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At least 1,387 records · Page 77

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↗

Structural maturation of myofilaments in engineered 3D cardiac microtissues characterized using small angle x-ray scattering

Abstract Understanding the structural and functional development of human-induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) is essential to engineering cardiac tissue that enables pharmaceutical testing, modeling diseases, and designing therapies. Here we use a method not commonly applied to biological materials, small angle x-ray scattering, to characterize the structural development of hiPSC-CMs within three-dimensional engineered tissues during their preliminary stages of maturation. An x-ray scattering experimental method enables the reliable characterization of the cardiomyocyte myofilament spacing with maturation time. The myofilament lattice spacing monotonically decreases as the tissue matures from its initial post-seeding state over the span of 10 days. Visualization of the spacing at a grid of positions in the tissue provides an approach to characterizing the maturation and organization of cardiomyocyte myofilaments and has the potential to help elucidate mechanisms of pathophysiology, and disease progression, thereby stimulating new biological hypotheses in stem cell engineering.

36 MATERIALS SCIENCE↗

Continuous Risk Management at NASA

NPG 7120.5A, "NASA Program and Project Management Processes and Requirements" enacted in April, 1998, requires that "The program or project manager shall apply risk management principles..." The Software Assurance Technology Center (SATC) at NASA GSFC has been tasked with the responsibility for developing and teaching a systems level course for risk management that provides information on how to comply with this edict. The course was developed in conjunction with the Software Engineering Institute at Carnegie Mellon University, then tailored to the NASA systems community. This presentation will briefly discuss the six functions for risk management: (1) Identify the risks in a specific format; (2) Analyze the risk probability, impact/severity, and timeframe; (3) Plan the approach; (4) Track the risk through data compilation and analysis; (5) Control and monitor the risk; (6) Communicate and document the process and decisions. This risk management structure of functions has been taught to projects at all NASA Centers and is being successfully implemented on many projects. This presentation will give project managers the information they need to understand if risk management is to be effectively implemented on their projects at a cost they can afford.

Hammer, Theodore F.↗

Deblurring

In most instances, traditional EEG methodology provides insufficient spatial detail to identify relationships between brain electrical events and structures and functions visualized by magnetic resonance imaging or positron emission tomography. This article describes a method called Deblurring for increasing the spatial detail of the EEG and for fusing neurophysiologic and neuroanatomic data. Deblurring estimates potentials near the outer convexity of the cortex using a realistic finite element model of the structure of a subject's head determined from their magnetic resonance images. Deblurring is not a source localization technique and thus makes no assumptions about the number or type of generator sources. The validity of Deblurring has been initially tested by comparing deblurred data with potentials measured with subdural grid recordings. Results suggest that deblurred topographic maps, registered with a subject's magnetic resonance imaging and rendered in three dimensions, provide better spatial detail than has heretofore been obtained with scalp EEG recordings. Example results are presented from research studies of somatosensory stimulation, movement, language, attention and working memory. Deblurred ictal EEG data are also presented, indicating that this technique may have future clinical application as an aid to seizure localization and surgical planning.

Non-NASA Center↗

Defining the S-Glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches

Protein S-glutathionylation (SSG) is a reversible post-translational modification (PTM) featuring the conjugation of glutathione to a protein cysteine thiol. SSG can alter protein structure, activity, subcellular localization, and interaction with small molecules and other proteins. Thus, it plays a critical role in redox signaling and regulation in various physiological activities and pathological events. In this review, we summarize current biochemical and analytical approaches for characterizing SSG at both the proteome level and at individual protein levels. To illustrate the mechanism underlying SSG-mediated redox regulation, we highlight recent examples of functional and structural consequences of SSG modifications. Finally, we discuss the analytical challenges in characterizing SSG and the thiol PTM landscape, future directions for understanding of the role of SSG in redox signaling and regulation and its interplay with other PTMs, and the potential role of computational approaches to accelerate functional discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Electronic Structure of InAs and InSb Surfaces: Density Functional Theory and Angle-Resolved Photoemission Spectroscopy

The electronic structure of surfaces plays a key role in the properties of quantum devices. However, surfaces are also the most challenging to simulate and engineer. Here, in this work, the electronic structure of InAs(001), InAs(111), and InSb(110) surfaces is studied using a combination of density functional theory (DFT) and angle-resolved photoemission spectroscopy (ARPES). Large-scale first principles simulations are enabled by using DFT calculations with a machine-learned Hubbard U correction [npj Comput. Mater. 6, 180 (2020)]. To facilitate direct comparison with ARPES results, a “bulk unfolding” scheme is implemented by projecting the calculated band structure of a supercell surface slab model onto the bulk primitive cell. For all three surfaces, a good agreement is found between DFT calculations and ARPES. For InAs(001), the simulations clarify the effect of the surface reconstruction. Different reconstructions are found to produce distinctive surface states, which may be detected by ARPES with low photon energies. For InAs(111) and InSb(110), the simulations help elucidate the effect of oxidation. Owing to larger charge transfer from As to O than from Sb to O, oxidation of InAs(111) leads to significant band bending and produces an electron pocket, whereas oxidation of InSb(110) does not. The combined theoretical and experimental results may inform the design of quantum devices based on InAs and InSb semiconductors, for example, topological qubits utilizing the Majorana zero modes.

42 ENGINEERING↗

Phase-Field Modeling of Materials Interfaces and Nanostructures

Nanostructured materials offer unique properties for a wide range of energy applications. Among various known processing methods, liquid metal dealloying (LMD)—the selective dissolution of a base alloy element into a metallic melt—has emerged as a powerful technique to produce a new class of nano-/meso-scale open porous and bicontinuous composite structures with ultra-high interfacial area. LMD has recently been complemented by the advent of vapor phase dealloying (VPD), a novel technique that exploits the selective evaporation of one element from a parent alloy containing elements with very different vapor pressures, thereby enabling to fabricate open nanoporous structures of various elements from less-noble metals to inorganic elements regardless of their chemical activity without requiring high LMD temperatures and chemical etching. Together LMD and VPD have greatly expanded the scope of dealloying techniques, limited by traditional electrochemical means to noble metals, and boosted the design of new functional and structural materials that combine a wide variety of elements. Topologically-connected open porous structures with ultra-high surface area allow mass transport within the structure while preserving structural integrity, enabling them to serve as catalysts, fuel cells, supercapacitors, or high-capacity battery materials. Bicontinuous composite structures in turn can display high strength and high ductility or superior radiation-damage resistance due to the ultra-high interface area between interpenetrating solid phases. This research program makes use of state-of-the-art computational methods to understand at a basic level the self-organizing dealloying process with main focus on dealloying kinetics and interfacial pattern formation at the dealloying front controlling initial structure size, topology, and phase compositions. Phase-field simulation studies of LMD focus on solid solutions, line compounds, and intermetallic systems that can form ternary composites by nucleation and growth of a new phase. Studies of VPD employ phase-field modeling and a hybrid method combining a kinetic Monte Carlo (KMC) model of evaporation and surface diffusion with molecular dynamics for vapor-phase transport inside nanopores. Simulations explore mechanisms of interface- and diffusion-controlled dealloying kinetics, both observed in VPD but not fundamentally understood. In addition, our newly developed multi-physics phase-field approach of large-volume-change phase transformations is being used to model novel 3D anode geometries based on dealloyed nanoporous structures including novel sandwiched graphene/Si/silica for highrate Li ion battery. Those studies are aimed at elucidating geometric design principles that improve mechanical stability. We expect this research to enhance the capability to tailor nano-/mesoscale structures for a wide range of energy-related materials applications and to yield further advances in computational methodologies that benefit a broad materials research community.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Latent Representation Learning for Structural Characterization of Catalysts

Supervised machine learning-enabled mapping of the X-ray absorption near edge structure (XANES) spectra to local structural descriptors offers new methods for understanding the structure and function of working nanocatalysts. We briefly summarize a status of XANES analysis approaches by supervised machine learning methods. We present an example of an autoencoder-based, unsupervised machine learning approach for latent representation learning of XANES spectra. This new approach produces a lower-dimensional latent representation, which retains a spectrum–structure relationship that can be eventually mapped to physicochemical properties. Furthermore, the latent space of the autoencoder also provides a pathway to interpret the information content “hidden” in the X-ray absorption coefficient. Our approach (that we named latent space analysis of spectra, or LSAS) is demonstrated for the supported Pd nanoparticle catalyst studied during the formation of Pd hydride. By employing the low-dimensional representation of Pd K-edge XANES, the LSAS method was able to isolate the key factors responsible for the observed spectral changes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure

The ribose 2'-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2'-OH orientation (H2'-C2'-O2'-HO2' torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2'-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3', 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2'-OD backbone-orientation. GAGA-tetraloop riboses display a 2'-OD base-orientation. An atypical C2'-endo sugar pucker is strictly correlated with a 2'-OD sugar-orientation. Neutrons reveal the strong preference of the 2'-OH to donate in H-bonds and that 2'-OH orientation affects both backbone geometry and ribose pucker. We discuss 2'-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.

59 BASIC BIOLOGICAL SCIENCES↗

Countermeasures for Maintenance of Cardiovascular and Muscle Function in Space Flight

In this session, Session FA2, the discussion focuses on the following topics: Effects of Repeated Long Duration +2Gz Load on Man's Cardiovascular Function; Certain Approaches to the Development of On-Board Automated Training System; Cardiac, Arterial, and Venous Adaptation to Og during 6 Month MIR-Spaceflights with and without "Thigh Cuffs" (93-95); Space Cycle(TM) Induced Physiologic Responses; Muscular Deconditioning During Long-term Spaceflight Exercise Recommendations to Optimize Crew Performance; Structure And Function of Knee Extensors After Long-Duration Spaceflight in Man, Effects of Countermeasure Exercise Training; Force and power characteristics of an exercise ergometer designed for use in space; and The simulating of overgravity conditions for astronauts' motor apparatus at the conditions of the training for orbital flights.

Source record↗

QCD hidden-color hexadiquark in the core of nuclei

Hidden-color configurations are a key prediction of QCD with important physical consequences. In this work we examine a QCD color-singlet configuration in nuclei formed by combining six scalar [ud] diquarks in a strongly bound SU (3) C channel. The resulting hexadiquark state is a charge-2, spin-0, baryon number-4, isospin-0, color-singlet state. It contributes to alpha clustering in light nuclei and to the additional binding energy not saturated by ordinary nuclear forces in as well as the alpha-nuclei sequence of interest for nuclear astrophysics. We show that the strongly bound combination of six scalar isospin-0 [ud] diquarks within the nuclear wave function - relative to free nucleons - provides a natural explanation of the EMC effect measured by the CLAS collaboration's comparison of nuclear parton distribution function ratios for a large range of nuclei. Overall, these experiments confirmed that the EMC effect; i.e., the distortion of quark distributions within nuclei, is dominantly identified with the dynamics of neutron-proton (“isophobic”) short-range correlations within the nuclear wave function rather than proton-proton or neutron-neutron correlations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division

ABSTRACT Cell elongation and division are essential aspects of the bacterial life cycle that must be coordinated for viability and replication. The impact of misregulation of these processes is not well understood as these systems are often not amenable to traditional genetic manipulation. Recently, we reported on the CenKR two-component system (TCS) in the Gram-negative bacterium Rhodobacter sphaeroides that is genetically tractable, widely conserved in α-proteobacteria, and directly regulates the expression of components crucial for cell elongation and division, including genes encoding subunit of the Tol-Pal complex. In this work, we show that overexpression of cenK results in cell filamentation and chaining. Using cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), we generated high-resolution two-dimensional (2D) images and three-dimensional (3D) volumes of the cell envelope and division septum of wild-type cells and a cenK overexpression strain finding that these morphological changes stem from defects in outer membrane (OM) and peptidoglycan (PG) constriction. By monitoring the localization of Pal, PG biosynthesis, and the bacterial cytoskeletal proteins MreB and FtsZ, we developed a model for how increased CenKR activity leads to changes in cell elongation and division. This model predicts that increased CenKR activity decreases the mobility of Pal, delaying OM constriction, and ultimately disrupting the midcell positioning of MreB and FtsZ and interfering with the spatial regulation of PG synthesis and remodeling. IMPORTANCE By coordinating cell elongation and division, bacteria maintain their shape, support critical envelope functions, and orchestrate division. Regulatory and assembly systems have been implicated in these processes in some well-studied Gram-negative bacteria. However, we lack information on these processes and their conservation across the bacterial phylogeny. In R. sphaeroides and other α-proteobacteria, CenKR is an essential two-component system (TCS) that regulates the expression of genes known or predicted to function in cell envelope biosynthesis, elongation, and/or division. Here, we leverage unique features of CenKR to understand how increasing its activity impacts cell elongation/division and use antibiotics to identify how modulating the activity of this TCS leads to changes in cell morphology. Our results provide new insight into how CenKR activity controls the structure and function of the bacterial envelope, the localization of cell elongation and division machinery, and cellular processes in organisms with importance in health, host-microbe interactions, and biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

Evolutionary changes in transcriptional regulation undoubtedly play an important role in creating morphological diversity. However, there is little information about the evolutionary dynamics of cis-regulatory sequences. This study examines the functional consequence of evolutionary changes in the Endo16 promoter of sea urchins. The Endo16 gene encodes a large extracellular protein that is expressed in the endoderm and may play a role in cell adhesion. Its promoter has been characterized in exceptional detail in the purple sea urchin, Strongylocentrotus purpuratus. We have characterized the structure and function of the Endo16 promoter from a second sea urchin species, Lytechinus variegatus. The Endo16 promoter sequences have evolved in a strongly mosaic manner since these species diverged approximately 35 million years ago: the most proximal region (module A) is conserved, but the remaining modules (B-G) are unalignable. Despite extensive divergence in promoter sequences, the pattern of Endo16 transcription is largely conserved during embryonic and larval development. Transient expression assays demonstrate that 2.2 kb of upstream sequence in either species is sufficient to drive GFP reporter expression that correctly mimics this pattern of Endo16 transcription. Reciprocal cross-species transient expression assays imply that changes have also evolved in the set of transcription factors that interact with the Endo16 promoter. Taken together, these results suggest that stabilizing selection on the transcriptional output may have operated to maintain a similar pattern of Endo16 expression in S. purpuratus and L. variegatus, despite dramatic divergence in promoter sequence and mechanisms of transcriptional regulation.

NASA Discipline Evolutionary Biology↗

Thin‐Film Ferroelectrics

Abstract Over the last 30 years, the study of ferroelectric oxides has been revolutionized by the implementation of epitaxial‐thin‐film‐based studies, which have driven many advances in the understanding of ferroelectric physics and the realization of novel polar structures and functionalities. New questions have motivated the development of advanced synthesis, characterization, and simulations of epitaxial thin films and, in turn, have provided new insights and applications across the micro‐, meso‐, and macroscopic length scales. This review traces the evolution of ferroelectric thin‐film research through the early days developing understanding of the roles of size and strain on ferroelectrics to the present day, where such understanding is used to create complex hierarchical domain structures, novel polar topologies, and controlled chemical and defect profiles. The extension of epitaxial techniques, coupled with advances in high‐throughput simulations, now stands to accelerate the discovery and study of new ferroelectric materials. Coming hand‐in‐hand with these new materials is new understanding and control of ferroelectric functionalities. Today, researchers are actively working to apply these lessons in a number of applications, including novel memory and logic architectures, as well as a host of energy conversion devices.

Fernandez, Abel↗

Hole–hole Tamm–Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation

The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole–hole Tamm–Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole–hole counterpart to the more established particle–particle TDA (pp-TDA) method, both of which are derived from the particle–particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. Furthermore, the treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. Additionally, we show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states—particularly those with both low-lying ππ* and nπ* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Review on Bioinspired Proton Exchange Membrane Fuel Cell: Design and Materials

With the climate crisis gathering recognition, there has been significant interest in clean energy. As a reliable and clean energy solution, markets transitioning toward sustainable energy have identified polymer electrolyte membrane fuel cells (PEMFCs) as a critical technology. The increasing interest in PEMFCs is primarily due to their high energy density, high efficiency and zero greenhouse gas emission. However, additional development is required to overcome the current barriers associated with fuel cell component design, high manufacturing cost, and insufficient stability. Bioinspired designs have the potential to provide new and valuable insights using novel techniques for extracting design inspirations from biological structures. Applying these design concepts to develop materials and structures for various fuel cell components can be transformative. The well–adapted structures and functional features of biological systems have been proven to greatly enhance the performance of current designs through novel and optimized pathways. Bioinspired designs have indeed lived up to performance expectations and even exceed them. Herein, the potential and value of using these bioinspired designs are discussed. Recent studies and advancements based on nature–inspired structures for components of PEMFCs and how these design considerations substantiate their claim as an attractive alternative to conventional designs are discussed.

25 ENERGY STORAGE↗

Correlating activities and defects in (photo)electrocatalysts using in-situ multi-modal microscopic imaging

Photo(electro)catalysts use sunlight to drive chemical reactions such as water splitting. A major factor limiting photocatalyst development is physicochemical heterogeneity which leads to spatially dependent reactivity. To link structure and function in such systems, simultaneous probing of the electrochemical environment at microscopic length scales and a broad range of timescales (ns to s) is required. Here, we address this challenge by developing and applying in- situ (optical) microscopies to map and correlate local electrochemical activity, with hole lifetimes, oxygen vacancy concentrations and photoelectrode crystal structure. Using this multi-modal approach, we study prototypical hematite (α-Fe 2 O 3 ) photoelectrodes. We demonstrate that regions of α-Fe 2 O 3 , adjacent to microstructural cracks have a better photoelectrochemical response and reduced back electron recombination due to an optimal oxygen vacancy concentration, with the film thickness and extended light exposure also influencing local activity. Our work highlights the importance of microscopic mapping to understand activity, in even seemingly homogeneous photoelectrodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

RANGERS: Modeling Report on Integrity and Performance Assessment of Engineered Barrier Systems in a Salt Repository for HLW/SNF

The Engineered Barrier System (EBS) plays an important role in ensuring the long-term safety and containment of high-level waste (HLW) and spent nuclear fuel (SNF) in deep geological repositories in salt formation. As part of a multi-barrier system, the EBS works alongside the natural barrier, which is the salt formation itself and the technical barrier comprising the disposal casks. The primary function of the EBS is to maintain containment during a defined period until the backfill used in the repository made of crushed salt, develops its sealing capacity through compaction. Over the time, the backfill eventually compacts to a state of low porosity and permeability, acting as a long-term seal. However, until this process is complete, the EBS must retain its structural and functional integrity. Regulatory guidelines in Germany currently require the EBS to remain effective for up to next ice age, that is expected in 50,000 years. The significant hydro-geological and topographic changes expected during an ice age could make it impossible to accurately predict the hydro-chemical conditions within the repository system at that time. In response to these challenges, BGE TECHNOLOGY GmbH (BGE TEC) and Sandia National Laboratories (SNL) have jointly developed a comprehensive methodology for the design and safety assessment of engineered barrier systems within the scope of the RANGERS project. This methodology is tailored for repositories in salt formations. The developed methodology provides a structured approach for designing and assessing the performance of the EBS in salt-based repositories. It begins with defining a sealing concept based on the geological characteristics of the selected site and the overall repository design. The entire repository system, comprising the geological site, repository infrastructure, and EBS, is then subjected to a Features, Events, and Processes (FEP) analysis, focusing solely on those FEPs that affect the EBS. The derived FEPs help identify the loads and stresses acting on the EBS, which serve as the foundation for conducting an integrity assessment. This analysis helps predict the EBS’s evolution and performance over the regulatory time frame, feeding into integrated performance assessment simulations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗