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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
NASA NTRS1989

ECUT (Energy Conversion and Utilization Technologies) program: Biocatalysis project

The Annual Report presents the fiscal year (FY) 1988 research activities and accomplishments, for the Biocatalysis Project of the U.S. Department of Energy, Energy Conversion and Utilization Technologies (ECUT) Division. The ECUT Biocatalysis Project is managed by the Jet Propulsion Laboratory, California Institute of Technology. The Biocatalysis Project is a mission-oriented, applied research and exploratory development activity directed toward resolution of the major generic technical barriers that impede the development of biologically catalyzed commercial chemical production. The approach toward achieving project objectives involves an integrated participation of universities, industrial companies and government research laboratories. The Project's technical activities were organized into three work elements: (1) The Molecular Modeling and Applied Genetics work element includes research on modeling of biological systems, developing rigorous methods for the prediction of three-dimensional (tertiary) protein structure from the amino acid sequence (primary structure) for designing new biocatalysis, defining kinetic models of biocatalyst reactivity, and developing genetically engineered solutions to the generic technical barriers that preclude widespread application of biocatalysis. (2) The Bioprocess Engineering work element supports efforts in novel bioreactor concepts that are likely to lead to substantially higher levels of reactor productivity, product yields and lower separation energetics. Results of work within this work element will be used to establish the technical feasibility of critical bioprocess monitoring and control subsystems. (3) The Bioprocess Design and Assessment work element attempts to develop procedures (via user-friendly computer software) for assessing the energy-economics of biocatalyzed chemical production processes, and initiation of technology transfer for advanced bioprocesses.

Baresi, Larry↗
DOE OSTI2024

Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline

Abstract As genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Designed 2D protein crystals as dynamic molecular gatekeepers for a solid-state device

The sensitivity and responsiveness of living cells to environmental changes are enabled by dynamic protein structures, inspiring efforts to construct artificial supramolecular protein assemblies. However, despite their sophisticated structures, designed protein assemblies have yet to be incorporated into macroscale devices for real-life applications. We report a 2D crystalline protein assembly of C98/E57/E66 L-rhamnulose-1-phosphate aldolase ( CEE RhuA) that selectively blocks or passes molecular species when exposed to a chemical trigger. CEE RhuA crystals are engineered via cobalt(II) coordination bonds to undergo a coherent conformational change from a closed state (pore dimensions <1 nm) to an ajar state (pore dimensions ~4 nm) when exposed to an HCN(g) trigger. When layered onto a mesoporous silicon (pSi) photonic crystal optical sensor configured to detect HCN (g) , the 2D CEE RhuA crystal layer effectively blocks interferents that would otherwise result in a false positive signal. The 2D CEE RhuA crystal layer opens in selective response to low-ppm levels of HCN (g) , allowing analyte penetration into the pSi sensor layer for detection. These findings illustrate that designed protein assemblies can function as dynamic components of solid-state devices in non-aqueous environments.

36 MATERIALS SCIENCE↗
NASA NTRS2006

Inspiring the Next Generation: Student Experiments and Educational Activities on the International Space Station, 2000-2006

One important objective of NASA has always been to inspire the next generation. NASA and human space flight have a unique ability to capture the imaginations of both students and teachers. The presence of humans onboard the International Space Station (ISS) for more than five years now has provided a foundation for numerous educational activities aimed at capturing the interest and motivating study in the sciences, technology, engineering, and mathematics. Yet even before the Expedition 1 crew arrived at station in November 2000, experiments with student participation were being conducted onboard ISS in support of NASA missions. One of NASA's protein crystal growth experiments had been delivered to station by the shuttle Atlantis during STS-106 in September 2000 and was returned to Earth six weeks later aboard the shuttle Discovery during the STS-92 mission. From very early on it was recognized that students would have a strong interest in the ISS, and that this would provide a unique opportunity for them to get involved and participate in science and engineering projects on ISS. It should be noted that participation is not limited to U.S. students but involves the 16 International Partner countries and various other countries under special commercial agree

Thomas, Donald A.↗
DOE OSTI2024

Vaccination induces broadly neutralizing antibody precursors to HIV gp41

A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Mechanism-guided engineering of a minimal biological particle for genome editing

The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here, we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs and demonstrated increased editing in cell lines and therapeutically relevant primary human T cells. These results show that virally derived particles can be streamlined to create efficacious genome editing delivery vehicles with simpler production and manufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DiMER

SAND2025-04145O DiMER is a Python based tool that helps researchers understand the functions of genes by searching through multiple biological databases. It takes user-provided data and scans various databases to find the best matches for gene functions, generating a clear summary of results. DiMER identifies the most relevant functional annotations and improves upon previous annotations by replacing instances of "unknown protein function" with more accurate descriptions. DiMER requires minimal setup. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Mageeney, Catherine [Sandia National Lab. (SNL-CA)↗
DOE OSTI2024

Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB

ABSTRACT Stenotrophomonas maltophilia expresses a type IV protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria and does so partly by secreting the effector TfcB. Here, we report the structure of TfcB, comprising an N-terminal domain similar to the catalytic domain of glycosyl hydrolase (GH-19) chitinases and a C-terminal domain for recognition and translocation by the T4SS. Utilizing a two-hybrid assay to measure effector interactions with the T4SS coupling protein VirD4, we documented the existence of five more T4SS substrates. One of these was protein 20845, an annotated nuclease. A S. maltophilia mutant lacking the gene for 20845 was impaired for killing Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa . Moreover, the cloned 20845 gene conferred robust toxicity, with the recombinant E. coli being rescued when 20845 was co-expressed with its cognate immunity protein. The 20845 effector was an 899 amino-acid protein, comprised of a GHH-nuclease domain in its N-terminus, a large central region of indeterminant function, and a C-terminus for secretion. Engineered variants of the 20845 gene that had mutations in the predicted catalytic site did not impede E. coli , indicating that the antibacterial effect of 20845 involves its nuclease activity. Using flow cytometry with DNA staining, we determined that 20845, but not its mutant variants, confers a loss in DNA content of target bacteria. Database searches revealed that uncharacterized homologs of 20845 occur within a range of bacteria. These data indicate that the S. maltophilia T4SS promotes interbacterial competition through the action of multiple toxic effectors, including a potent, novel DNase. IMPORTANCE Stenotrophomonas maltophilia is a multi-drug-resistant, Gram-negative bacterium that is an emerging pathogen of humans. Patients with cystic fibrosis are particularly susceptible to S. maltophilia infection. In hospital water systems and various types of infections, S. maltophilia co-exists with other bacteria, including other pathogens such as Pseudomonas aeruginosa . We previously demonstrated that S. maltophilia has a functional VirB/D4 type VI protein secretion system (T4SS) that promotes contact-dependent killing of other bacteria. Since most work on antibacterial systems involves the type VI secretion system, this observation remains noteworthy. Moreover, S. maltophilia currently stands alone as a model for a human pathogen expressing an antibacterial T4SS. Using biochemical, genetic, and cell biological approaches, we now report both the discovery of a novel antibacterial nuclease (TfdA) and the first structural determination of a bactericidal T4SS effector (TfcB).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Architector 2.0: Expanded Capabilities for Metal Complex Engineering

Automated three-dimensional molecular construction from two-dimensional graph representations is critical to high-throughput discovery eIorts. Software capabilities in this area have accelerated research across fields ranging from protein design and drug discovery to transition metal catalyst development. When Architector was first introduced, it uniquely enabled high-throughput, chemically relevant three-dimensional construction of f-element complexes. Since its introduction, Architector has been applied in large-scale computational campaigns, targeted studies in critical mineral extraction, and artificial intelligence-driven discovery eIorts.

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

Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain

Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Here, through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

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

TCF Base Technology-Specific Final Report: Engineering Enzymes for Crystalline PET Substrate

The primary objective of this project was to develop a new polyethylene terephthalate (PET) hydrolase enzyme to depolymerize relevant PET substrates for Birch Biosciences, using high-throughput protein expression, purification, and assaying systems and machine learning-guided enzyme design. As a secondary project objective, we also aimed to develop a more energy-efficient ethylene glycol (EG) recovery strategy relative to distillation.

09 BIOMASS FUELS↗
DOE OSTI2026

Engineered Membrane Vesicle Production via oprF or oprI Deletion Has Distinct Phenotypic Effects in Pseudomonas putida -putative knockouts table

Table S1, putative gene knockout targets in P. putida KT2440 to enhance vesiculation; Table S2, protein sequence identity of OmpA from E. coli K12 to P. putida KT2440 genes; Table S3, strains utilized in this study and corresponding construction details; Table S4, oligonucleotides utilized in this study; Table S5, plasmids utilized in this study; Table S6, sequences for mNeonGreen, tags, and codon-optimized genes; Figure S1, particle count per gCDW for KT2440 and knockout strains corresponding to data presented in Figure 1B; Figure S2, OD600 measurements of extracted MVs from KT2440 and knockout strains; Figure S3, particle count per gCDW for WT, ΔPP_4669, and ΔPP_1502; Figure S4, particle count per gCDW for KT2440 and knockout strains corresponding to data presented in Figure 3C; Figure S5, sizes of MVs corresponding to particle counts in Figure S4; Figure S6, particle count per gCDW for KT2440 grown on 20 mM glucose alone or 20 mM glucose plus 12.5 mM p-coumarate and 12.5 mM ferulate; Figure S7 and Figure S8, principal component analysis of the cellular fractions; Figure S9, heatmap of outer membrane proteins with differential abundance; and Figure S10, mNeonGreen (mNG) fluorescence signal for the cellular fraction and the extracellular fraction

hypervesiculation↗
DOE OSTI2025

Engineering Pseudomonas putida for production of 3-hydroxyacids using hybrid type I polyketide synthases

Engineered type I polyketide synthases (T1PKSs) are a potentially transformative platform for the biosynthesis of small molecules. Due to their modular nature, T1PKSs can be rationally designed to produce a wide range of bulk or specialty chemicals. While heterologous PKS expression is best studied in microbes of the genus Streptomyces, recent studies have focused on the exploration of non-native PKS hosts. The biotechnological production of chemicals in fast growing and industrial relevant hosts has numerous economic and logistic advantages. With its native ability to utilize alternative feedstocks, Pseudomonas putida has emerged as a promising workhorse for the sustainable production of small molecules. Here, we outline the assessment of P. putida as a host for the expression of engineered T1PKSs and production of 3-hydroxyacids. After establishing the functional expression of an engineered T1PKS, we successfully expanded and increased the pool of available acyl-CoAs needed for the synthesis of polyketides using transposon sequencing and protein degradation tagging. This work demonstrates the potential of T1PKSs in P. putida as a production platform for the sustainable biosynthesis of unnatural polyketides.

Schmidt, Matthias↗
DOE OSTI2025

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗
NASA NTRS2004

Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.

Stolc, Viktor↗