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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

Effects of Convective Asymmetries on Hurricane Intensity: A Numerical Study

The influence of the uniform large-scale flow, beta effect, and vertical shear of the environmental flow on hurricane intensity is investigated in the context of the induced convective or potential vorticity asymmetries with a hydrostatic primitive equation hurricane model. In agreement with the previous studies, imposing of one of these environmental effects can substantially weaken the simulated tropical cyclones. In response t o the environmental influence, significant asymmetries develop with a structure similar to the spiral bands in real hurricanes, which are dominated by wavenumber-one components. The tendencies of the mean radial, azimuthal winds and temperature associated with the environment-induced convective asymmetries are evaluated respectively. The resulting asymmetries can effectively reduce hurricane intensity by directly producing the negative tendency of the mean tangential wind in the vicinity of the radius of maximum wind, and by weakening the mean radial circulation. The reduction effects are closely associated with the spiral structure of the induced asymmetries. The time lag observed between the imposition of the environmental influence and the resulting rise in the minimum central pressure is the time required for developing the spiral structure. This study also confirms the axisymmetrization process associated with the induced wavenumber-one components of potential vorticity asymmetries, but it exists only within the radius of maximum wind.

Wu, Liguang↗
DOE OSTI2025

Interface-sensitive microwave loss in superconducting tantalum films sputtered on c-plane sapphire

Quantum coherence in superconducting circuits has increased steadily over the last decades because of a growing understanding of the various loss mechanisms. Recently, tantalum (Ta) emerged as a promising material to address microscopic sources of loss found on niobium (Nb) or aluminum (Al) surfaces. However, the effects of film and interface microstructure on low-temperature microwave loss are still not well understood. Here, in this study, we present a systematic study of the structural and electrical properties of Ta and Nb films sputtered on c-plane sapphire at varying growth temperatures. As growth temperature was increased, our results show that the onset of epitaxial growth of α -phase Ta correlates with lower Ta surface roughness, higher critical temperature, and higher residual resistivity ratio, but surprisingly also correlates with a significant increase in loss at microwave frequency. Notably, this high level of loss is not observed in Nb films prepared in the same way and having very similar structure. By experimentally controlling the surface on which the Ta film is nucleated, we determine that the source of loss was only present in samples having an epitaxial Ta/sapphire interface and show that it was apparently mitigated by either growing a thin, epitaxial Nb interlayer between the Ta film and the substrate or by intentionally treating, and effectively damaging, the sapphire surface with an in situ argon plasma before Ta growth. In addition to elucidating this interfacial microwave loss, this work provides adequate process details to aid reproducible growth of low-loss Ta films across fabrication facilities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues

Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues. These measurements were framed by atomistic molecular dynamic simulations to provide a complementary physical picture of the gas–polymer interface. Simulations and SFG measurements show that methacrylate backbones are buried beneath a layer of trifluoroethyl containing side groups that result in structurally similar interfaces regardless of the polymer molecular weight or architecture. The average orientational angles of the trifluoroethyl containing side groups differ depending on polymer linear and bottlebrush architectures, suggesting that the surface groups can reorient via available rotational degrees of freedom. Results show that the surfaces of the bottlebrush and linear polymer samples do not strongly depend on molecular weight or architecture. As such, one cannot rely on increasing the molecular weight or altering the architecture to tune surface properties. This insight into the polymer interfacial structure is expected to advance the design of new material interfaces with tailored chemical/functional properties.

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

Identification of Unique Fragmentation Patterns of Fentanyl Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry

The opioid crisis in the United States is being fueled by the rapid emergence of new fentanyl analogs and precursors that can elude traditional library-based screening methods, which require data from known reference compounds. Since reference compounds are unavailable for new fentanyl analogs, we examined if fentanyls (fentanyl + fentanyl analogs) could be identified in a reference-free manner using a combination of electrospray ionization (ESI), high-resolution ion mobility (IM) spectrometry, high-resolution mass spectrometry (MS), and higher-energy collision-induced dissociation (MS/MS). We analyzed a mixture containing nine fentanyls and W-15 (a structurally similar molecule) and found that the protonated forms of all fentanyls uniquely exhibited two baseline separated IM distributions that produced different MS/MS patterns. Upon fragmentation, both IM distributions of all fentanyls produced two high intensity fragments resulting from amine site cleavages. The higher mobility distributions of all fentanyls also produced several low intensity fragments, but surprisingly, these same fragments exhibited much greater intensities in the lower mobility distributions. This observation demonstrates that many fragments of fentanyls predominantly originate from one of two different gas-phase structures (suggestive of protomers). Furthermore, increasing the water concentration in the ESI solution increased the intensity of the lower mobility distribution relative to the higher mobility distribution, which further supports that fentanyls exist as two gas-phase protomers. In conclusion, our new observations on the IM and MS/MS properties of fentanyls can be exploited to positively identify them as fentanyls without requiring reference libraries and will hopefully assist first responders and law enforcement in combating new and emerging fentanyls.

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

Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains

Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)–to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. Furthermore, these results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.

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

Wintertime Arctic Oscillation and North Atlantic Oscillation and their impacts on the Northern Hemisphere climate in E3SM

The characteristics of the wintertime Arctic Oscillation (AO) and North Atlantic Oscillation (NAO) and their impacts on climate variability over the Northern Hemisphere are important metrics for evaluating a climate system model. Observational analyses reveal that the horizontal and vertical structures in the AO and NAO exhibit a meridional dipole and a large-scale barotropic pattern between the Arctic and mid-latitudes. Historical model simulations from the Energy Exascale Earth System Model (E3SM-HIST) are used to identify how well it captures these major climate modes. It is found that the simulated AO and NAO modes have spatial structures similar to the observed features. In addition, the observed frequency bands in the AO and NAO-related time variability are captured well in the E3SM-HIST simulation. Associated with the positive phase in wintertime AO and NAO, zonal flow and warm advection in mid-latitude continents are enhanced, along with stronger cold flow from enhanced northerly winds over high latitudes. These features are linked to the atmospheric circulation pattern reflected by lower SLP anomalies over the Arctic and higher SLP anomalies over the mid-latitudes. In E3SM-HIST, these spatial associations and main structural features are analogous to those in observations. In the time-height evolution related to winter AO and NAO modes, it can also be seen that the simulations reproduce the downward propagating patterns in observations. Nevertheless, the vertical structures associated with AO and NAO in E3SM-HIST exhibit substantial biases in the lower stratosphere. The cause of these stratospheric biases is investigated using the strength of climatological stratospheric polar vortex (SPV) and wave activity fluxes. The results herein suggest that E3SM-HIST has a reasonable skill in reproducing the observed characteristics related to the winter AO and NAO, although there exist systematic biases in the associated climate variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Chemical Recommender System: Replacement Suggestions for Small Molecules

The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.

Nair, Parthiv Anand [Sandia National Laboratories ↗
NASA NTRS1990

Characterization and distribution of a maize cDNA encoding a peptide similar to the catalytic region of second messenger dependent protein kinases

Maize (Zea mays) roots respond to a variety of environmental stimuli which are perceived by a specialized group of cells, the root cap. We are studying the transduction of extracellular signals by roots, particularly the role of protein kinases. Protein phosphorylation by kinases is an important step in many eukaryotic signal transduction pathways. As a first phase of this research we have isolated a cDNA encoding a maize protein similar to fungal and animal protein kinases known to be involved in the transduction of extracellular signals. The deduced sequence of this cDNA encodes a polypeptide containing amino acids corresponding to 33 out of 34 invariant or nearly invariant sequence features characteristic of protein kinase catalytic domains. The maize cDNA gene product is more closely related to the branch of serine/threonine protein kinase catalytic domains composed of the cyclic-nucleotide- and calcium-phospholipid-dependent subfamilies than to other protein kinases. Sequence identity is 35% or more between the deduced maize polypeptide and all members of this branch. The high structural similarity strongly suggests that catalytic activity of the encoded maize protein kinase may be regulated by second messengers, like that of all members of this branch whose regulation has been characterized. Northern hybridization with the maize cDNA clone shows a single 2400 base transcript at roughly similar levels in maize coleoptiles, root meristems, and the zone of root elongation, but the transcript is less abundant in mature leaves. In situ hybridization confirms the presence of the transcript in all regions of primary maize root tissue.

NASA Program Space Biology↗
DOE OSTI2025

AAPM Truth‐based CT (TrueCT) reconstruction grand challenge

Background: This Special Report summarizes the 2022, AAPM grand challenge on Truth-based CT image reconstruction. Purpose: To provide an objective framework for evaluating CT reconstruction methods using virtual imaging resources consisting of a library of simulated CT projection images of a population of human models with various diseases. Methods: Two hundred unique anthropomorphic, computational models were created with varied diseases consisting of 67 emphysema, 67 lung lesions, and 66 liver lesions. The organs were modeled based on clinical CT images of real patients. The emphysematous regions were modeled using segmentations from patient CT cases in the COPDGene Phase I dataset. For the lung and liver lesion cases, 1–6 malignant lesions were created and inserted into the human models, with lesion diameters ranging from 5.6 to 21.9 mm for lung lesions and 3.9 to 14.9 mm for liver lesions. The contrast defined between the liver lesions and liver parenchyma was 82 ± 12 HU, ranging from 50 to 110 HU. Similarly, the contrast between the lung lesions and the lung parenchyma was defined as 781 ± 11 HU, ranging from 725 to 805 HU. For the emphysematous regions, the defined HU values were −950 ± 17 HU ranging from −918 to −979 HU. The developed human models were imaged with a validated CT simulator. The resulting CT sinograms were shared with the participants. The participants reconstructed CT images from the sinograms and sent back their reconstructed images. Further, the reconstructed images were then scored by comparing the results against the corresponding ground truth values. The scores included both task-generic (root mean square error [RMSE] and structural similarity matrix [SSIM]), and task-specific (detectability index [d’] and lesion volume accuracy) metrics. For the cases with multiple lesions, the measured metric was averaged across all the lesions. To combine the metrics with each other, each metric was normalized to a range of 0 to 1 per disease type, with “0” and “1” being the worst and best measured values across all cases of the disease type for all received reconstructions. Results: The True-CT challenge attracted 52 participants, out of which 5 successfully completed the challenge and submitted the requested 200 reconstructions. Across all participants and disease types, SSIM absolute values ranged from 0.22 to 0.90, RMSE from 77.6 to 490.5 HU, d’ from 0.1 to 64.6, and volume accuracy ranged from 1.2 to 753.1 mm3. The overall scores demonstrated that participant “A” had the best performance in all categories, except for the metrics of d’ for lung lesions and RMSE for liver lesions. Participant “A” had an average normalized score of 0.41 ± 0.22, 0.48 ± 0.32, and 0.42 ± 0.33 for the emphysema, lung lesion, and liver lesion cases, respectively. Conclusions: The True-CT challenge successfully enabled objective assessment of CT reconstructions with the unique advantage of access to a diverse population of diseased human models with known ground truth. This study highlights the significant potential of virtual imaging trials in objective assessment of medical imaging technologies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

First Resolved Scattered-light Images of Four Debris Disks in Scorpius-Centaurus with the Gemini Planet Imager

In this work, we present the first spatially resolved scattered-light images of four debris disks around members of the Scorpius-Centaurus (Sco-Cen) OB association with high-contrast imaging and polarimetry using the Gemini Planet Imager (GPI). All four disks are resolved for the first time in polarized light, and one disk is also detected in total intensity. The three disks imaged around HD 111161, HD 143675, and HD 145560 are symmetric in both morphology and brightness distribution. The three systems span a range of inclinations and radial extents. The disk imaged around HD 98363 shows indications of asymmetries in morphology and brightness distribution, with some structural similarities to the HD 106906 planet–disk system. Uniquely, HD 98363 has a wide comoving stellar companion, Wray 15-788, with a recently resolved disk with very different morphological properties. HD 98363 A/B is the first binary debris disk system with two spatially resolved disks. All four targets have been observed with ALMA, and their continuum fluxes range from one nondetection to one of the brightest disks in the region. With the new results, a total of 15 A/F stars in Sco-Cen have resolved scattered-light debris disks, and approximately half of these systems exhibit some form of asymmetry. Combining the GPI disk structure results with information from the literature on millimeter fluxes and imaged planets reveals a diversity of disk properties in this young population. Overall, the four newly resolved disks contribute to the census of disk structures measured around A/F stars at this important stage in the development of planetary systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

The ChiS-Family DNA-Binding Domain Contains a Cryptic Helix-Turn-Helix Variant

Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Structure and dynamics of the Arizona monsoon boundary

The structure and dynamics of the Arizona monsoon boundary, defined as the boundary separating two distinctly different air masses over Mexico and the adjacent Pacific during the summer, are analyzed. The cross-sectional analysis was based on the following three data sources: a composite cross section through the boundary, constructed from the Fleet Numerical Oceanography Center analysis for 1985; a time-height cross section, obtained using radiosonde observations at the time the boundary passed through Tucson in 1984; and a cross section through the boundary of July 22, 1985, using high-resolution fields of temperature, moisture, and geopotential height obtained from the VISSR Atmospheric Sounder. All three sources yielded similar structure, showing that the Arizona monsoon boundary resembles a midlatitude front forced almost entirely by confluence. The possible role this frontlike system may play in the development of disturbances in the southwestern United States during summer is discussed.

Adang, Thomas C.↗
DOE OSTI2023

Phonon mixing in the charge density wave state of ScV6Sn6

Abstract Kagomé metals are widely recognized, versatile platforms for exploring topological properties, unconventional electronic correlations, magnetic frustration, and superconductivity. In the R V 6 Sn 6 family of materials ( R = Sc, Y, Lu), ScV 6 Sn 6 hosts an unusual charge density wave ground state as well as structural similarities with the A V 3 Sb 5 system ( A = K, Cs, Rb). In this work, we combine Raman scattering spectroscopy with first-principles lattice dynamics calculations to reveal phonon mixing processes in the charge density wave state of ScV 6 Sn 6 . In the low temperature phase, we find at least four new peaks in the vicinity of the V-containing totally symmetric mode near 240 cm −1 suggesting that the density wave acts to mix modes of P 6/ m m m and $$R\bar{3}m$$ R 3 ¯ m symmetry - a result that we quantify by projecting phonons of the high symmetry state onto those of the lower symmetry structure. We also test the stability of the short-range ordered density wave state under compression and propose that both physical and chemical pressure quench the effect. We discuss these findings in terms of symmetry and the structure-property trends that can be unraveled in this system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Subaru Near-infrared Imaging Polarimetry of Misaligned Disks around the SR 24 Hierarchical Triple System

The SR 24 multistar system hosts both circumprimary and circumsecondary disks, which are strongly misaligned with each other. The circumsecondary disk is circumbinary in nature. Interestingly, both disks are interacting, and they possibly rotate in opposite directions. To investigate the nature of this unique twin disk system, we present 0.″1 resolution near-infrared polarized intensity images of the circumstellar structures around SR 24, obtained with HiCIAO mounted on the Subaru 8.2 m telescope. Both the circumprimary disk and the circumsecondary disk are resolved and have elongated features. While the position angle of the major axis and radius of the near-IR (NIR) polarization disk around SR 24S are 55° and 137 au, respectively, those around SR 24N are 110° and 34 au, respectively. With regard to overall morphology, the circumprimary disk around SR 24S shows strong asymmetry, whereas the circumsecondary disk around SR 24N shows relatively strong symmetry. Our NIR observations confirm the previous claim that the circumprimary and circumsecondary disks are misaligned from each other. Both the circumprimary and circumsecondary disks show similar structures in {sup 12}CO observations in terms of its size and elongation direction. This consistency is because both NIR and {sup 12}CO are tracing surface layers of the flared disks. As the radius of the polarization disk around SR 24N is roughly consistent with the size of the outer Roche lobe, it is natural to interpret the polarization disk around SR 24N as a circumbinary disk surrounding the SR 24Nb–Nc system.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2019

Subaru Near-Infrared Imaging Polarimetry of Misaligned Disks Around the SR 24 Hierachical Triple System

The SR 24 multistar system hosts both circumprimary and circumsecondary disks, which are strongly misaligned with each other. The circumsecondary disk is circumbinary in nature. Interestingly, both disks are interacting, and they possibly rotate in opposite directions. To investigate the nature of this unique twin disk system, we present 0.″1 resolution near-infrared polarized intensity images of the circumstellar structures around SR 24, obtained with HiCIAO mounted on the Subaru 8.2 m telescope. Both the circumprimary disk and the circumsecondary disk are resolved and have elongated features. While the position angle of the major axis and radius of the near-IR (NIR) polarization disk around SR 24S are 55° and 137 au, respectively, those around SR 24N are 110° and 34 au, respectively. With regard to overall morphology, the circumprimary disk around SR 24S shows strong asymmetry, whereas the circumsecondary disk around SR 24N shows relatively strong symmetry. Our NIR observations confirm the previous claim that the circumprimary and circumsecondary disks are misaligned from each other. Both the circumprimary and circumsecondary disks show similar structures in 12CO observations in terms of its size and elongation direction. This consistency is because both NIR and 12CO are tracing surface layers of the flared disks. As the radius of the polarization disk around SR 24N is roughly consistent with the size of the outer Roche lobe, it is natural to interpret the polarization disk around SR 24N as a circumbinary disk surrounding the SR 24Nb─Nc system.

Satoshi Mayama↗
NASA NTRS1992

Protein changes associated with reprotonation of the Schiff base in the photocycle of Asp96-->Asn bacteriorhodopsin. The MN intermediate with unprotonated Schiff base but N-like protein structure

The difference Fourier transform infrared spectrum for the N intermediate in the photoreaction of the light-adapted form of bacteriorhodopsin can be recorded at pH 10 at 274 K (Pfefferle, J.-M., Maeda, A., Sasaki, J., and Yoshizawa, T. (1991) Biochemistry 30, 6548-6556). Under these conditions, Asp96-->Asn bacteriorhodopsin gives a photoproduct which shows changes in protein structure similar to those observed in N of wild-type bacteriorhodopsin. However, decreased intensity of the chromophore bands and the single absorbance maximum at about 400 nm indicate that the Schiff base is unprotonated, as in the M intermediate. This photoproduct was named MN. At pH 7, where the supply of proton is not as restricted as at pH 10, Asp96-->Asn bacteriorhodopsin yields N with a protonated Schiff base. The Asn96 residue, which cannot deprotonate as Asp96 in wild-type bacteriorhodopsin, is perturbed upon formation of both MN at pH 10 and N at pH 7. We suggest that the reprotonation of the Schiff base is preceded by a large change in the protein structure including perturbation of the residue at position 96.

Non-NASA Center↗
DOE OSTI2022

Mechanism of the cadherin–catenin F-actin catch bond interaction

Mechanotransduction at cell–cell adhesions is crucial for the structural integrity, organization, and morphogenesis of epithelia. At cell–cell junctions, ternary E-cadherin/β-catenin/αE-catenin complexes sense and transmit mechanical load by binding to F-actin. The interaction with F-actin, described as a two-state catch bond, is weak in solution but is strengthened by applied force due to force-dependent transitions between weak and strong actin-binding states. Here, we provide direct evidence from optical trapping experiments that the catch bond property principally resides in the αE-catenin actin-binding domain (ABD). Consistent with our previously proposed model, the deletion of the first helix of the five-helix ABD bundle enables stable interactions with F-actin under minimal load that are well described by a single-state slip bond, even when αE-catenin is complexed with β-catenin and E-cadherin. Our data argue for a conserved catch bond mechanism for adhesion proteins with structurally similar ABDs. We also demonstrate that a stably bound ABD strengthens load-dependent binding interactions between a neighboring complex and F-actin, but the presence of the other αE-catenin domains weakens this effect. These results provide mechanistic insight to the cooperative binding of the cadherin–catenin complex to F-actin, which regulate dynamic cytoskeletal linkages in epithelial tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quantifying T Cell Cross-Reactivity: Influenza and Coronaviruses

If viral strains are sufficiently similar in their immunodominant epitopes, then populations of cross-reactive T cells may be boosted by exposure to one strain and provide protection against infection by another at a later date. This type of pre-existing immunity may be important in the adaptive immune response to influenza and to coronaviruses. Patterns of recognition of epitopes by T cell clonotypes (a set of cells sharing the same T cell receptor) are represented as edges on a bipartite network. We describe different methods of constructing bipartite networks that exhibit cross-reactivity, and the dynamics of the T cell repertoire in conditions of homeostasis, infection and re-infection. Cross-reactivity may arise simply by chance, or because immunodominant epitopes of different strains are structurally similar. We introduce a circular space of epitopes, so that T cell cross-reactivity is a quantitative measure of the overlap between clonotypes that recognize similar (that is, close in epitope space) epitopes.

59 BASIC BIOLOGICAL SCIENCES↗