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Results for “Complexity bounding”

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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen

Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRAS G12V peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Kinetics and mechanisms of polycondensation reactions between aryl halides and bisphenol A

Aryl chlorides (ArCl) or aryl fluorides (ArF) were used in polycondensation reactions to form poly(arylene ether sulfone)s (PAES). Interestingly, the kinetics of the ArF reaction fit a third-order rate law, which is attributed to the activation of the carbon–fluorine bond by two potassium cations (at least one bound to phenolate), which form a three-body complex. Here, the ArCl monomer follows a second-order rate law, where a two-body complex forms at the initial state of the aromatic nucleophilic substitution (S N Ar) pathway. These metal cation-activated complexes act as intermediates during the attack by the nucleophile. This finding was reproduced with either the potassium or the sodium counterion (introduced via potassium carbonate or sodium carbonate). Through a combination of experimental analysis of reaction kinetics and computational calculations with density functional theory (DFT) methods, the present work extends the fundamental understanding of polycondensation mechanisms for two aryl halides and highlights the importance of the CX–metal interaction(s) in the S N Ar reaction, which is translational to other ion-activated substitution reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

BODIPY and dipyrrin as unexpected robust anchoring groups on TiO 2 nanoparticles

Covalent attachment of molecules to metal oxide surfaces typically demands the presence of an anchoring group that in turn requires synthetic steps to introduce. BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) chromophores have long been used in dye-sensitized solar cells, but carboxylic acid groups typically had to be installed to act as surface anchors. We now find that even without the introduction of such anchors, the unmodified BODIPY can bind to TiO 2 surfaces via its BF 2 group through boron–oxygen surface bonds. Dipyrrin, the parent molecule of BODIPY, is also capable of binding directly to TiO 2 surfaces, likely through its chelating nitrogen atoms. These binding modes prove to be even more robust than that of an installed carboxylate and offer a new way to attach molecular complexes to surfaces for (photo)catalytic applications since, once bound, we show that surface bound BODIPY and dipyrrin derivatives exhibit ultrafast photoinjection of electrons into the conduction band of TiO 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine

Ribosome serves as a universal molecular machine capable of synthesis of all the proteins in a cell. Small-molecule inhibitors, such as ribosome-targeting antibiotics, can compromise the catalytic versatility of the ribosome in a context-dependent fashion, preventing transpeptidation only between particular combinations of substrates. Classic peptidyl transferase center inhibitor chloramphenicol (CHL) fails to inhibit transpeptidation reaction when the incoming A site acceptor substrate is glycine, and the molecular basis for this phenomenon is unknown. Here, we present a set of high-resolution X-ray crystal structures that explain why CHL is unable to inhibit peptide bond formation between the incoming glycyl-tRNA and a nascent peptide that otherwise is conducive to the drug action. Our structures reveal that fully accommodated glycine residue can co-exist in the A site with the ribosome-bound CHL. Moreover, binding of CHL to a ribosome complex carrying glycyl-tRNA does not affect the positions of the reacting substrates, leaving the peptide bond formation reaction unperturbed. These data exemplify how small-molecule inhibitors can reshape the A-site amino acid binding pocket rendering it permissive only for specific amino acid residues and rejective for the other substrates extending our detailed understanding of the modes of action of ribosomal antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones

Diffusible small molecule microbial hormones drastically alter the expression profiles of antibiotics and other drugs in actinobacteria. For example, avenolide (a butenolide) regulates the production of avermectin, derivatives of which are used in the treatment of river blindness and other parasitic diseases. Butenolides and γ-butyrolactones control the production of pharmaceutically important secondary metabolites by binding to TetR family transcriptional repressors. Here, we describe a concise, 22-step synthetic strategy for the production of avenolide. We present crystal structures of the butenolide receptor AvaR1 in isolation and in complex with avenolide, as well as those of AvaR1 bound to an oligonucleotide derived from its operator. Biochemical studies guided by the co-crystal structures enable the identification of 90 new actinobacteria that may be regulated by butenolides, two of which are experimentally verified. These studies provide a foundation for understanding the regulation of microbial secondary metabolite production, which may be exploited for the discovery and production of novel medicines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Molecular-Scale Understanding of Sulfate Exchange from Schwertmannite by Chromate Versus Arsenate

Schwertmannite effectively sorbs chromate (Cr(VI)), yet the sorption mechanisms remain elusive. We determined the Cr(VI) sorption mechanisms on schwertmannite at pH 3.2 and 5 using combined macroscopic sorption experiments with molecularscale characterization and by comparing them to arsenate (As(V)) sorption. Cr(VI) adsorbs as bidentate-binuclear (BB) inner-sphere complexes through exchanging more sulfate and less >Fe–OH/OH 2 , with 0.59–0.71 sulfate released per Cr(VI) sorbed. While As(V) also forms BB complexes, it exchanges sulfate and >Fe–OH/OH 2 equally with 0.49–0.52 sulfate released per As(V) sorbed. At high As(V) loadings, As(V) precipitates as amorphous FeAsO 4 , particularly at low pH. The abovementioned differences between Cr(VI) and As(V) can be related to their different ionic radii and binding strength. Moreover, Cr(VI) and As(V) preferentially exchange sulfate innersphere complexes, increasing the proportion of sulfate outer-sphere complexes in schwertmannite. In turn, the concentration of sulfate outer-sphere complexes increases and then decreases with increasing Cr(VI) loading. Results suggest that an oxyanion, which would form inner-sphere complexes on a mineral surface, preferentially exchanges inner-spherically bound oxyanions than outerspherically bound ones on the surface, even though both are exchanged. Furthermore, this study improves our understanding of the sorption of oxyanions on schwertmannite and their capabilities to template schwertmannite formation and stabilize its structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine

Pfs230 domain 1 (Pfs230D1) is an advanced malaria transmission-blocking vaccine antigen demonstrating high functional activity in clinical trials. However, the structural and functional correlates of transmission-blocking activity are not defined. Here, we characterized a panel of human monoclonal antibodies (hmAbs) elicited in vaccinees immunized with Pfs230D1. These hmAbs exhibited diverse transmission-reducing activity, yet all bound to Pfs230D1 with nanomolar affinity. We compiled epitope-binning data for seventeen hmAbs and structures of nine hmAbs complexes to construct a high-resolution epitope map and revealed that potent transmission-reducing hmAbs bound to one face of Pfs230D1, while non-potent hmAbs bound to the opposing side. The structure of Pfs230D1D2 revealed that non-potent transmission-reducing epitopes were occluded by the second domain. The hmAb epitope map delineated binary hmAb combinations that synergized for extremely high-potency, transmission-reducing activity. Finally, this work provides a high-resolution guide for structure-based design of enhanced immunogens and informs diagnostics that measure the transmission-reducing response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain

The monomeric catalytic domain (residues 1–199) of SARS-CoV-2 main protease (MPro 1-199 ) fused to 25 amino acids of its flanking nsp4 region mediates its autoprocessing at the nsp4-MPro 1-199 junction. We report the catalytic activity and the dissociation constants of MPro 1-199 and its analogs with the covalent inhibitors GC373 and nirmatrelvir (NMV), and the estimated monomer-dimer equilibrium constants of these complexes. Mass spectrometry indicates the presence of the accumulated adduct of NMV bound to MPro WT and MPro 1-199 and not of GC373. A room temperature crystal structure reveals a native-like fold of the catalytic domain with an unwound oxyanion loop (E state). In contrast, the structure of a covalent complex of the catalytic domain-GC373 or NMV shows an oxyanion loop conformation (E* state) resembling the full-length mature dimer. These results suggest that the E-E* equilibrium modulates autoprocessing of the main protease when converting from a monomeric polyprotein precursor to the mature dimer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Coupled Cluster Study of the Interactions of AnO 2 , AnO 2 + , and AnO 2 2+ (An = U, Np) with N 2 and CO

We report thermochemical and spectroscopic properties for actinyl complexes involving UO 2 2+/1+/0 and NpO 2 2+/1+/0 with N 2 and CO, together with the UO 2 -O 2 , UO 2 + -O 2 , and UO 2 + -NO complexes, have been studied for the first time using an accurate composite coupled cluster approach. Two general bonding motifs were investigated, end-on (η 1 ) and side-on (η 2 ) relative to the metal center of the actinyls. For end-on CO complexes, both C-coordinated (An-C) and O-coordinated (An-O) structures were examined, with the former always being lower in energy. All of the η 1 complexes were calculated to be stable, with dissociation energies ranging from 2 to 36 kcal/mol, except for that of UO 2 + -O 2 (the η 1 orientation for UO 2 + -NO was not amenable to single reference coupled cluster). In agreement with a previous study, the η 2 structure for UO 2 + -O 2 was calculated to be relatively strongly bound, by 22.3 kcal/mol in this work. The closely related NO complex, however, had a calculated dissociation energy of just 4.0 kcal/mol. The binding energy of O 2 to neutral UO 2 in a η 2 orientation was calculated to be very strong, 75.4 kcal/mol, and strongly resembled a UO 2 + (O 2 – ) complex at equilibrium. The N–N and C–O bonds were found to be somewhat activated for all the side-on (η 2 ) neutral An(IV) complexes, with stretching frequencies of N 2 or CO being red-shifted by as much as 480 cm –1 with a 0.06 Å bond length elongation. Dissociation energies for the η 1 complexes are strongly correlated with the extent of electron transfer from ligand to actinyl. The nature of bonding in the actinyl complexes is examined using natural resonance theory (NRT). The correlation between bonding motif and small molecule activation is in agreement with experiments in condensed phases.

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

Reassessing the Origins and Contemporary Relevance of ck Acceptability Parameters: Evolving Perspectives on Similarity

“Sensitivity and Uncertainty Analyses Applied to Criticality Safety Validation,” introduces sensitivity and uncertainty methods to address challenges in defining and extending areas of applicability for criticality safety validation. These areas are traditionally defined by the bounds or limits on key parameters, but establishing valid ranges and managing complex parameter variations remain challenging. NUREG/CR-6655 introduces ck and other integral indices, as well as concepts such as the completeness of benchmark coverage, to better quantify system similarities. The work proposed herein seeks to evaluate these foundational concepts to ensure that the bounds remain effective in guiding the assessment of similarity and applicability in modern applications. The concept of completeness, along with other parameters envisioned within the framework, serves as an example of the foundational ideas that have been established, though their effectiveness in practice may not be fully understood. Advancements in scripting tools, coupled with the speed and efficiency of modern computing and statistical models, now allow for faster and more thorough assessments than previously possible. These advancements also enable the identification of trends within the data, which could provide additional insight into system behavior and further broaden the scope of previously performed benchmarks. By leveraging these capabilities, we will revisit and expand the scope of these foundational methods to determine whether the necessary elements for robust similarity evaluation are already embedded, partially realized, or remain untapped.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Complexity Phase Diagram for Interacting and Long-Range Bosonic Hamiltonians

Here, we classify phases of a bosonic lattice model based on the computational complexity of classically simulating the system. We show that the system transitions from being classically simulable to classically hard to simulate as it evolves in time, extending previous results to include on-site number-conserving interactions and long-range hopping. Specifically, we construct a complexity phase diagram with easy and hard “phases” and derive analytic bounds on the location of the phase boundary with respect to the evolution time and the degree of locality. We find that the location of the phase transition is intimately related to upper bounds on the spread of quantum correlations and protocols to transfer quantum information. Remarkably, although the location of the transition point is unchanged by on-site interactions, the nature of the transition point does change. Specifically, we find that there are two kinds of transitions, sharp and coarse, broadly corresponding to interacting and noninteracting bosons, respectively. Our Letter motivates future studies of complexity in many-body systems and its interplay with the associated physical phenomena.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF

Tumour necrosis factor (TNF) is a trimeric protein which signals through two membrane receptors, TNFR1 and TNFR2. Previously, we identified small molecules that inhibit human TNF by stabilising a distorted trimer and reduce the number of receptors bound to TNF from three to two. Here we present a biochemical and structural characterisation of the small molecule-stabilised TNF-TNFR1 complex, providing insights into how a distorted TNF trimer can alter signalling function. We demonstrate that the inhibitors reduce the binding affinity of TNF to the third TNFR1 molecule. In support of this, we show by X-ray crystallography that the inhibitor-bound, distorted, TNF trimer forms a complex with a dimer of TNFR1 molecules. This observation, along with data from a solution-based network assembly assay, leads us to suggest a model for TNF signalling based on TNF-TNFR1 clusters, which are disrupted by small molecule inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The complex momentum representation approach and its application to low-lying resonances in ${^{17}}$O and ${^{29,31}}$F

Approaches for predicting low-lying resonances, uniformly treating bound, and resonant levels have been a long-standing goal in nuclear theory. Accordingly, we explored the viability of the complex momentum representation (CMR) approach coupled with new potentials. We focus on predicting the energy of the low-lying 2p 3/2 resonance in 17 O, which is critical for s-process nucleosynthesis and missing in previous theoretical research. Here, using a Woods-Saxon potential based on the Koning-Delaroche optical model and constrained by the experimental one-neutron separation energy, we successfully predicted the resonant energy of this level for the first time. Our predictions of the bound levels and 1d 3/2 resonance agree well with the measurement results. Additionally, we utilize this approach to study the near-threshold resonances that play a role when forming a two-neutron halo in 29,31 F. We found that the CMR-based predictions of the bound-level energies and unbound 1f 7/2 level agree well with the results obtained using the scattering phase shift method. Subsequently, we successfully found a solution for the 2p 3/2 resonance with energy just above the threshold, which is decisive for halo formation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Data for Simultaneous Suppression of Lignin, Tricin and Wall-Bound Phenolic Biosynthesis via the Expression of Monolignol 4- O -Methyltransferases in Rice

Grass lignocelluloses feature complex compositions and structures. In addition to the presence of conventional lignin units from monolignols, acylated monolignols and flavonoid tricin also incorporate into lignin polymer; moreover, hydroxycinnamates, particularly ferulate, cross-link arabinoxylan chains with each other and/or with lignin polymers. These structural complexities make grass lignocellulosics difficult to optimize for effective agro-industrial applications. In the present study, we assess the applications of two engineered monolignol 4- O -methyltransferases (MOMTs) in modifying rice lignocellulosic properties. Two MOMTs confer regiospecific para-methylation of monolignols but with different catalytic preferences. The expression of MOMTs in rice resulted in differential but drastic suppression of lignin deposition, showing more than 50% decrease in guaiacyl lignin and up to an 90% reduction in syringyl lignin in transgenic lines. Moreover, the levels of arabinoxylan-bound ferulate were reduced by up to 50%, and the levels of tricin in lignin fraction were also substantially reduced. Concomitantly, up to 11 μmol/g of the methanol-extractable 4- O -methylated ferulic acid and 5–7 μmol/g 4- O -methylated sinapic acid were accumulated in MOMT transgenic lines. Both MOMTs in vitro displayed discernible substrate promiscuity towards a range of phenolics in addition to the dominant substrate monolignols, which partially explains their broad effects on grass phenolic biosynthesis. The cell wall structural and compositional changes resulted in up to 30% increase in saccharification yield of the de-starched rice straw biomass after diluted acid-pretreatment. These results demonstrate an effective strategy to tailor complex grass cell walls to generate improved cellulosic feedstocks for the fermentable sugar-based production of biofuel and bio-chemicals.

Biomass Analytics↗
DOE OSTI2024

Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda

Abstract Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32–Dda–ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda–peptide complex was consistent with the corresponding interaction in the gp32–Dda–ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32–Dda–ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32–Dda–ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Implications of the Upper Bound on h → μ + μ - on the Baryon Asymmetry of the Universe

The upper bounds from the ATLAS and CMS experiments on the decay rate of the Higgs boson to two muons provide the strongest constraint on an imaginary part of the muon Yukawa coupling. This bound is more than an order of magnitude stronger than bounds from $\mathcal{CP}$-violating observables, specifically the electric dipole moment of the electron. It excludes a scenario $-$ which had been viable prior to these measurements $-$ that a complex muon Yukawa coupling is the dominant source of the baryon asymmetry. Even with this bound, the muon source can still contribute ${\cal O}(16\%)$ of the asymmetry.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Analytic continuation of the relativistic three-particle scattering amplitudes

We investigate the relativistic scattering of three identical scalar bosons interacting via pair-wise interactions. Extending techniques from the nonrelativistic three-body scattering theory, we provide a detailed and general prescription for solving and analytically continuing integral equations describing the three-body reactions. We use these techniques to study a system with zero angular momenta described by a single scattering length leading to a bound state in a two-body subchannel. We obtain bound-state-particle and three-particle amplitudes in the previously unexplored kinematical regime; in particular, for real energies below elastic thresholds and complex energies in the physical and unphysical Riemann sheets. We extract positions of three-particle bound-states that agree with previous finite-volume studies, providing further evidence for the consistency of the relativistic finite-volume three-body quantization conditions. We also determine previously unobserved virtual bound states in this theory. Lastly, we find numerical evidence of the breakdown of the two-body finite-volume formalism in the vicinity of the left-hand cuts and argue for the generalization of the existing formalism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗