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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Out of the Dark and Into the Light: A New View of Phytochrome Photobodies

Light is a critical environmental stimulus for plants, serving as an energy source via photosynthesis and a signal for developmental programming. Plants perceive light through various light-responsive proteins, termed photoreceptors. Phytochromes are red-light photoreceptors that are highly conserved across kingdoms. In the model plant Arabidopsis thaliana , phytochrome B serves as a light and thermal sensor, mediating physiological processes such as seedling germination and establishment, hypocotyl growth, chlorophyll biogenesis, and flowering. In response to red light, phytochromes convert to a biologically active form, translocating from the cytoplasm into the nucleus and further compartmentalizes into subnuclear compartments termed photobodies. PhyB photobodies regulate phytochrome-mediated signaling and physiological outputs. However, photobody function, composition, and biogenesis remain undefined since their discovery. Based on photobody cellular dynamics and the properties of internal components, photobodies have been suggested to undergo liquid-liquid phase separation, a process by which some membraneless compartments form. Here, we explore photobodies as environmental sensors, examine the role of their protein constituents, and outline the biophysical perspective that photobodies may be undergoing liquid-liquid phase separation. Understanding the molecular, cellular, and biophysical processes that shape how plants perceive light will help in engineering improved sunlight capture and fitness of important crops.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein–water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ~0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Influence of the irradiated pulmonary microenvironment on macrophage and T cell dynamics

The lung is sensitive to radiation, which increases the risk of normal tissue toxicity following radiation therapy. Adverse outcomes include pneumonitis and pulmonary fibrosis, which are thought to result from dysregulated intercellular communication within the pulmonary microenvironment. Macrophage accumulation in the lung following radiation exposure is implicated in these pathogenic outcomes. Here we investigate the role of the microenvironment in macrophage and T cell dynamics. Materials and methods C57Bl/6 mice received 6Gyx5 x-ray irradiation to the right lung. Macrophage and T cell dynamics were investigated in ipsilateral right lungs, contralateral left lungs and compared to those from non-irradiated control subjects at 4-26wk post exposure. Lungs were evaluated by flow cytometry, histology and proteomics. Results In uni-lung irradiated subjects, focal regions of macrophage accumulation were noted in both lungs by 8wk, however fibrotic lesions were observed only in ipsilateral lungs by 26wk. Both infiltrating and alveolar macrophages populations transiently expanded in both lungs, however a transitional CD11b+ alveolar macrophage population persisted only in ipsilateral lungs and expressed lower CD206. Concurrently, arginase-1+ macrophages were noted within areas of macrophage accumulation in ipsilateral but not contralateral lungs at 8 and 26wk post exposure, while CD206+ macrophages were absent from these accumulations. While CD8+ T cells were present in both lungs of irradiated subjects, T regulatory cells were only increased in ipsilateral lungs. Unbiased proteomics analysis of immune cells revealed a substantial number of differentially expressed proteins in ipsilateral lungs when compared to either contralateral or non-irradiated lungs, as well as between contralateral lungs from irradiated subjects and non-irradiated controls. Conclusions Pulmonary macrophage and T cell dynamics are impacted by the microenvironmental conditions that develop in the lung following radiation exposure, both locally and systemically. Our findings demonstrate that while macrophages and T cells infiltrate and expand in both lungs, they diverge phenotypically depending on their environment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Solvent Mediated Excited State Proton Transfer in Indigo Carmine

Excited state proton transfer (ESPT) is thought to be responsible for the photostability of biological molecules, including DNA and proteins, and natural dyes such as indigo. However, the mechanistic role of the solvent interaction in driving ESPT is not well understood. Here, the electronic excited state deactivation dynamics of indigo carmine (InC) is mapped by visible pump-infrared probe and two-dimensional electronic-vibrational (2DEV) spectroscopy and complemented by electronic structure calculations. The observed dynamics reveal notable differences between InC in a protic solvent, D$_2$O , and an aprotic solvent, deuterated dimethyl sulfoxide (dDMSO). Notably, an acceleration in the excited state decay is observed in D$_2$O (<10 ps) compared to dDMSO (130 ps). Our data reveals clear evidence for ESPT in D$_2$O accompanied by a significant change in dipole moment, which is found not to occur in dDMSO. We conclude that the ability of protic solvents to form intermolecular H-bonds with InC enables ESPT, which facilitates a rapid nonradiative S$_1$ → S$_0$ transition via the monoenol intermediate.

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

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

State-dependent motion of a genetically encoded fluorescent biosensor

Genetically encoded biosensors can measure biochemical properties such as small-molecule concentrations with single-cell resolution, even in vivo. Despite their utility, these sensors are “black boxes”: Very little is known about the structures of their low- and high-fluorescence states or what features are required to transition between them. We used LiLac, a lactate biosensor with a quantitative fluorescence-lifetime readout, as a model system to address these questions. X-ray crystal structures and engineered high-affinity metal bridges demonstrate that LiLac exhibits a large interdomain twist motion that pulls the fluorescent protein away from a “sealed,” high-lifetime state in the absence of lactate to a “cracked,” low-lifetime state in its presence. Understanding the structures and dynamics of LiLac will help to think about and engineer other fluorescent biosensors.

Rosen, Paul C. (ORCID:000000017414454X)↗
DOE OSTI2021

No ordinary proteins: Adsorption and molecular orientation of monoclonal antibodies

The interaction of monoclonal antibodies (mAbs) with air/water interfaces plays a crucial role in their overall stability in solution. We aim to understand this behavior using pendant bubble measurements to track the dynamic tension reduction and x-ray reflectivity to obtain the electron density profiles (EDPs) at the surface. Native immunoglobulin G mAb is a rigid molecule with a flat, “Y” shape, and simulated EDPs are obtained by rotating a homology construct at the surface. Comparing simulations with experimental EDPs, we obtain surface orientation probability maps showing mAbs transition from flat-on Y-shape configurations to side-on or end-on configurations with increasing concentration. The modeling also shows the presence of β sheets at the surface. Overall, the experiments and the homology modeling elucidate the orientational phase space during different stages of adsorption of mAbs at the air/water interface. These finding will help define new strategies for the manufacture and storage of antibody-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Lipid Droplets: Packing Hydrophobic Molecules Within the Aqueous Cytoplasm

Lipid droplets, also known as oil bodies or lipid bodies, are plant organelles that compartmentalize neutral lipids as a hydrophobic matrix covered by proteins embedded in a phospholipid monolayer. Some of these proteins have been known for decades, such as oleosins, caleosins, and steroleosins, whereas a host of others have been discovered more recently with various levels of abundance on lipid droplets, depending on the tissue and developmental stage. In addition to a growing inventory of lipid droplet proteins, the subcellular machinery that contributes to the biogenesis and degradation of lipid droplets is being identified and attention is turning to more mechanistic questions regarding lipid droplet dynamics. While lipid droplets are mostly regarded as storage deposits for carbon and energy in lipid-rich plant tissues such as seeds, these organelles are present in essentially all plant cells, where they display additional functions in signaling, membrane remodeling, and the compartmentalization of a variety of hydrophobic components. Remarkable metabolic engineering efforts have demonstrated the plasticity of vegetative tissues such as leaves to synthesize and package large amounts of storage lipids, which enable future applications in bioenergy and the engineering of high-value lipophilic compounds. Here, we review the growing body of knowledge about lipid droplets in plant cells, describe the evolutionary similarity and divergence in their associated subcellular machinery, and point to gaps that deserve future attention.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Closed-loop control of active nematic flows

Stabilizing and shaping autonomous flows of active fluids is a fundamental challenge and a prerequisite for applications. We embed a light-responsive microtubule-based nematic in a proportional-integral control loop that adjusts the applied light intensity in response to real-time measurements of the spatially averaged flow speed. The self-regulating hardware/software/wetware system maintains a target flow speed against external or internal perturbations, including protein aging and aggregation, sample-to-sample variability, and temperature variation. Varying the controller’s gains reveals antagonistic roles between feedback and intrinsic processes, leading to nontrivial dynamics observed in fluctuation spectra. In particular, oscillations emerge from the interplay between the controller, motor binding kinetics, and active hydrodynamic relaxation. Accounting for the underlying binding timescale, our coarse-grained model and nematohydrodynamics simulations corroborate these observations. This work provides insight into the coupled dynamics of controlled active matter, laying the foundation for spatiotemporal patterning of active stress to generate and stabilize new dynamical configurations.

Nishiyama, Katsu [Brandeis Univ., Waltham, MA (Uni↗
DOE OSTI2021

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus

The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here, in this work, we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution, which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This “inversion” is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP ⁢1⁢𝛼-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.

biomolecular & subcellular processes↗
DOE OSTI2021

Condensed Phase Water Molecular Multipole Moments from Deep Neural Network Models Trained on Ab Initio Simulation Data

Ionic solvation phenomena in liquids involve intense interactions in the inner solvation shell. For interactions beyond the first shell, the ion–solvent interaction energies result from the sum of many smaller-magnitude contributions that can still include polarization effects. Deep neural network (DNN) methods have recently found wide application in developing efficient molecular models that maintain near-quantum accuracy. In this work, we extend the DeePMD-kit code to produce accurate molecular multipole moments in the bulk and near interfaces. The new method is validated by comparing the DNN moments with those generated by ab initio simulations. The moments are used to compute the electrostatic potential at the center of a molecular-sized hydrophobic cavity in water. The results show that the fields produced by the DNN models are in quantitative agreement with the AIMD-derived values. These efficient methods will open the door to more accurate solvation models for large solutes such as proteins.

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

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗
DOE OSTI2022

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗
DOE OSTI2025

Enhancing chemical bioproduction with rational control of bacterial post-translational modifications

Efficient conversion of inexpensive feedstocks to valuable chemicals by microbes is critical for a robust bioeconomy, but the ability to rationally design bacteria is hampered by insufficient knowledge of how post translational modifications (PTMs) control bacterial protein function and thus bioproduction phenotypes. Our study will focus on the lysine acetylation, a ubiquitous bacterial PTM that can affect the function of enzymes in central metabolism that are often critical for bioproduction processes, disrupt transcriptional regulation, and reduce translation. However, most lysine acetylation data is observational, which means that we do not know when, how, and what specific acetylated residues affect protein function and bacterial physiology. For our model host, we will use a Pseudomonas putida strain that we previously engineered to convert lignocellulosic feedstocks into chemicals such as itaconic acid (ITA). With this strain, we use a dynamic two-stage bioproduction process in which ITA is produced during a non-growth associated production phase. Production is highest during growth stages when lysine acetylation is low in other organisms (early stationary phase) and stalls in conditions where acetylation is highest (late stationary phase). The switch from high to stalled ITA production is also correlated with an unexpected increase in acetate levels – the precursor to non-enzymatic lysine acetylation. As such, we predict that lysine acetylation plays a substantial role in regulating the metabolic pathways required for ITA production. We will develop a generalizable approach that combines high-throughput genetic screens and cutting-edge genome engineering with state-of-the-art proteomics, metabolomics, and genetic code expansion methods to identify and modulate lysine acetylation patterns in bacteria. Ultimately, these strategies aim to manipulate protein expression and acetylation patterns to enhance bioproduction phenotypes (e.g., sustained ITA production in late stationary phase).

60 APPLIED LIFE SCIENCES↗