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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer

Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an ‘occluded-open’ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Vanilloid-dependent TRPV1 opening trajectory from cryo EM ensemble analysis

Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational trajectory is not trivial. Here, we use thermal titration methods and cryo-EM in an attempt to obtain temporal resolution of the conformational trajectory of the vanilloid receptor TRPV1 with resiniferatoxin (RTx) bound. Based on our cryo-EM ensemble analysis, RTx binding to TRPV1 appears to induce intracellular gate opening first, followed by selectivity filter dilation, then pore loop rearrangement to reach the final open state. This apparent conformational wave likely arises from the concerted, stepwise, additive structural changes of TRPV1 over many subdomains. Greater understanding of the RTx-mediated long-range allostery of TRPV1 could help further the therapeutic potential of RTx, which is a promising drug candidate for pain relief associated with advanced cancer or knee arthritis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

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

A structural framework for unidirectional transport by a bacterial ABC exporter

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4 eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by NaAtm1. One of the disulfide crosslinked NaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system

NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ 54 -dependent activator NifA to control the transcription of nitrogen fixation (nif) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL–NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph,Azotobacter vinelandii.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
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 OSTI2026

Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound

Here, we report the X-ray structural analysis of dihydroorotase from Methanococcus jannaschii co-crystallized with dihydroorotate at pH 6.5. The crystals are isomorphous with the crystals of the apoenzyme, with space group P3 2 21 and unit-cell dimensions a = b = 111.4, c = 101.2 Å. The structure was refined to R = 0.169 and R free = 0.186 at a resolution of 1.87 Å at room temperature. During crystallization the degradative reaction took place, and the electron density in the active site corresponds to the substrate carbamoyl aspartate. Carbamoyl aspartate interacts with the protein in the active site in a manner similar to that observed for Escherichia coli and human dihydroorotases. However, the flexible loop (residues 140–151) adopts both conformations in the crystal, loop-out and loop-in, with the loop-out conformation having higher occupancy. This contrasts with our expectations for the flexible loop to be exclusively in the loop-in conformation, which is the conformation that it adopts to stabilize the binding of the substrate in the known systems. Additional studies with substrate analogs that resemble carbamoyl aspartate and different crystallization conditions would provide further insight into the conformation of the flexible loop in this system.

Methanococcus jannaschii↗
DOE OSTI2022

Gating choreography and mechanism of the human proton-activated chloride channel $\mathrm{ASOR}$

The proton-activated chloride channel ASOR (TMEM206/PAC) permeates anions across cellular membranes in response to acidification, thereby enhancing acid-induced cell death and regulating endocytosis. The molecular mechanisms of pH-dependent control are not understood, in part because structural information for an activated conformation of ASOR is lacking. Here, we reconstitute function from purified protein and present a 3.1-Å-resolution cryo–electron microscopy structure of human ASOR at acidic pH in an activated conformation. The work contextualizes a previous acidic pH structure as a desensitized conformation. Combined with electrophysiological studies and high-resolution structures of resting and desensitized states, the work reveals mechanisms of proton sensing and ion pore gating. Clusters of extracellular acidic residues function as pH sensors and coalesce when protonated. Ensuing conformational changes induce metamorphosis of transmembrane helices to fashion an ion conduction pathway unique to the activated conformation. The studies identify a new paradigm of channel gating in this ubiquitous ion channel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Local Topological Free Energy of the SARS-CoV-2 Spike Protein

The novel coronavirus SARS-CoV-2 infects human cells using a mechanism that involves binding and structural rearrangement of its Spike protein. Understanding protein rearrangement and identifying specific amino acids where mutations affect protein rearrangement has attracted much attention for drug development. In this manuscript, we use a mathematical method to characterize the local topology/geometry of the SARS-CoV-2 Spike protein backbone. Our results show that local conformational changes in the FP, HR1, and CH domains are associated with global conformational changes in the RBD domain. The SARS-CoV-2 variants analyzed in this manuscript (alpha, beta, gamma, delta Mink, G614, N501) show differences in the local conformations of the FP, HR1, and CH domains as well. Finally, most mutations of concern are either in or in the vicinity of high local topological free energy conformations, suggesting that high local topological free energy conformations could be targets for mutations with significant impact of protein function. Namely, the residues 484, 570, 614, 796, and 969, which are present in variants of concern and are targeted as important in protein function, are predicted as such from our model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Inflaton Decay in No-Scale Supergravity and Starobinsky-like Models

We consider the decay of the inflaton in Starobinsky-like models arising from either an R+R 2 theory of gravity or N = 1 no-scale supergravity models. If Standard Model matter is simply introduced to the R+R 2 theory, the inflaton (which appears when the theory is conformally transformed into the Einstein frame) couples to matter predominantly in Standard Model Higgs kinetic terms. This will typically lead to a reheating temperature of ~3 × 10 9 GeV. However, if the Standard Model Higgs is conformally coupled to curvature, the decay rate may be suppressed and vanishes for conformal coupling ζ = 1/6. Nevertheless, the inflaton decays through the conformal anomaly, leading to a reheating temperature of the order of 10 8 GeV. The Starobinsky potential may also arise in no-scale supergravity. In this case, the inflaton decays if there is a direct coupling of the inflaton to matter in the superpotential or to gauge fields through the gauge kinetic function. We also discuss the relation between the theories and demonstrate the correspondence between the no-scale models and the conformally coupled R+R 2 theory (with ζ = 1/6).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Structurally controlled deposition of silicon onto nanowires

Provided herein are nanostructures for lithium ion battery electrodes and methods of fabrication. In some embodiments, a nanostructure template coated with a silicon coating is provided. The silicon coating may include a non-conformal, more porous layer and a conformal, denser layer on the non-conformal, more porous layer. In some embodiments, two different deposition processes, e.g., a PECVD layer to deposit the non-conformal layer and a thermal CVD process to deposit the conformal layer, are used. Anodes including the nanostructures have longer cycle lifetimes than anodes made using either a PECVD or thermal CVD method alone.

25 ENERGY STORAGE↗
DOE OSTI2022

Structurally controlled deposition of silicon onto nanowires

Provided herein are nanostructures for lithium ion battery electrodes and methods of fabrication. In some embodiments, a nanostructure template coated with a silicon coating is provided. The silicon coating may include a non-conformal, more porous layer and a conformal, denser layer on the non-conformal, more porous layer. In some embodiments, two different deposition processes, e.g., a PECVD layer to deposit the non-conformal layer and a thermal CVD process to deposit the conformal layer, are used. Anodes including the nanostructures have longer cycle lifetimes than anodes made using either a PECVD or thermal CVD method alone.

Wang, Weijie↗
DOE OSTI2023

Structurally controlled deposition of silicon onto nanowires

Provided herein are nanostructures for lithium ion battery electrodes and methods of fabrication. In some embodiments, a nanostructure template coated with a silicon coating is provided. The silicon coating may include a non-conformal, more porous layer and a conformal, denser layer on the non-conformal, more porous layer. In some embodiments, two different deposition processes, e.g., a PECVD layer to deposit the non-conformal layer and a thermal CVD process to deposit the conformal layer, are used. Anodes including the nanostructures have longer cycle lifetimes than anodes made using either a PECVD or thermal CVD method alone.

Wang, Weijie↗
DOE OSTI2026

Beyond Point Estimates: Benchmarking Uncertainty Quantification Methods on the AION-1 Astronomical Foundation Model

Foundation models for astronomical surveys offer powerful learned representations that can be transferred to downstream regression tasks such as galaxy property estimation. However, point predictions alone are insufficient for scientific inference; reliable uncertainty quantification (UQ) is essential. We compare seven UQ methods on galaxy property regression using frozen AION-1 foundation-model embeddings, predicting redshift, stellar mass, stellar-population age, gas-phase metallicity, and specific star-formation rate, from Legacy Survey photometry/imaging and DESI spectra, with PROVABGS-derived labels. Distribution-free conformal methods achieve marginal coverage within $\sim$1 pp of the nominal 90% across all properties, while non-conformal baselines (Deep Ensembles, MC~Dropout) fail to calibrate reliably. Among conformal approaches, Conformalized Quantile Regression (CQR) delivers the best coverage in the bin with the poorest model predictions. More importantly, only the Locally Valid and Discriminative (LVD) framework -- particularly when operating on AION-1 embeddings -- also provides finite-sample \emph{local validity}, producing intervals that adapt to each galaxy's local prediction difficulty rather than relying on marginal guarantees alone. These results establish conformal prediction, and LVD in particular, as the preferred UQ framework for uncertainty-aware inference on foundation-model embeddings in astrophysics.

Tame-Narvaez, Karla [Fermilab] (ORCID:000000022249↗
DOE OSTI2023

Bootstrapping boundaries and branes

The study of conformal boundary conditions for two-dimensional conformal field theories (CFTs) has a long history, ranging from the description of impurities in one-dimensional quantum chains to the formulation of D-branes in string theory. Nevertheless, the landscape of conformal boundaries is largely unknown, including in rational CFTs, where the local operator data is completely determined. We initiate a systematic bootstrap study of conformal boundaries in 2d CFTs by investigating the bootstrap equation that arises from the open-closed consistency condition of the annulus partition function with identical boundaries. We find that this deceivingly simple bootstrap equation, when combined with unitarity, leads to surprisingly strong constraints on admissible boundary states. In particular, we derive universal bounds on the tension (boundary entropy) of stable boundary conditions, which provide a rigorous diagnostic for potential D-brane decays. We also find unique solutions to the bootstrap problem of stable branes in a number of rational CFTs. Along the way, we observe a curious connection between the annulus bootstrap and the sphere packing problem, which is a natural extension of previous work on the modular bootstrap. We also derive bounds on the boundary entropy at large central charge. These potentially have implications for end-of-the-world branes in pure gravity on AdS 3 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Universal bounds on CFT Distance Conjecture

For any unitary conformal field theory in two dimensions with the central charge c, we prove that, if there is a nontrivial primary operator whose conformal dimension ∆ vanishes in some limit on the conformal manifold, the Zamolodchikov distance t to the limit is infinite, the approach to this limit is exponential ∆ = exp(−αt + O(1)), and the decay rate obeys the universal bounds c−1/2 ≤ α ≤ 1. In the limit, we also find that an infinite tower of primary operators emerges without a gap above the vacuum and that the conformal field theory becomes locally a tensor product of a sigma-model in the large radius limit and a compact theory. As a corollary, we establish a part of the Distance Conjecture about gravitational theories in three-dimensional anti-de Sitter space. In particular, our bounds on α indicate that the emergence of exponentially light states is inevitable as the moduli field corresponding to t rolls beyond the Planck scale along the steepest path and that this phenomenon can begin already at the curvature scale of the bulk geometry. We also comment on implications of our bounds for gravity in asymptotically flat spacetime by taking the flat space limit and compare with the Sharpened Distance Conjecture.

AdS-CFT Correspondence↗
DOE OSTI2025

Nonrenormalization theorem for $\mathcal{N}$ = (4, 4) interface entropy

We derive a formula for the half-BPS interface entropy between any pair of $\mathcal{N}$ = (4, 4) theories on the same conformal manifold. This generalizes the diastasis formula derived in [1] for $\mathcal{N}$ = (2, 2) theories, which is restricted to the conformal submanifolds generated by either chiral or twisted chiral multiples of $\mathcal{N}$ = (2, 2) supersymmetry. To derive the $\mathcal{N}$ = (4, 4) formula, we use the fact that the conformal manifold of $\mathcal{N}$ = (4, 4) theories is symmetric and quaternionic-Kähler and that its isotropy group contains the SU(2) ⊗ SU(2) external automorphism of the $\mathcal{N}$ = (4, 4) superconformal algebra. As an application of the formula, we prove a supersymmetric non-renormalization theorem, which explains the observation in [2] that the interface entropy for half-BPS Janus solutions in type IIB supergravity on AdS 3 × S 3 × T 4 coincides with the corresponding quantity in their free conformal field limits.

AdS-CFT correspondence↗