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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A Post-translational Histidine–Histidine Cross-Link Enhances Enzymatic Oxygen Reduction Activity with Greater pH Adaptability

Cross-linked protein residues exist as enzyme cofactors to enable or enhance catalytic activities. Despite their importance in nature, the chemical identity of the cross-links is limited to certain amino acid combinations, whose function and the formation mechanism remain insufficiently understood due to the difficulty in isolating native enzymes without the cross-links. Herein, we report the formation and characterization of both His-Tyr and His-His cross-links under oxidative enzymatic turnover conditions in L29H/F33Y/F43H Mb, a structural and functional model of heme-copper oxidase (HCO). The connectivity of the cross-link was characterized as Ne ε2 (His29)-Cd δ2 (His43) by mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR). Interestingly, formation of the cross-link significantly enhances the oxygen reduction activity of the enzyme at neutral or basic pH with higher product specificity. X-ray crystallography has identified a novel Tyr-His cross-link through a Tyr-O-His linkage. Our mechanistic studies indicate the involvement of high-valent heme-iron and the neighboring tyrosine in an oxidative self-processing pathway to generate the cross-link. In conclusion, this work serves as a new example while providing insights into the enzyme cross-link formation, allowing the design of artificial biocatalysts containing these novel cross-links with higher activity and pH adaptability.

Liu, Yiwei [Univ. of Texas, Austin, TX (United Sta↗
DOE OSTI2021

An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications

We present an updated analysis of the linker and core histone proteins and their proteoforms in the green microalga Chlamydomonas reinhardtii by top-down mass spectrometry (TDMS). The combination of high-resolution liquid chromatographic separation, robust fragmentation high, mass spectral resolution, the application of a custom search algorithm, and extensive manual analysis enabled the characterization of 86 proteoforms across all four core histones H2A, H2B, H3 and H4, and the linker histone H1. All canonical H2A paralogs, which vary in their C-termini, were identified, along with an unreported non-canonical variant that had both high levels of acetylation and C-terminal truncations. Similarly, a majority of the canonical H2B paralogs were identified, along with a smaller non-canonical variant, H2B.v, that was highly acetylated. Histone H4 exhibited a novel acetylation profile that differs significantly from that found in other organisms. A majority of H3 was monomethylated at K4, while a small fraction of H3 was trimethylated at K4 and also highly acetylated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Defect detection in atomic-resolution images via unsupervised learning with translational invariance

Abstract Crystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A broken translational symmetry state in an infinite-layer nickelate

A defining signature of strongly correlated electronic systems is a rich phase diagram, which consists of multiple broken symmetries, such as magnetism, superconductivity, and charge order. In the recently discovered nickelate superconductors a large antiferromagnetic exchange energy has been reported, which implies the existence of strong electronic correlations. However, signatures of a broken-symmetry state other than superconductivity have not yet been observed. Here, we observe charge ordering in infinite-layer nickelates La 1-x Sr x NiO 2 using resonant x-ray scattering. The parent compound orders along the Ni-O bond direction with an incommensurate wave vector, distinct from the stripe order observed in other nickelates that propagates along a direction 45º to the Ni-O bond. The resonance profile we measure indicates that ordering originates from the nickelate layers and induces a parasitic charge modulation of lanthanum electrons. After doping, the charge order diminishes and its wave vector shifts toward commensurate, indicating that strong electronic correlations are likely to be responsible for the ordered state. Our results suggest that the existence of charge order and its potential interplay with antiferromagnetic fluctuations and superconductivity are important themes in nickel-based superconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Advances in bioelectronics: Materials, devices, and translational applications

Modern electronics and materials science are bringing revolutionary advances to biointerface design and are shattering the limits of what is possible in the areas of biomedical diagnostics and sensing, neuroscience, and prosthetics. Furthermore, this special issue highlights the rapid progress in all areas of bioelectronics and includes contributions that explore the interfaces between electronics, materials science, and other engineering disciplines, as well as biochemistry, biophysics, and general biology.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Ab initio translationally invariant nucleon-nucleus optical potentials

We combine the ab initio symmetry-adapted no-core shell model (SA-NCSM) with the single-particle Green's function approach to construct optical potentials rooted in first principles. Specifically, we show that total cross sections and phase shifts for neutron elastic scattering from a 4 He target with projectile energies between 0.5 and 10 MeV closely reproduce the experiment. In addition, we discuss an important new development that resolves a long-standing issue with spurious center-of-mass motion in the Green's function formalism for many-body approaches. Furthermore, the new development opens a path for first-principle predictions of cross sections for elastic scattering of single-nucleon projectiles, nucleon capture, and deuteron breakup reactions, feasible for a broad range of open-shell spherical and deformed nuclei in the SA-NCSM approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗