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At least 919 records · Page 51

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

Nonbonded interactions in membrane active cyclic biopolymers. IV - Cation dependence

Interactions of valinomycin and form of its analogs in several conformations with the central ions Li(+), Na(+), K(+), Rb(+) and Cs(+) are investigated as part of a study of the specific preference of valinomycin for potassium and the mechanisms of carrier-mediated ion transport across membranes. Ion binding energies and conformational potential energies are calculated taking into account polarization energy formulas and repulsive energy between the central ion and the ligand atoms for conformations representing various stages in ion capture and release for each of the two ring chiralities of valinomycin and its analogs. Results allow the prediction of the chirality and conformation most likely to be observed for a given analog, and may be used to synthesize analogs with a desired rigidity or flexibility. The binding energies with the alkali metal cations are found to decrease with increasing ion size, and to be smaller than the corresponding ion hydration energies. It is pointed out that the observed potassium preference may be explainable in terms of differences between binding and hydration energies. Binding energies are also noted to depend on ligand conformation.

Radhakrishnan, R.↗

A finite element-boundary integral method for cavities in a circular cylinder

Conformal antenna arrays offer many cost and weight advantages over conventional antenna systems. However, due to a lack of rigorous mathematical models for conformal antenna arrays, antenna designers resort to measurement and planar antenna concepts for designing non-planar conformal antennas. Recently, we have found the finite element-boundary integral method to be very successful in modeling large planar arrays of arbitrary composition in a metallic plane. We extend this formulation to conformal arrays on large metallic cylinders. In this report, we develop the mathematical formulation. In particular, we discuss the shape functions, the resulting finite elements and the boundary integral equations, and the solution of the conformal finite element-boundary integral system. Some validation results are presented and we further show how this formulation can be applied with minimal computational and memory resources.

Kempel, Leo C.↗

Higher Order Modeling In the BEM/FEM Hybrid Formulation

Hybrid formulations using low order curl-conforming bases to represent the total electric field within a finite element region and low order divergence-conforming bases to represent equivalent electric and magnetic currents on the boundary are well known. However, higher-order divergence and curl-conforming bases have been shown to provide significant benefits in convergence rates and accuracy when employed in strictly integral equation and strictly finite element formulations. In this paper, a hybrid electric field formulation employing higher order bases is presented. The paper addresses benefits and issues associated with using higher order divergence-and curl-conforming bases in the hybrid finite element/boundary element electric field formulation. The method of singularity subtraction may be used to compute the self terms of the boundary integral when the bases are of low order. But this method becomes laborious and requires great care when the divergence conforming bases are of higher order. In order to handle these singularities simply and accurately, a generalized Gaussian quadrature method is employed in which the expansion functions account for the singularity. In preliminary tests of the higher order hybrid formulation, the equivalent electric current induced by scattering of a plane wave from a square dielectric cylinder is examined. Accurate results are obtained using only a two-triangle mesh when the current basis is of order 4 or 5. Additional results are presented comparing the error obtained using higher order bases to that obtained using lower order bases when the number of unknowns is approximately equal. Also, convergence rates obtained with higher order bases are compared to those obtained with lower order bases for selected sample problems.

Fink, Patrick W.↗

Vertical Field of View Reference Point Study for Flight Path Control and Hazard Avoidance

Researchers within the eXternal Visibility System (XVS) element of the High-Speed Research (HSR) program developed and evaluated display concepts that will provide the flight crew of the proposed High-Speed Civil Transport (HSCT) with integrated imagery and symbology to permit path control and hazard avoidance functions while maintaining required situation awareness. The challenge of the XVS program is to develop concepts that would permit a no-nose-droop configuration of an HSCT and expanded low visibility HSCT operational capabilities. This study was one of a series of experiments exploring the 'design space' restrictions for physical placement of an XVS display. The primary experimental issues here was 'conformality' of the forward display vertical position with respect to the side window in simulated flight. 'Conformality' refers to the case such that the horizon and objects appear in the same relative positions when viewed through the forward windows or display and the side windows. This study quantified the effects of visual conformality on pilot flight path control and hazard avoidance performance. Here, conformality related to the positioning and relationship of the artificial horizon line and associated symbology presented on the forward display and the horizon and associated ground, horizon, and sky textures as they would appear in the real view through a window presented in the side window display. No significant performance consequences were found for the non-conformal conditions.

Comstock, J. Raymond, Jr.↗

Thermal Protection System to Enable Ice Giant Aerocapture Mission for Delivering Both an Orbiter and an In Situ Probe

The Ice Giants have been identified as high priority science destinations in the last Decadal Survey [1] and could benefit from aerocapture as the primary method for orbit insertion [2]. A mass-efficient aerocapture system will enable the delivery of an orbiter along with an atmospheric probe (for in situ measurements to anchor global data collected by the orbiter) and possibly a lander at Triton [3]. Aerocapture could be executed either using low L/D rigid aeroshell with lift modulation (LMA) [4] or using deployable aeroshell using drag modulation (DMA) [3]. Nearly two decades ago, a NASA-funded team performed Neptune-Triton aerocapture studies with a mid-L/D lifting configuration [5] for achieving orbit using LMA. This study showed aerocapture challenges. Due to very high peak entry conditions combined with very high heat-load, a suite of TPS materials was required and this suite was deemed problematic from a qualification perspective, due test facility limitations. In the past 20 years, progress made in GN&C for lift-guided entry missions such as MSL, Orion EFT1, Mars 2020 and the upcoming Artemis missions, and the expertise in blunt body aerodynamics at large scale (~ 5m) has led the EDL community to conclude that aerocapture is a “go do” engineering activity and most technologies are in hand to propose missions with aerocapture [6] [7]. Aerocapture using DMA, currently in development, is an option for Ice Giant Missions. While DMA is simpler in some sense, due to ballistic entry and no need for lift-guided maneuvering, it has challenges and it’s maturity is lower. LMA and DMA both require one or more ablative Thermal Protection System (TPS) materials for the rigid aeroshell element. The ablative TPS needs to be robust and mass efficient due to the high heat loads and size of the rigid aeroshell. Currently, there are capable ablative thermal protection materials, e.g., Heatshield for Extreme Entry Environments Technology (HEEET), 3-D woven Mid-Density Carbon- Phenolic (3MDCP), and PICA (Phenolic-Impregnated Carbon Ablator) that are mature, i.e., at TRL 6 or higher. NASA also invested in Conformal PICA that was matured to TRL 5. Our goal is to evaluate the applicability of high TRL TPS and consider other design options. We first establish bounding aerocapture trajectories for a wide range of arrival conditions and the associated aerothermal environment. Based on the environments, we then determine the predicted TPS mass for the aeroshell [4]. In this presentation, we will outline the process by which we establish bounding aerocapture trajectories for hyperbolic excess velocities ranging from 27 km/s to 35 km/s, which are shown to be a range of velocities that can reduce the trip time from ~14 years to 8 years. The above velocity range translates to ~12 km/s to ~24 km/s arrival velocities at the planetary entry interface [2]. The velocity reduction required to achieve orbit ranges between ~2.5 km/s to 9.5 km/s for both Neptune and Triton. Propulsive insertion alone, due to the amount of fuel required to achieve the required velocity reduction, limits the science returned [2]. We establish the bounding aerocapture trajectories for a low L/D (~ 0.4) configuration for three different ballistic coefficients. The ballistic coefficient range is determined from three different aeroshell diameters of 3m, 4m and 5m and with an entry system mass of 2200 kg. With the above range of design parameters, we then determine conservative/bounding estimates of aerothermal environments by using a combination of CFD simulations and stagnation point heating estimates [7]. This engineering approach allows us to first assess the TPS need vs. TPS capability and determine the applicability of existing TPS. Once an applicable suite of TPS is determined, the TPS thickness and mass are computed. We show that the TPS mass fraction can be as low as 5% to as high as 20%, depending on total trip time reduction and other design parameters for a range of TPS. This is a large range for TPS mass fraction. We show PICA and HEEET can indeed enable aerocapture missions, but the missions incur a mass penalty. TPS mass savings, can be further reduced with the use of conformal PICA. Advancing the development of Conformal PICA to make it robust across the entire aerothermal environment (peak heat-flux, pressure and shear) range will result in TPS mass fractions of < 10% for Ice Giant aerocapture missions such as the Neptune-Triton mission. Aerocapture allows for not only shortening the trip time but enables larger mass to be placed in orbit. Furthermore, probes deployed from orbit will benefit in reduced entry environments allowing for a lower risk TPS implementation as compared to mission designs where the probe is released prior to orbit insertion. One of the challenges for the Ice Giant community is to ensure mission designs that maximize science and allow flexibility in the placement of the entry probe. The traditional approach to release the probe ahead of the orbiter may not optimize returned science. In this presentation, we will make the case for mature TPS such as HEEET and PICA. While these materials can enable aerocapture missions, completing the development of conformal PICA and extending Conformal PICA to be more robust, will have significant impact to TPS mass efficiency and significantly enhance science return for future Gas- and Ice-Giant missions.

E Venkatapathy↗

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↗

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↗

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↗

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↗