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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Zhao, Yanyan (ORCID:0000000323021763)↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
DOE OSTI2025

Carbon Storage in Fold‐and‐Thrust Belts: An Overlooked Gigatonne Storage Opportunity

This study presents numerical investigations of the trapping characteristics of fold-and-thrust belt structures, defining three carbon capture and storage (CCS) play types that could be used to store commercial volumes (millions of tonnes) of CO 2 . Specifically, we present simulations of CO 2 storage in three fold-and-thrust belt models comprising a thrust-ramp, duplex, and thrust-fold geometry. To constrain these play types in realistic geology, each model is based on a study site, including a novel investigation of a greenfield saline reservoir in Virginia, USA, being considered for commercial carbon storage and two well-characterized petroleum fields: the Wilburton field in Oklahoma, USA, and the Incahuasi field in Bolivia. Our results provide insight into several key parameters, such as the long-term security of injected CO 2 in these geologies and injection strategies for maximizing storage efficiency while reducing pressure-related risk. These results improve the understanding of CCS in fold-and-thrust belt storage sites globally by describing general storage parameters that may be applied to site-specific projects. We find that thrust-ramp geometries may securely trap CO 2 through solubility and hydrodynamic trapping under suitable reservoir conditions, duplex structures may store some quantities of CO 2 but are pressure-constrained, and that thrust-ramp structures may store large quantities of CO 2 by maximizing fetch volume, which simultaneously lowers geomechanical risk by reducing pressure buildup along zones of weakness.

42 ENGINEERING↗
DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗
DOE OSTI2025

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

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

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗
DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Atomic-Scale Dynamics of Five-Fold Twin Mediated Coalescence: Pathway-Dependent and Defect-Governed Nonclassical Growth Mechanisms

Defective crystals with distinct properties have been discovered in many systems. However, the growth mechanism of defective crystals is still poorly understood. Here, in this work, using a 5-fold twinned gold (Au) nanocrystal (NC) as a model system, three new coalescence pathways involving detwinning or twinning have been uncovered through atomic-scale dynamic observations in an aberration-corrected transmission electron microscope coupled with atomistic simulations. This demonstrates that beyond crystal size, coalescence growth dynamics involving 5-fold twins (5-FTs) are highly dependent on crystal defect density and the approach pathways of the crystals. When a 5-FT encounters a smaller 5-FT or a smaller NC in a face-to-face way, a new, larger 5-FT is produced at a relatively fast coalescence growth rate; while in a corner-to-corner way, the coalescence dynamics are more retarded and sluggish, which is conducive to the formation of complex multitwined structures rather than 5-FTs. This highlights that the planar defect density and crystal approach pathway influence the coalescence dynamics of crystals containing 5-FT. Moreover, a column-by-column grain boundary (GB) migration mechanism, which results in bent GBs, was also unveiled during the crystal coalescence process. These results enrich the general understanding of the crystal growth theory and provide new insights into the controllable fabrication of 5-FTs by crystal coalescence mechanisms.

crystallization↗
DOE OSTI2025

Designing Peptide Fossils That Model the Evolution of the Bacterial Ferredoxin Fold

Electron transfer coupled to redox chemistry is at the heart of metabolism. The proteins responsible for moving electrons (protein electron carriers) must have emerged at the origin of life. The small iron–sulfur-binding bacterial ferredoxins were likely among these first proteins. Embedded within the ferredoxin sequence and structure is a symmetry that points to an ancient gene duplication event. Little is understood about the nature of ferredoxins prior to this duplication event or what environmental factors may have driven the selection for more complex forms. The deep-time molecular history of ferredoxins goes back billions of years and cannot be reconstructed by phylogenetic analyses based on amino acid sequences. Here, we use structure-guided protein design to model a fossil half-ferredoxin stage in the evolution of this fold, the semidoxins, and their symmetric full-length counterparts, the symdoxins. Semidoxin designs homodimerize, exhibiting structural, thermodynamic, and electrochemical behaviors in most cases identical to cognate symdoxins. However, the semi- and symdoxin fossil stages behave differently when incorporated into an in vivo electron transfer complementation assay. Both can support bacterial growth dependent on protein expression. Growth rates of bacteria expressing the semidoxins are much more sensitive to oxygen than those of bacteria expressing symdoxins. Motivated by the in vivo functionality of designed semidoxins, we identified putative naturally occurring semidoxins in extant anaerobic microorganisms. This is consistent with the observed in vivo oxygen sensitivity of the semidoxin designs. One natural semidoxin is shown to be folded and redox active. However, it exists as a mixture of monomers and dimers, suggesting a potential connection between semidoxins and even simpler single iron–sulfur cluster-binding peptides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exotic edge states of C 3 high-fold fermions in honeycomb lattices

A generalization of the graphene honeycomb model to the case where each site in the honeycomb lattice contains a n -fold degenerate set of eigenstates of the C 3 symmetry has been recently proposed to describe several systems, including triangulene crystals and photonic lattices. These generalized honeycomb models are defined by ( n a , n b ) , the number of C 3 eigenstates in the a and b sites of the unit cell, resulting in n a + n b bands. Thus, the (1,1) case gives the coventional honeycomb model that describes the two low-energy bands in graphene. Generalizations, such as (2,1), (2,2), and (3,3) display several nontrivial features, such as coexisting graphenelike Dirac cones with flat bands, both at zero and finite energy, as well as robust degeneracy points where a flat band and a parabolic band meet at the Γ point. Here we explore the edge states of this class of crystals, using as reference triangulene crystals, and we find several types of edge states absent in the conventional (1,1) honeycomb case, associated to the nontrivial features of the two-dimensional bands of the high-fold case. First, we find dispersive edge states associated to the finite-energy flat bands, that occur both at the armchair and zigzag termination. Second, in the case of noncentrosymmetric triangulene crystals that lead to a S = 1 Dirac band, we have a bonding-antibonding pair of dispersive edge states, localized in the same edge so that their energy splitting is reduced as their localization increases, opposite to the conventional behavior of pairs of states localized in opposite edges. Third, for the (3,3) case, that hosts a gap separating a pair of flat conduction and valence bands, we find nondispersive edge states with E = 0 in all edge terminations. Published by the American Physical Society 2024

Madail, L. (ORCID:0000000208457748)↗
DOE OSTI2025

Unaccounted-for look-elsewhere effect in k-fold cross adaptive anomaly searches

Recently a technique based on k-fold cross validation has become popular in anomaly detection in HEP, as a way to search for a wide class of anomalies in the data, without paying an associated penalty in sensitivity-depth. In this work, we point out that the breadth-depth tradeoff is an unavoidable aspect of anomaly detection, and cannot be overcome using the aforementioned k-fold cross adaptive search technique. Furthermore, we show that the technique leads to unaccounted-for look elsewhere effect, i.e., the underestimation of p-values or the overestimation of significances of observed anomalies.

Shyamsundar, Prasanth [Fermilab]↗
DOE OSTI2025

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Disordered hydrogen adsorption at the three-fold site of W(110)

Hydrogen often forms disordered phases on metals; however, deciphering the atomic-scale behavior requires experimental and modeling techniques that directly probe the short-range order between neighboring hydrogen adsorbates. Here, to address this challenge, we applied direct recoil spectroscopy (DRS) to investigate hydrogen adsorption on the W(110) surface. We show that the recoiled hydrogen flux measured during DRS is sensitive to the short range order of the adsorbed hydrogen. Ordered hydrogen neighbors are much more efficient at dechanneling incident ions along low-index surface channels, strongly suppressing the recoiled hydrogen flux along these directions. By modeling the DRS measurements with molecular dynamics for ordered and disordered hydrogen phases, we find that at a hydrogen surface coverage of approximately Θ = 0.6, the hydrogen adsorbates are bound to three-fold sites in a disordered phase at room temperature. This finding is consistent with transfer-matrix scaling model calculations that suggest the transition to an ordered hydrogen phase occurs at a greater surface coverage of Θ = 0.83.

08 HYDROGEN↗
DOE OSTI2026

Noncanonical folding of peptoid oligomers: Formation of a closed conformation in nonpolar solvent

Peptoids provide a versatile platform for foldamer design, yet their conformational behavior in low-dielectric media remains poorly understood. The structural characteristics of N-1-phenylethylglycine (Nspe) homo-oligomers were inves-tigated in chloroform, a solvent that mimics the interior of lipid bilayers, using nuclear magnetic resonance (NMR) spec-troscopy and molecular dynamics (MD) simulations. Nspe7 populated two distinct compact conformations, while Nspe10 adopted a single homogeneous conformation related to the previously reported Nspe9 threaded-loop structure. Integrated experimental and computational analysis reveals that these structures are stabilized by cooperative end-to-end intramo-lecular hydrogen bonding, cis-trans backbone isomerism, and hydrophobic side-chain shielding. The resulting structures minimize exposed polar surface area, demonstrating a closed conformation in the low-dielectric environment. These find-ings establish specific chain-length requirements for achieving well-defined closed conformations. This work provides insights into peptoid folding in nonpolar media, enabling rational design strategies for solvent-directed conformational switching systems.

Oh, Jinyoung↗
DOE OSTI2024

Asymmetric fluctuations and self-folding of active interfaces

We study the structure and dynamics of the interface separating a passive fluid from a microtubule-based active fluid. Turbulent-like active flows power giant interfacial fluctuations, which exhibit pronounced asymmetry between regions of positive and negative curvature. Experiments, numerical simulations, and theoretical arguments reveal how the interface breaks up the spatial symmetry of the fundamental bend instability to generate local vortical flows that lead to asymmetric interface fluctuations. The magnitude of interface deformations increases with activity: In the high activity limit, the interface self-folds invaginating passive droplets and generating a foam-like phase, where active fluid is perforated with passive droplets. These results demonstrate how active stresses control the structure, dynamics, and break-up of soft, deformable, and reconfigurable liquid–liquid interfaces.

active fluid↗
DOE OSTI2026

Instant folded strings, dark energy and a cyclic bouncing universe

We present a wholly self-consistent, complete cyclic bouncing cosmology based on components drawn from string theory and constructed in a way that is under perturbative control throughout (e.g., with temperature much less than the string scale and string coupling g s ≪ 1 at all times). The cyclic evolution is governed by standard dilaton-gravity in (3+1)-dimensions with a perturbatively generated potential and a coupling between the dilaton and a second field that becomes massless at ϕ = ϕ ESP , resulting in an enhanced symmetry point (ESP) that prevents the dilaton from running all the way to zero coupling. A central role is played by instant folded strings (IFSs) — fundamental strings with the unusual property of being much lighter than the string mass while extending far beyond the string length, and violating the Null Energy Condition (NEC). IFSs are produced classically when the string coupling grows with time, which occurs at two critical points in each cycle. In turn, they fulfill a dual function: Enabling cosmological bounces and initiating transient epochs of dark-energy domination that naturally transition into slow contraction. The resulting cosmology eliminates the cosmic singularity and multiverse problems of big bang inflationary models and robustly predicts time-varying IFS-induced dark energy and the absence of primordial B-mode polarization in the cosmic microwave background.

alternatives to inflation↗
DOE OSTI2025

A conserved viral RNA fold enables nuclease resistance across kingdoms of life

Abstract Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence variability among xrRNAs from distantly related viruses raises questions about the shared molecular features that enable these RNAs to withstand the strong unwinding forces of exoribonucleases. Here, we present the first structure of a plant-virus xrRNA in its active conformation and uncover universal principles of xrRNA folding. Comparison with the structure of a human-pathogenic flavivirus xrRNA reveals that both share a core structural motif—a protective ring encircling the RNA’s 5′ end—despite lacking sequence similarity. Disrupting this core motif through targeted mutagenesis eliminates exoribonuclease-resistance and attenuates viral infection. We identify hundreds of related structures across multiple virus families, supporting the conservation of this mechanism. Our study demonstrates how distantly related RNA viruses have converged on a common structural strategy to inhibit cellular nucleases, with a universal ring topology as the defining feature of viral xrRNAs.

Biochemistry & Molecular Biology↗