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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Deep Sequencing-guided Design of a High Affinity Dual Specificity Antibody to Target Two Angiogenic Factors in Neovascular Age-related Macular Degeneration

The development of dual targeting antibodies promises therapies with improved efficacy over mono-specific antibodies. Here, we engineered a Two-in-One VEGF/angiopoietin 2 antibody with dual action Fab (DAF) as a potential therapeutic for neovascular age-related macular degeneration. Crystal structures of the VEGF/angiopoietin 2 DAF in complex with its two antigens showed highly overlapping binding sites. To achieve sufficient affinity of the DAF to block both angiogenic factors, we turned to deep mutational scanning in the complementarity determining regions (CDRs). By mutating all three CDRs of each antibody chain simultaneously, we were able not only to identify affinity improving single mutations but also mutation pairs from different CDRs that synergistically improve both binding functions. Furthermore, insights into the cooperativity between mutations allowed us to identify fold-stabilizing mutations in the CDRs. The data obtained from deep mutational scanning reveal that the majority of the 52 CDR residues are utilized differently for the two antigen binding function and permit, for the first time, the engineering of several DAF variants with sub-nanomolar affinity against two structurally unrelated antigens. Here, the improved variants show similar blocking activity of receptor binding as the high affinity mono-specific antibodies against these two proteins, demonstrating the feasibility of generating a dual specificity binding surface with comparable properties to individual high affinity mono-specific antibodies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Accelerating the Design of Solar Thermal Fuel Materials through High Throughput Simulations

Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastable structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.

Liu, Y↗
NASA NTRSDate not supplied

VIPER: Introduction to the Resource Prospecting Mission

With the Artemis Program, NASA plans to return humans to the Moon to stay, which means if there are local materials available, they could be deployed to help support extended lunar stays. Since the moon’s polar regions have confirmed the presence of volatiles, as revealed by LCROSS, LRO and other lunar missions, the next step is to understand the nature and distribution of those candidate resources and how they might be extracted. Recent studies have even indicated local volatiles could be processed into propellants and human life-supporting resources, significantly aiding in sustaining humans on the Moon, and eventually and later to support missions to Mars. The Volatiles Investigating Polar Exploration Resource (VIPER) is an in-situ resource utilization (ISRU) mission within NASA’s Science Mission Directorate (SMD), based on the pathfinding development of the Resource Prospector (RP) mission concept. This clever mission is targeting late 2023 and may spend over 100 days mapping and surveying four different Ice Stability Regions to understand the nature and distribution of water and volatiles already confirmed to be there, including measuring mineralogical content such as silicon and light metals from lunar regolith. The knowledge attained by a mission like VIPER could have many-fold benefits for space exploration, but also commercial applications. VIPER is an essential, early mission supporting the “moon rush” which has developed over the past few years, with both governments and commercial entities making their cases for lunar exploration. VIPER aims to understand just how the water-ice and other volatiles are distributed, both horizontally and vertically, enabling creation of volatiles resource maps, which will guide what might be required to harvest those resources at scale. With sufficient infrastructural investment, led by governments and then optimized by the commercial marketplace, VIPER will be a pathfinder mission addressing key decadal lunar science and early strategic knowledge gaps.

Daniel Andrews↗
DOE OSTI2022

Infrared spectroscopic signature of a hydroperoxyalkyl radical (•QOOH)

Infrared (IR) action spectroscopy is utilized to characterize a prototypical carbon-centered hydroperoxyalkyl radical (•QOOH) transiently formed in the oxidation of volatile organic compounds. The •QOOH radical formed in isobutane oxidation, 2-hydroperoxy-2-methylprop-1-yl, •CH 2 (CH 3 ) 2 COOH, is generated in the laboratory by H-atom abstraction from tert-butyl hydroperoxide (TBHP). IR spectral features of jet-cooled and stabilized •QOOH radicals are observed from 2950 to 7050 cm –1 at energies that lie below and above the transition state barrier leading to OH radical and cyclic ether products. The observed •QOOH features include overtone OH and CH stretch transitions, combination bands involving OH or CH stretch and a lower frequency mode, and fundamental OH and CH stretch transitions. Most features arise from a single vibrational transition with band contours well simulated at a rotational temperature of 10 K. In each case, the OH products resulting from unimolecular decay of vibrationally activated •QOOH are detected by UV laser-induced fluorescence. Assignments of observed •QOOH IR transitions are guided by anharmonic frequencies computed using second order vibrational perturbation theory, a 2 + 1 model that focuses on the coupling of the OH stretch with two low-frequency torsions, as well as recently predicted statistical •QOOH unimolecular decay rates that include heavy-atom tunneling. Most of the observed vibrational transitions of •QOOH are readily distinguished from those of the TBHP precursor. Furthermore, the distinctive IR transitions of •QOOH, including the strong fundamental OH stretch, provide a general means for detection of •QOOH under controlled laboratory and real-world conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Activity and Thermostability of GH5 Endoglucanase Chimeras from Mesophilic and Thermophilic Parents

Cellulases from glycoside hydrolase family 5 (GH5) are key endoglucanase enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical (βα) 8 -barrel structure, where each (βα) module is essential for the enzyme’s stability and activity. Despite their shared topology, the thermostability of GH5 endoglucanase enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications. Based on the previously characterized thermophilic GH5 endoglucanase Egl5A from Talaromyces emersonii ( Te Egl5A), which has an optimal temperature of 90°C, we created 10 hybrid enzymes with elements of the mesophilic endoglucanase Cel5 from Stegonsporium opalus ( So Cel5) to determine which elements are responsible for enhanced thermostability. Five of the expressed hybrid enzymes exhibit enzyme activity. Two of these hybrids exhibited pronounced increases in the temperature optimum (10 and 20°C), the temperature at which the protein lost 50% of its activity ( T 50 ) (15 and 19°C), and the melting temperature ( T m ) (16.5 and 22.9°C) and extended half-lives ( t 1/2 ) (~240- and 650-fold at 55°C) relative to the values for the mesophilic parent enzyme and demonstrated improved catalytic efficiency on selected substrates. The successful hybridization strategies were validated experimentally in another GH5 endoglucanase, Cel5 from Aspergillus niger ( An Cel5), which demonstrated a similar increase in thermostability. Based on molecular dynamics (MD) simulations of both the So Cel5 and Te Egl5A parent enzymes and their hybrids, we hypothesize that improved hydrophobic packing of the interface between α 2 and α 3 is the primary mechanism by which the hybrid enzymes increase their thermostability relative to that of the mesophilic parent So Cel5.Thermal stability is an essential property of enzymes in many industrial biotechnological applications, as high temperatures improve bioreactor throughput. Many protein engineering approaches, such as rational design and directed evolution, have been employed to improve the thermal properties of mesophilic enzymes. Structure-based recombination has also been used to fuse TIM barrel fragments, and even fragments from unrelated folds, to generate new structures. However, little research has been done on GH5 endoglucanases. In this study, two GH5 endoglucanases exhibiting TIM barrel structure, So Cel5 and Te Egl5A, with different thermal properties, were hybridized to study the roles of different (βα) motifs. This work illustrates the role that structure-guided recombination can play in helping to identify sequence function relationships within GH5 enzymes by supplementing natural diversity with synthetic diversity.

09 BIOMASS FUELS↗
DOE OSTI2019

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

Human liver glycerol 3-phosphate dehydrogenase (hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme–substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. Here, these results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

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

End-to-end Analytics for Grid Arch Design & All-hazard Assessment

Resiliency, reliability, and security of the next-generation smart grid depend upon leveraging advanced communication and computing technologies, integrating them with physical power systems, and developing real-time, fast, data-based applications to help in wide-area monitoring and control of the grid. Using a high sampling data rate from phasor measurement units (PMUs) to develop applications has opened the door to achieving the next-generation grid requirements. The North American Synchrophasor Initiative Network (NASPlnet) was developed in 2007-09 to create a standard and guide for PMU data exchanges. With the advancement in both networking and grid requirements, it is necessary to evaluate the performance of different NASPInet versions and their impact on applications. Therefore, we need a cyber-power cosimulation framework that supports very large-scale co-simulation capable of running in parallel, high-performance computing platforms and capturing real-life network behavior. This work presents a cyber-physical co-simulation testbed using NS3 to model the communication network, GridPACK to model the power grid, and HELICS as a co-simulation engine. Comparative analysis of latency in synchrophasor networks and a performance evaluation of a power system stabilizer application based on PMU data in an Institute of Electrical and Electronics Engineers 39-bus test system is presented using this co-simulation testbed.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Toward efficient single-atom catalysts for renewable fuels and chemicals production from biomass and CO 2

Transformation of biomass and CO 2 into renewable value-added chemicals and fuels has been identified as a promising strategy to fulfill high energy demands, lower greenhouse gas emissions, and exploit under-utilized resources. Cost-effective and performance-efficient catalysts are of great importance to lowering the conversion cost of biomass and CO 2 . Significant progress has been made to advance the catalyst design for these processes, with metal catalysts playing a critical role in many involved catalytic reactions. Traditional nanoparticle-based metal catalysts still require improvement in metal utilization rates, stability, and selectivity tunability. Single-atom catalysts, which have maximum atomic efficiency and a uniform and tunable metal center, as well as an adjustable metal-support interaction, provide potential opportunities to boost catalyst efficiency and thermal stability. Their well-defined and uniform structure also provides advantages to fundamental studies for understanding of the intrinsic reaction mechanism and site requirement in biomass and CO 2 conversion. In this article, we summarize and highlight the recent advances in converting biomass and CO 2 to renewable fuels and chemicals using single-atom catalysts. We discuss the design principles of single-atom catalysts and their potential applications to biomass and CO 2 upgrading as well as the origins of catalytic activity. Moreover, we compare the catalytic efficiency of various catalysts reported thus to provide a fair assessment of these catalysts. Finally, perspectives are given on the interesting fields that may guide future studies.

09 BIOMASS FUELS↗
NASA NTRSDate not supplied

Petrologic Sub-types, Sub-groups, and Pairing for CV Chondrites in the US Antarctic Meteorite Collection

Carbonaceous chondrites of the Vigarano group (CV) are primitive meteorites that provide a wealth of information about the early solar system, including constraints on chondrule formation, origin of calcium-aluminum inclusions, stability of organic compounds, and redox conditions. The US Antarctic meteorite collection contains 119 CV samples from 15 dense collection areas (DCAs) from the Trans-Antarctic Mountains. These samples have been assigned a preliminary classification as CVs, but have not been assigned to the subgroups Oxidized A, Oxidized B, and Reduced. Additionally, variation in petrologic grade can be determined non-destructively using Raman spectroscopy. In order to update classification of both subgroups and petrologic types in the collection, we have acquired magnetic susceptibility, metal and sulfide compositions, and Raman spectra, for as many samples as possible. We use the recent assessment and delineation of CV sub-groups of as a guide.

solar nebula↗
DOE OSTI2026

Solvation-guided inhibition of manganese dissolution of lithium- and manganese- rich cathode via cyclic carbonate molecular engineering

Lithium and manganese-rich (LMR) layered oxides represent a leading class of high-energy cathode materials, but their practical realization is fundamentally limited by severe manganese (Mn) dissolution, a process that triggers structural degradation and rapid capacity fade. While mitigation efforts have predominantly focused on interfacial engineering, the intrinsic contribution of bulk electrolyte solvation to this degradation pathway remains largely unexplored, primarily due to the difficulty of deconvolving its effects from concurrent cathode-electrolyte interphase (CEI) formation. Here, we report an experimental design to isolate the role of solvation. We systematically varied the electrolyte solvent solvation power by substituting the strongly coordinating ethylene carbonate (EC) with its weaker coordinating fluorinated derivatives, fluoroethylene carbonate (FEC) and trans-4,5-Difluoro-1,3-dioxolan-2-one (DFEC), while maintaining a consistent interfacial chemistry. Remarkably, the electrolyte formulated with the weakest solvent, DFEC, exhibits superior cycling stability, suppressing Mn dissolution by up to 63% relative to the conventional EC-based system. Post-mortem analysis unequivocally attributes this performance enhancement to the preservation of the LMR cathode's structural integrity, a direct consequence of mitigated Mn dissolution. This work provides conclusive evidence that modulating bulk electrolyte solvation is a potent and direct strategy for stabilizing LMR cathodes, establishing a vital design principle for next-generation battery systems.

25 ENERGY STORAGE↗
DOE OSTI2015

Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. Here, as anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Out of the Lab: 3D Printing on Non-Ideal Surfaces

In this work, coaxial direct ink writing is utilized to print sensitive or encapsulated materials onto heterogeneous and rough substrates. By enclosing the core fluid within a rigid ceramic shell, continuity is maintained even when printing on substrates traditionally considered challenging. This work presents the development of a coaxial ceramic direct ink writing system and investigates co-flow dynamics through microfluidic principles. A specially designed coaxial nozzle enables the co-extrusion of an alumina shell, with indium-tin-oxide inks serving as the core material. This approach allows the fabrication of core-shell ceramic structures suitable for future high-temperature applications on rough surfaces. The colloidal inks are tailored to achieve the necessary rheological properties and sintering performance. Additionally, flow simulations, guided by microfluidic co-flow principles, are employed to define the processing parameters for coaxial printing, ensuring precise control over the core-shell architectures. Physical modeling is further applied to study core deformation and eccentricity. These simulations are experimentally validated, supporting the successful deposition of coaxial ceramic features on heterogeneous, high-temperature ceramic substrates.

20 FOSSIL-FUELED POWER PLANTS↗
NASA NTRSDate not supplied

Design and Technology Maturation of the Stratospheric Projectile Experiment of Entry Dynamics

The supersonic and transonic dynamic stability of blunt-body reentry vehicles currently poses large risks in all of NASA’s ongoing entry missions (MSR SRL, MSR EES, and Dragonfly). These projects have allocated millions of dollars to testing and modeling efforts to buy down risk by using the current state-of-the-art (SoA) facilities at NASA’s disposal. While these facilities have heritage in supplying dynamics data to reentry missions, their availability is severely limited – particularly with the high number of concur-rent projects requesting simultaneous testing– and are costly when considering the science density per dollar. None of the current SoA facility methodologies allow the test model to have the dynamics fully develop through a flight relevant free-stream profile and as such require extrapolations with resultant high uncertainties in order to relate the test dynamics to flight expectations. SPEED is a NASA Ames Center Innovation Fund (CIF) project that is developing a highly tailorable and cost-effective test methodology to better assess the dynamic stability of blunt-body reentry vehicles via a stratospheric balloon flight. This is accomplished by dropping a suite of instrumented capsules from a stratospheric balloon to gain a statistically relevant dataset of scaled reentry vehicles in mission relevant free-flight conditions. This presentation will walk through how the test methodology is being implemented specifically for the Mars Sample Return (MSR) Earth Entry System (EES) geometry in an awarded Flight Opportunities Program (FOP) test flight in early CY24. SPEED Application to MSR: SPEED consists of three main mechanical systems: the Drop Platform, the Projectile, and the test Capsule. SPEED is being developed as a set of guidelines and recommendations for how to test with the proposed Concept of Operations (Conops) since the specific design parameters will vary depending on the specific project’s reference trajectory and entry vehicle design. As such, this presentation will walk through the development time-line as shown in Fig. 2. This is meant to serve as a blueprint for further missions as desired. Mechanical and Avionics Design. The SPEED test platform designed for the MSR-EES capsule geometry with nominal entry parameters has the ability to carry 10 Capsules to altitude instrumented with: 1. 3-Axis Accelerometer 2. IMU 3. Gyroscope 4. Magnetometer 5. Pressure Transducer cruciform 6. Uplook and Horizon Cameras To package the avionics/instrumentation suite, the capsule is approximately 1’ in diameter with the Outer Mold Line (OML) centroid-scaled from the full EES design. The internal volume is gutted and custom-shaped to fit the desired instrumentation suite, as well as to allow for the positioning of ballast mass such that the Center of Gravity is analogous to the flight vehicle. All structural components in the Capsule and Projectile are 3D printed, which significantly reduces the cost of each flight unit to around $1500 including all instrumentation, avionics, and structural components. Flight Conops. The test Capsule is accelerated to the desired altitude and Mach number while stowed in the Projectile, a missile-like vehicle consisting of steel ballast in the nose, a low-drag OML, and an Ejection Mechanism to reliably release the Capsule into the free-flow supersonic conditions. For the MSR-EES design, the capsule employs ~3kg of ballast mass at the nose to accelerate the 1.25kg test Capsule to ~Mach 1.7 at 23km altitude. This requires an initial release altitude of 40km, the quoted limit of a 80kg payload by the FOP-contracted balloon provider. Once the Ejection Mechanism avionics detect the proper conditions, the spring-loaded Ejection Mechanism will release and – guided by the sabot – expose the test Capsule to the desired test conditions for ~5 seconds of free-flight in the supersonic/transonic regimes. Dynamics in the subsonic regime will also be captured with the instrumentation suite with post-flight recovery operations aimed at recovering the high-G-load capable SD cards after the planned hard impact landings. Testing and Development: In the few months the SPEED project has worked the development of MSR-EES flight test, the team has performed lab and drone based testing which this presentation will overview. After the first design phase, the team fabricated Engineering Demonstration Units (EDUs) of all subsystems to perform validation testing shown in Fig. 5. After validation was completed on the subsystem level, a drone-drop test was performed at the recreational flight ceiling of 400ft altitude to assess the SPEED systems in a flight environment. Parameters such as in-flight stability, hard impact landing performance, and avionics performance were quantified and qualified. The FY23 CIF will culminate in a helicopter drop test aboard an Air National Guard Blackhawk. This will prepare the team for the CY24 FOP stratospheric balloon flight that should provide the final verification to begin offering the test platform for mission support. Focus of Presentation: This presentation will outline the technology maturation path of the SPEED implementation to the MSR-EES capsule baseline as well as the details regarding the mechanical system, avionics and instrumentation, and flight operations. Note that a complementary presentation is being submitted for a methodology overview of the SPEED test platform, introducing the testing technique and benefits as well as the full application space of the technology.

pitch damping coefficient↗
DOE OSTI2021

Adding Tree Rings to North America's National Forest Inventories: An Essential Tool to Guide Drawdown of Atmospheric CO 2

Tree-ring time series provide long-term, annually resolved information on the growth of trees. When sampled in a systematic context, tree-ring data can be scaled to estimate the forest carbon capture and storage of landscapes, biomes, and—ultimately—the globe. A systematic effort to sample tree rings in national forest inventories would yield unprecedented temporal and spatial resolution of forest carbon dynamics and help resolve key scientific uncertainties, which we highlight in terms of evidence for forest greening (enhanced growth) versus browning (reduced growth, increased mortality). We describe jump-starting a tree-ring collection across the continent of North America, given the commitments of Canada, the United States, and Mexico to visit forest inventory plots, along with existing legacy collections. Failing to do so would be a missed opportunity to help chart an evidence-based path toward meeting national commitments to reduce net greenhouse gas emissions, urgently needed for climate stabilization and repair.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

In-situ transmission electron microscopy investigation on surface oxides thermal stability of niobium

Niobium is commonly used for superconducting quantum systems as readout resonators, capacitors, and interconnects. Structural defects at the Nb/Si and air/Nb interface may be a major source of two-level systems (TLS), which are detrimental to the device's coherence time. Thus, identifying and understanding the microscopic origin of possible TLS in Nb-based devices and their relationship to processing is key to superconducting qubit performance improvement. Here this work studied the structure and thermal stability of surface oxide on physical vapor deposited Nb films on Si wafers, using aberration-corrected (scanning) transmission electron microscopy and spectroscopy. Here, all Nb films exhibit columnar growth with strong [110] textures. After in-situ heating of the heterostructure at 360 °C inside the microscope, the initial amorphous niobium surface oxides decompose into face-centered cubic Nb nanograins in the amorphous Nb-O matrix, which may reduce microwave dissipation. Despite changes in the microstructure and chemistry of the niobium oxide surface layer due to heat treatment, the interface between the Nb and the surface oxide layer remains almost unchanged. Our comprehensive study of the Nb surface oxide decomposition mechanism may guide future superconducting qubit device optimization through interfacial scattering center and TLS minimization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Enzymatic reconstitution of ribosomal peptide backbone thioamidation

Methyl-coenzyme M reductase (MCR) is an essential enzyme found strictly in methanogenic and methanotrophic archaea. MCR catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α-subunit of this enzyme (McrA) contains several unusual posttranslational modifications, including the only known naturally occurring example of protein thioamidation. We have recently demonstrated by genetic deletion and mass spectrometry that the tfuA and ycaO genes of Methanosarcina acetivorans are involved in thioamidation of Gly465 in the MCR active site. Modification to thioGly has been postulated to stabilize the active site structure of MCR. Herein, we report the in vitro reconstitution of ribosomal peptide thioamidation using heterologously expressed and purified YcaO and TfuA proteins from M. acetivorans . Like other reported YcaO proteins, this reaction is ATP-dependent but requires an external sulfide source. We also reconstitute the thioamidation activity of two TfuA-independent YcaOs from the hyperthermophilic methanogenic archaea Methanopyrus kandleri and Methanocaldococcus jannaschii . Using these proteins, we demonstrate the basis for substrate recognition and regioselectivity of thioamide formation based on extensive mutagenesis, biochemical, and binding studies. Finally, we report nucleotide-free and nucleotide-bound crystal structures for the YcaO proteins from M. kandleri . Sequence and structure-guided mutagenesis with subsequent biochemical evaluation have allowed us to assign roles for residues involved in thioamidation and confirm that the reaction proceeds via backbone O -phosphorylation. We conclude these data assign a new biochemical reaction to the YcaO superfamily and paves the way for further characterization of additional peptide backbone posttranslational modifications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Biological Small Angle Scattering: Techniques, Strategies and Tips

This book provides a clear, comprehensible and up-to-date description of how Small Angle Scattering (SAS) can help structural biology researchers. SAS is an efficient technique that offers structural information on how biological macromolecules behave in solution. SAS provides distinct and complementary data for integrative structural biology approaches in combination with other widely used probes, such as X-ray crystallography, Nuclear magnetic resonance, Mass spectrometry and Cryo-electron Microscopy. The development of brilliant synchrotron small-angle X-ray scattering (SAXS) beam lines has increased the number of researchers interested in solution scattering. SAS is especially useful for studying conformational changes in proteins, highly flexible proteins, and intrinsically disordered proteins. Small-angle neutron scattering (SANS) with neutron contrast variation is ideally suited for studying multi-component assemblies as well as membrane proteins that are stabilized in surfactant micelles or vesicles. SAS is also used for studying dynamic processes of protein fibrillation in amyloid diseases, and pharmaceutical drug delivery. The combination with size-exclusion chromatography further increases the range of SAS applications.The book is written by leading experts in solution SAS methodologies. The principles and theoretical background of various SAS techniques are included, along with practical aspects that range from sample preparation to data presentation for publication. Topics covered include techniques for improving data quality and analysis, as well as different scientific applications of SAS. With abundant illustrations and practical tips, we hope the clear explanations of the principles and the reviews on the latest progresses will serve as a guide through all aspects of biological solution SAS.The scope of this book is particularly relevant for structural biology researchers who are new to SAS. Advanced users of the technique will find it helpful for exploring the diversity of solution SAS methods and applications.

Chaudhuri, Barnali↗