the PFNS spectrum, which obtained an average energy of 1.70 ± 0.34 MeV. These two papers, previously unavailable outside of Los Alamos, are reproduced in the Supplementary Appendix. From these data, at the beginning of the project in 1943 Serber estimated an average 235 U PFNS energy of 2 MeV, and indeed this agrees with today’s best estimate. The challenges facing the scientists involved both the availability of only very small samples of enriched uranium and plutonium targets, and fast neutron detection technologies. During the project, 235 U and 239 Pu PFNS were measured by Nicodemus and Staub. These also proved to be quite accurate and gave an average spectrum energy of 2 MeV for 235 U. [This is not reproduced in the Appendix because it was published after the war in Physical Review 89, 1288 (1953)]. New methods were developed to enable more accurate measurements, and this paper describes how the PFNS was determined surprisingly well by 1945. We end by describing the post-war measurements in the 50s, including the PFNS data used by Ford and Wheeler in their simulations in 1951, the Bonner 1952 data, the seminal 1952 Watt paper with a new empirical parametrization of the PFNS, and the accurate PFNS measurement undertaken at Los Alamos by Cranberg et al. in 1956. We compare the measurements with our best understanding today as embodied in the Evaluated Nuclear Data File ENDF/B-VIII.0. Some images from historical documents in our Los Alamos National Security Research Center (NSRC) archives are shown.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality (“greenness”) as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Ps and Qs: Quantization-Aware Pruning for Efficient Low Latency Neural Network Inference

Efficient machine learning implementations optimized for inference in hardware have wide-ranging benefits, depending on the application, from lower inference latency to higher data throughput and reduced energy consumption. Two popular techniques for reducing computation in neural networks are pruning, removing insignificant synapses, and quantization, reducing the precision of the calculations. In this work, we explore the interplay between pruning and quantization during the training of neural networks for ultra low latency applications targeting high energy physics use cases. Techniques developed for this study have potential applications across many other domains. We study various configurations of pruning during quantization-aware training, which we term quantization-aware pruning, and the effect of techniques like regularization, batch normalization, and different pruning schemes on performance, computational complexity, and information content metrics. We find that quantization-aware pruning yields more computationally efficient models than either pruning or quantization alone for our task. Further, quantization-aware pruning typically performs similar to or better in terms of computational efficiency compared to other neural architecture search techniques like Bayesian optimization. Surprisingly, while networks with different training configurations can have similar performance for the benchmark application, the information content in the network can vary significantly, affecting its generalizability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Phase Behavior and Ionic Conductivity of Blended, Ion-Condensed Electrolytes with Ordered Morphologies

In this study, the amphiphilic salt lithium trifluoromethanesulfonylimide octadecane (C18LiTFSI) was used as a basis to investigate the effects of anion density and cation coordination sites within blended electrolytes with strong ionic aggregation. C18LiTFSI was previously reported as a single-component, ion-condensed electrolyte with a wide layered liquid crystalline phase regime. Three additive molecules with varyingly sized polar sulfonyl groups attached to an octodecane-tail were synthesized and mixed with C18LiTFSI. The thermal properties, morphology, and ionic conductivity of the blended electrolytes were characterized. It was found that the blended electrolytes exhibited layered liquid crystalline morphology over a narrower temperature range than the pure salt, and the ionic conductivity of the blended liquid crystalline electrolytes were generally lower than that of the pure salt. Surprising, the additives were found to have the greatest effect on the bulk ionic conductivity of the semicrystalline phase of the electrolytes. Addition of minor fractions of methylsulfonyloctadecane to C18LiTFSI resulted in increases in conductivity of over two orders of magnitude at room temperature, while addition of ethylsulfonyloctadecane or isopropylsulfonyloctadecane with the larger head group resulted in decreased ionic conductivity over the entire composition space and temperature range investigated.

Collins, Hannah (ORCID:0000000338858136)↗
DOE OSTI2026

Strategies for Enhancing Battery Life Under Fast Charging: Insights from NMC-Based Cell Cycling

Fast charging improves the usability of consumer electronics and electric vehicles (EVs) by reducing range anxiety and downtime but accelerates battery degradation and raises safety concerns. Optimizing operational conditions during fast-charging is critical to mitigating aging and ensuring safety. This study evaluated multilayer Gr/NMC811 cells under various conditions, including depths of discharge (DODs of 68%, 84%, and 100%), upper charge cutoff voltages (4.1–4.2 V), and post-charge rest periods (2–30 min), using a 20 min fast charging protocol for up to 500 cycles (up to 150,000 miles of EV use assuming 3.3 mi/kWh vehicle level energy efficiency). Surprisingly, higher DODs under fast charging improved battery life and performance compared to lower DODs. Reducing the upper charge cut-off voltage helped mitigate degradation. A brief 2 min rest period after charging further reduced aging effects. The primary aging modes were loss of lithium inventory and cathode active material. Although minor lithium plating was observed within 500 cycles, it did not affect performance significantly. These findings suggest that, with optimized conditions, cells can sustain hundreds of fast charge cycles—equivalent to over 100,000 miles of EV use—without significant adverse effects on performance or longevity.

25 - ENERGY STORAGE↗
DOE OSTI2023

Microstructural, Corrosion, and Mechanical Characterization of Friction Stir Welded Al 6022-to-ZEK100 Mg Joints

Friction stir welded (FSW) aluminum–magnesium lightweight vehicle joints have gained significant interest due to their high strength-to-weight ratio. In this work, the corrosion resistance of this material is analyzed through electrochemical tests, which include open circuit potential (OCP) inspection and potentiodynamic polarization (PD) scanning. Weight loss measurements tested the corrosion rate of the FSW weld through cyclic corrosion testing (CCT) according to the standard SAEJ 2334. Mechanical properties were also investigated, including lap-shear strength, micro- and nano-hardness mapping, and true stress–strain curves as a function of local processing history. The electrochemical results indicate that the center weld zone’s corrosion property stays between the two base alloys. Indentation-based testing demonstrated that the weld zone behaves differently from base alloys. Lap shear strength surprisingly did not drop much even after eight weeks of cyclic corrosion tests, indicating that the joint did not allow any ingress of the electrolyte.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure and Anharmonicity of α- and β -Sb 2 O 3 at Low Temperature

Antimony oxides are important materials for catalysis and flame-retardant applications. The two most common phases, α-Sb 2 O 3 (senarmontite) and β-Sb 2 O 3 (valentinite), have been studied extensively. Specific focus has been placed recently on their lattice dynamics properties and how they relate to the α-β phase transformation and their potential anharmonicity. However, there has not been any direct investigation of anharmonicity in these systems, and a surprising lack of low-temperature structural information has prevented further study. Here, we report the powder neutron diffraction data of both phases of Sb 2 O 3 , as well as structural information. α-Sb 2 O 3 behaved as expected, but β-Sb 2 O 3 revealed a small region of zero thermal expansion along the c axis. Additionally, while the β phase matched well with reported atomic displacement parameters, the α phase displayed a marked deviation. This data will enable further investigations into these systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Dilute Paramagnetism and Non-Trivial Topology in Quasicrystal Approximant Fe4Al13

A very fundamental property of both weakly and strongly interacting materials is the nature of their magnetic response. In this work, we detail the growth of crystals of the quasicrystal approximant Fe4Al13 with an Al flux solvent method. We characterize our samples using electrical transport and heat capacity, yielding results consistent with a simple non-magnetic metal. However, magnetization measurements portray an extremely unusual response for a dilute paramagnet and do not exhibit the characteristic Curie behavior expected for a weakly interacting material at high temperature. Electronic structure calculations confirm metallic behavior but also indicate that each isolated band near the Fermi energy hosts non-trivial topologies, including strong, weak, and nodal components, with resultant topological surface states distinguishable from bulk states on the (001) surface. With half-filled flat bands apparent in the calculation, but an absence of long-range magnetic order, the unusual quasi-paramagnetic response suggests the dilute paramagnetic behavior in this quasicrystal approximant is surprising and may serve as a test of the fundamental assumptions that are taken for granted for the magnetic response of weakly interacting systems.

Avers, Keenan E. (ORCID:0000000223441939)↗
DOE OSTI2024

The Information Length Concept Applied to Plasma Turbulence

A methodology to study statistical properties of anomalous transport in fusion plasma is investigated. Three time traces generated by the full-f gyrokinetic code GKNET are analyzed for this purpose. The time traces consist of heat flux as a function of the radial position, which is studied in a novel manner using statistical methods. The simulation data exhibit transport processes with both medium and long correlation length along the radius. A typical example of a phenomenon with long correlation length is avalanches. In order to investigate the evolution of the turbulent state, two basic configurations are studied, one flux-driven and one gradient-driven with decaying turbulence. The information length concept in tandem with Boltzmann–Gibbs and Tsallis entropy is used in the investigation. It is found that the dynamical states in both flux-driven and gradient-driven cases are surprisingly similar, but the Tsallis entropy reveals differences between them. This indicates that the types of probability distribution function are nevertheless quite different since the higher moments are significantly different.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

AI-Based Protein Interaction Screening and Identification (AISID)

In this study, we presented an AISID method extending AlphaFold-Multimer’s success in structure prediction towards identifying specific protein interactions with an optimized AISIDscore. The method was tested to identify the binding proteins in 18 human TNFSF (Tumor Necrosis Factor superfamily) members for each of 27 human TNFRSF (TNF receptor superfamily) members. For each TNFRSF member, we ranked the AISIDscore among the 18 TNFSF members. The correct pairing resulted in the highest AISIDscore for 13 out of 24 TNFRSF members which have known interactions with TNFSF members. Out of the 33 correct pairing between TNFSF and TNFRSF members, 28 pairs could be found in the top five (including 25 pairs in the top three) seats in the AISIDscore ranking. Surprisingly, the specific interactions between TNFSF10 (TNF-related apoptosis-inducing ligand, TRAIL) and its decoy receptors DcR1 and DcR2 gave the highest AISIDscore in the list, while the structures of DcR1 and DcR2 are unknown. The data strongly suggests that AlphaFold-Multimer might be a useful computational screening tool to find novel specific protein bindings. This AISID method may have broad applications in protein biochemistry, extending the application of AlphaFold far beyond structure predictions.

59 BASIC BIOLOGICAL SCIENCES↗