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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Sum frequency generation (SFG) microscopy analysis of cellulose microfibrils in Physcomitrium patens gametophore leaf

Physcomitrium patens is a good model system to study the structure and function relationships of cellulose synthase (CESA) proteins since the life cycle of moss is short and genetic modification is relatively easy. Here, we report a microscopic sum frequency generation (SFG) vibrational spectroscopy analysis of P. patens leaves in a never-dried and fully hydrated state. Using imaging-SFG spectroscopy, cellulose microfibril (CMF) organization in the midrib, laminar, and marginal regions of the gametophore leaf were analyzed separately. The azimuth angle dependence of SFG signals showed that CMFs in the thick stereid cell walls in the midrib are highly aligned along the microfibril angle of ~ 30° with respect to the midrib axis. CMFs in the marginal cell walls also are preferentially tilted toward the longitudinal axis of leaf with the characteristic features of secondary cell walls. On the other hand, CMFs in the lamina cell walls have no preferential orientation and their SFG intensity is low, which is consistent with the primary cell wall property. Finally, the thick walls and highly aligned CMFs in the midrib and marginal cells of P. patens leaves are consistent with their support function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species that play a key role in the environmental consumption of methane across gradients of dioxygen tensions. In this work, we approached the question of howMethylobacter copes with hypoxia, via laboratory manipulation. Through comparative transcriptomics of cultures grown under high dioxygen partial pressure versus cultures exposed to hypoxia, we identified a gene cluster encoding a hybrid cluster protein along with sensing and regulatory functions. Through mutant analysis, we demonstrated that this gene cluster is involved in the hypoxia stress response. Through additional transcriptomic analyses, we uncovered a complex interconnection between the NO-mediated stress response, quorum sensing, the secondary metabolite tundrenone, and methanol dehydrogenase functions. This novel and complex hypoxia stress response system is so far unique to Methylobacter species, and it may play a role in the environmental fitness of these organisms and in their cosmopolitan environmental distribution.Here, we describe a novel and complex hypoxia response system in a methanotrophic bacterium that involves modules of central carbon metabolism, denitrification, quorum sensing, and a secondary metabolite, tundrenone. This intricate stress response system, so far unique to Methylobacter species, may be responsible for the persistence and activity of these species across gradients of dioxygen tensions and for the cosmopolitan distribution of these organisms in freshwater and soil environments in the Northern Hemisphere, including the fast-melting permafrosts.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Isolation and characterization of a novel gene sfig in rat skeletal muscle up-regulated by spaceflight (STS-90)

We obtained the skeletal muscle of rats exposed to weightless conditions during a 16-day-spaceflight (STS-90). By using a differential display technique, we identified 6 up-regulated and 3 down-regulated genes in the gastrocnemius muscle of the spaceflight rats, as compared to the ground control. The up-regulated genes included those coding Casitas B-lineage lymphoma-b, insulin growth factor binding protein-1, titin and mitochondrial gene 16 S rRNA and two novel genes (function unknown). The down-regulated genes included those encoding RNA polymerase II elongation factor-like protein, NADH dehydrogenase and one novel gene (function unknown). In the present study, we isolated and characterized one of two novel muscle genes that were remarkably up-regulated by spaceflight. The deduced amino acid sequence of the spaceflight-induced gene (sfig) comprises 86 amino acid residues and is well conserved from Drosophila to Homo sapiens. A putative leucine-zipper structure located at the N-terminal region of sfig suggests that this gene may encode a transcription factor. The up-regulated expression of this gene, confirmed by Northern blot analysis, was observed not only in the muscles of spaceflight rats but also in the muscles of tail-suspended rats, especially in the early stage of tail-suspension when gastrocnemius muscle atrophy initiated. The gene was predominantly expressed in the kidney, liver, small intestine and heart. When rat myoblastic L6 cells were grown to 100% confluence in the cell culture system, the expression of sfig was detected regardless of the cell differentiation state. These results suggest that spaceflight has many genetic effects on rat skeletal muscle.

STS-90 Shuttle Project↗
DOE OSTI2021

Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding

The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (O axis 2 ) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. In this work, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM–peptide complexes. O axis 2 of CaM in the ligand-free (O axis,U 2 ) and ligand-bound (O axis,B 2 ) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. ΔO axis 2 = O axis,B 2 – O axis,U 2 follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced O axis,U 2 → O axis,B 2 transition decreases with increasing magnitude of ΔO axis 2 , indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between ΔOaxis2 and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein–ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein–ligand binding.

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

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗
NASA NTRSDate not supplied

Engineering 6-Phosphogluconate Improves Grain Yield in Heat-Stressed Maize

Endosperm starch synthesis is a primary determinant of grain yield and is sensitive to high-temperature stress. The maize chloroplast-localized 6-phosphogluconate dehydrogenase (6PGDH), PGD3, is critical for endosperm starch accumulation. Maize also has two cytosolic isozymes, PGD1 and PGD2, that are not required for kernel development. We found that cytosolic PGD1 and PGD2 isozymes have heat-stable activity, while amyloplast-localized PGD3 activity is labile under heat stress conditions. We targeted heat-stable 6PGDH to endosperm amyloplasts by fusing the Waxy1 chloroplast targeting the peptide coding sequence to the Pgd1 and Pgd2 open reading frames (ORFs). These WPGD1 and WPGD2 fusion proteins import into isolated chloroplasts, demonstrating a functional targeting sequence. Transgenic maize plants expressing WPGD1 and WPGD2 with an endosperm-specific promoter increased 6PGDH activity with enhanced heat stability in vitro. WPGD1 and WPGD2 transgenes complement the pgd3-defective kernel phenotype, indicating the fusion proteins are targeted to the amyloplast. In the field, the WPGD1 and WPGD2 transgenes can mitigate grain yield losses in high-nighttime-temperature conditions by increasing kernel number. These results provide insight into the subcellular distribution of metabolic activities in the endosperm and suggest the amyloplast pentose phosphate pathway is a heat-sensitive step in maize kernel metabolism that contributes to yield loss during heat stress.

Synthetic Biology↗
DOE OSTI2020

Heterotrimeric G‐protein, Gi1, is involved in the regulation of proliferation, neuronal migration, and dendrite morphology during cortical development in vivo

Abstract Heterotrimeric G‐proteins are composed of α, β, and γ subunits, and function as signal transducers. Critical roles of the α‐subunits of Gi/o family heterotrimeric G‐proteins, Gαi2, and Gαo1, have so far been reported in brain development and neurodevelopmental disorders. In this study, we tried to clarify the role of Gαi1, α‐subunit of another Gi/o family member Gi1, during corticogenesis, based on the recent identification of its gene abnormalities in neurodevelopmental disorders. In western blot analyses, Gαi1 was found to be expressed in mouse brain in a developmental stage‐dependent manner. Morphological analyses revealed that Gαi1 was broadly distributed in cerebral cortex with relatively high expression in the ventricular zone (VZ) at embryonic day (E) 14. Meanwhile, Gαi1 was enriched in membrane area of yet unidentified early mitotic cells in the VZ and the marginal zone at E14. Acute knockdown of Gαi1 with in utero electroporation in cerebral cortex caused cell cycle elongation of the neural progenitor cells and promoted their cell cycle exit. Gαi1‐deficient cortical neurons also exhibited delayed radial migration during corticogenesis, with abnormally elongated leading processes and hampered nucleokinesis. In addition, silencing of Gαi1 prevented basal dendrite development. The migration and dendritic phenotypes were at least partially rescued by an RNAi‐resistant version of Gαi1. Collectively, these results strongly suggest a crucial role of Gi1 in cortical development, and disturbance of its function may cause deficits in synaptic network formation, leading to neurodevelopmental disorders. image

Hamada, Nanako↗
DOE OSTI2021

Bacterial effectors mimicking ubiquitin-proteasome pathway tweak plant immunity

Plant pathogenic Gram-negative bacteria evade the host plant immune system by secreting Type III (T3E) and Type IV effector (T4E) proteins into the plant cytoplasm. Mostly T3Es are secreted into the plant cells to establish pathogenicity by affecting the vital plant process viz. metabolic pathways, signal transduction and hormonal regulation. Ubiquitin-26S proteasome system (UPS) exists as one of the important pathways in plants to control plant immunity and various cellular processes by employing several enzymes and enzyme components. Pathogenic and non-pathogenic bacteria are found to secrete effectors into plants with structural and/or functional similarity to UPS pathway components like ubiquitin E3 ligases, F-box domains, cysteine proteases, inhibitor of host UPS or its components, etc. The bacterial effectors mimic UPS components and target plant resistance proteins for degradation by proteasomes, thereby taking control over the host cellular activities as a strategy to exert virulence. Thus, the bacterial effectors circumvent plant cellular pathways leading to infection and disease development. Finally, this review highlights known bacterial T3E and T4E proteins that function and interfere with the ubiquitination pathway to regulate the immune system of plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗
DOE OSTI2022

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

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

Probing substrate water access through the O1 channel of Photosystem II by single site mutations and membrane inlet mass spectrometry

Abstract Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO 2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn 4 CaO 5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated fromThermosynechococcus vestitus(T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn 4 CaO 5 cluster during its S 2 →S 3 and S 3 →S 4 →S 0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacteriumSynechocystis sp.PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitusnumbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn 4 CaO 5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn 4 CaO 5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

Plant Sciences↗
DOE OSTI2022

Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD

Serotonin (5-hydroxytryptamine [5-HT]) 5-HT2-family receptors represent essential targets for lysergic acid diethylamide (LSD) and all other psychedelic drugs. Although the primary psychedelic drug effects are mediated by the 5-HT 2A serotonin receptor (HTR2A), the 5-HT 2B serotonin receptor (HTR2B) has been used as a model receptor to study the activation mechanisms of psychedelic drugs due to its high expression and similarity to HTR2A. Here, in this study, we determined the cryo-EM structures of LSD-bound HTR2B in the transducer-free, Gq-protein-coupled, and β-arrestin-1-coupled states. These structures provide distinct signaling snapshots of LSD’s action, ranging from the transducer-free, partially active state to the transducer-coupled, fully active states. Insights from this study will both provide comprehensive molecular insights into the signaling mechanisms of the prototypical psychedelic LSD and accelerate the discovery of novel psychedelic drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Bioexcitons by Design: How Do We Get There?

Biological pigment-protein complexes (PPCs) exhibit a remarkable ability to tune the optical properties of biological excitons (bioexcitons) through specific pigment-protein interactions. While such fine-tuning allows natural systems (e.g., photosynthetic proteins) to carry out their native functions with near-optimal performance, native function itself is often suboptimal for applications such as biofuel production or quantum technology development. Furthermore, this perspective offers a look at near-term prospects for the rational reoptimization of PPC bioexcitons for new functions using site-directed mutagenesis. The primary focus is on the "structure-spectrum" challenge of understanding the relationships between structural features and spectroscopic properties. While recent examples demonstrate that site-directed mutagenesis can be used to tune nearly all key bioexciton parameters (e.g., site energies, inter-pigment couplings, and electronic-vibrational interactions), critical challenges remain before we achieve truly rational design of bioexciton properties.

09 BIOMASS FUELS↗
DOE OSTI2023

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗
DOE OSTI2022

Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology

Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Computational ranking identifies Plexin-B2 in circulating tumor cell clustering with monocytes in breast cancer metastasis

Abstract Multicellular circulating tumor cell (CTC) clusters can be up to 50 times more efficient than single CTCs in mediating viable metastasis. Here, combining computational ranking and functional determination, we identify the transmembrane protein Plexin-B2 (PLXNB2) as one of the top molecular targets associated with unfavorable distant metastasis-free survival, showing enriched expression in CTC clusters versus single CTCs from patients with advanced breast cancer (mostly female). Loss of PLXNB2 (Plxnb2) reduces the formation of homotypic tumor cell clusters and heterotypic tumor-myeloid cell clusters, reducing spontaneous metastases in female mice bearing human (mouse) breast cancer. Interactions of PLXNB2 with its ligands SEMA4C on tumor cells and SEMA4A on myeloid cells (monocytes) promote homotypic and heterotypic CTC cluster formation, respectively, thereby driving lung metastasis. Global proteomic analysis reveals downstream effectors of the PLXNB2 pathway associated with tumor cell clustering. Thus, PLXNB2 is a therapeutic target for preventing new metastasis in breast cancer.

Science & Technology - Other Topics↗