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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis Xylan O-acetyltransferase XOAT1

Xylans are a major component of plant cell walls. O-Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis (Arabidopsis thaliana) xylan O-acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the a/ß/a topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac–Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.

acetylation↗
DOE OSTI2025

Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree

The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase fromHevea brasiliensis(HbHNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-typeHbHNL, the C α positions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Crystal structures of 40- and 71-substitution variants of hydroxynitrile lyase from rubber tree

Hydroxynitrile lyase fromHevea brasiliensis(HbHNL) and the esterase SABP2 fromNicotiana tabacumshare the α/β-hydrolase fold, a Ser–His–Asp catalytic triad and 44% sequence identity, yet catalyze different reactions. Prior studies showed that three active-site substitutions inHbHNL conferred weak esterase activity. To investigate how regions beyond the active site influence catalytic efficiency and active-site geometry, we engineeredHbHNL variants with increasing numbers of substitutions to match SABP2. Variant HNL16 has all amino acids within 6.5 Å of the active site identical to SABP2, HNL40 those within 10 Å and HNL71 those within 14 Å. HNL16 exhibited poor esterase activity, whereas both HNL40 and HNL71 showed efficient esterase catalysis, demonstrating that residues beyond the immediate active site are critical for functional conversion. X-ray structures of HNL40 and HNL71 reveal a progressive shift in backbone positions toward those of SABP2, with r.m.s.d. values of 0.51 Å (HNL40) and 0.41 Å (HNL71) over the C α atoms, and even smaller r.m.s.d.s within the active-site region. Both HNL40 and HNL71 show a restored oxyanion hole and an additional tunnel connecting the active site to the protein surface. This work demonstrates the essential role of distant, indirectly acting residues to catalysis in α/β-hydrolase enzymes.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Knocking out the carboxyltransferase interactor 1 (CTI1) in Chlamydomonas boosted oil content by fivefold without affecting cell growth

Summary The first step in chloroplast de novo fatty acid synthesis is catalysed by acetyl‐CoA carboxylase (ACCase). As the rate‐limiting step for this pathway, ACCase is subject to both positive and negative regulation. In this study, we identify a Chlamydomonas homologue of the plant carboxyltransferase interactor 1 (CrCTI1) and show that this protein interacts with the Chlamydomonas α‐carboxyltransferase (Crα‐CT) subunit of the ACCase by yeast two‐hybrid protein–protein interaction assay. Three independent CRISPR‐Cas9 mediated knockout mutants for CrCTI1 each produced an ‘enhanced oil’ phenotype, accumulating 25% more total fatty acids and storing up to fivefold more triacylglycerols (TAGs) in lipid droplets. The TAG phenotype of the crcti1 mutants was not influenced by light but was affected by trophic growth conditions. By growing cells under heterotrophic conditions, we observed a crucial function of CrCTI1 in balancing lipid accumulation and cell growth. Mutating a previously mapped in vivo phosphorylation site (CrCTI1 Ser108 to either Ala or to Asp), did not affect the interaction with Crα‐CT. However, mutating all six predicted phosphorylation sites within Crα‐CT to create a phosphomimetic mutant reduced this pairwise interaction significantly. Comparative proteomic analyses of the crcti1 mutants and WT suggested a role for CrCTI1 in regulating carbon flux by coordinating carbon metabolism, antioxidant and fatty acid β‐oxidation pathways, to enable cells to adapt to carbon availability. Taken together, this study identifies CrCTI1 as a negative regulator of fatty acid synthesis in algae and provides a new molecular brick for the genetic engineering of microalgae for biotechnology purposes.

Li, Zhongze [Aix‐Marseille Université, CEA, CNRS, ↗
DOE OSTI2024

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

Abstract Background Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions. Results To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13 C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13 C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts. Conclusions Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

Abstract Background A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. Results Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp 614 Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro 323 Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. Conclusions These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI1994

Nuclear Safety [Vol. 35, No. 2, July-December 1994]

Nuclear Safety is a journal that covers significant issues in the field of nuclear safety. Its primary scope is safety in the design, construction, operation, and decommissioning of nuclear power reactors worldwide and the research and analysis activities that promote this goal, but it also encompasses the safety aspects of the entire nuclear fuel cycle, including fuel fabrication, spent-fuel processing and handling, and nuclear waste disposal, the handling of fissionable materials and radioisotopes, and the environmental effects of all these activities. Table of Contents for this issue follows. GENERAL SAFETY CONSIDERATIONS: 179 Consideration of Postaccident Consequences in the Determination of Safety Objectives for Future Nuclear Power Plants in France, D. Queniart, A. Sugier, and J. Lochard; ACCIDENT ANALYSIS: 187 Nuclear Safety Research: The Phebus FP Severe Accident Experimental Program, P. von der Hardt, A. V. Jones, C. Lecomte, and A. Tattegrain; 205 Containment Performance Analysis of the Advanced Neutron Source Reactor at the Oak Ridge National Laboratory, S. H. Kim, R. P. Taleyarkhan, and V. Georgevich; 213 Assessment of Fission Product Deposits in the Reactor Coolant System: The DEVAP Program, G. Le Marois and M. Megnin; 222 Erratum to “A Review of the Available Information on the Triggering Stage of a Steam Explosion," Vol. 35, No. 1, CONTROL AND INSTRUMENTATION: 223 Effects of Normal Aging on Calibration and Response Time of Nuclear Plant Resistance Temperature Detectors and Pressure Sensors, H. M. Hashemian; DESIGN FEATURES: 235 Defense in Depth Against the Hydrogen Risk—A European Research Program, F. Fineschi; ENVIRONMENTAL EFFECTS: 246 Technical Note: A Preliminary Analysis of the Risks to Hong Kong Resulting from Potential Accidents of Daya Bay Nuclear Power Plant, Z. Shi and X. Wei; OPERATING EXPERIENCES: 253 Reactor Shutdown Experience, Compiled by J. W. Cletcher; SPECIAL SECTION ON TMI-2 VESSEL INVESTIGATION PROJECT: 256 Three Mile Island—New Findings 15 Years After the Accident A. M. Rubin and E. Beckjord; 269 Relocation of Molten Material to the TMI-2 Lower Head, J. R. Wolf, D. W. Akers, and L. A. Neimark; 280 Insight Into the TMI-2 Core Material Relocation Through Examination of Instrument Tube Nozzles, L. A. Neimark; 288 Physical and Radiochemical Examinations of Debris from the TMI-2 Lower Head, D. W. Akers and B. K. Schuetz; 301 Results of Metallographic Examinations and Mechanical Tests of Pressure Vessel Samples from the TMI-2 Lower Head, D. R. Diercks and G. E. Korth; 313 Margin-to-Failure Calculations for the TMI-2 Vessel, J. Rempe, L. Stickler, S. Chavez, G. Thinnes, R. Witt, and M. Corradini; U.S. NUCLEAR REGULATORY COMMISSION INFORMATION AND ANALYSES: 328 1993 Accident Sequence Precursor (ASP) Program Results, L. N. Vanden Heuvel, J. W. Cletcher, D. A. Copinger, J. W. Minarick, B. W. Dolan, and P. D. O’Reilley; RECENT DEVELOPMENTS: 339 Reports, Standards, and Safety Guides, D. S. Queener; 345 Proposed Rule Changes as of June 30, 1994; ANNOUNCEMENTS: 234 Thirty-First Annual Meeting of the National Council on Radiation Protection and Measurements; 356 1995 International Incineration Conference; 358 Fifth International Controls and Instrumentation Conference; 359 ANS International Topical Meeting on Safety of Operating Reactors; 359 Fifth International Conference on Nuclear Criticality Safety; 360 International Conference on Probabilistic Safety Assessment Methodology and Applications; 351 The Authors; 357 Reviewers of Nuclear Safety, Vol. 35.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Analysis of DWPF Sludge Batch 6 (Macrobatch 7): Pour Stream Glass Samples

The Defense Waste Processing Facility (DWPF) began processing Sludge Batch 6 (SB6), also referred to as Macrobatch 7 (MB7), in June 2010. SB6 is a blend of the heel of Tank 40 from Sludge Batch 5 (SB5), H-Canyon Np transfers and SB6 that was transferred to Tank 40 from Tank 51.1 SB6 was processed using Frit 418. Sludge is received into the DWPF Chemical Processing Cell (CPC) and is processed through the Sludge Receipt and Adjustment Tank (SRAT) and Slurry Mix Evaporator Tank (SME). The treated sludge slurry is then transferred to the Melter Feed Tank (MFT) and fed to the melter. During processing of each sludge batch, the DWPF is required to take at least one glass sample to meet the objectives of the Glass Product Control Program (GPCP) and to complete the necessary Production Records so that the final glass product may be disposed of at a Federal Repository. The DWPF requested various analyses of radioactive glass samples obtained from the melter pour stream during processing of SB6 as well as reduction/oxidation (REDOX) analysis of MFT samples to determine the impact of Argon bubbling. Sample analysis followed the Task Technical and Quality Assurance Plan (TTQAP) and an Analytical Study Plan (ASP). Four Pour Stream (PS) glass samples and two MFT slurry samples were delivered to the Savannah River National Laboratory (SRNL) from the DWPF. Table 1-1 lists the sample information for each pour stream glass sample. SB6 PS3 (S03472) was selected as the official pour stream sample for SB6 and full analysis was requested. This report details the visual observations of the as-received SB6 PS No.3 glass sample as well as results for the chemical composition, Product Consistency Test (PCT), radionuclide content, noble metals, and glass density. REDOX results will be provided for all four pour stream samples and vitrified samples of MFT-558 and MFT-568A. Where appropriate, data from other pour stream samples will be provided.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity

We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe 2+ utilizing H 2 O 2 (not O 2 ) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H 2 O 2 -mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H 2 O 2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe 2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H 2 O 2 or O 2 but requires divalent cations and 12-mer Pa Dps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanical Properties of a Solvated Biomolecule: RGD (1FUV) Peptide

The mechanical properties of proteins/peptides play an essential role in their functionalities and implications, as well as their structure and dynamic properties. Understanding mechanical properties is pivotal to our knowledge of protein folding and the molecular basis of diverse cellular processes. Herein, we present a computational approach using ab initio quantum mechanical calculations to determine the mechanical properties—such as bulk modulus, shear modulus, Young’s modulus, and Poisson’s ratio—of a solvated Arg-Gly-Asp (RGD) peptide model. Since this peptide serves as the RGD-directed integrin recognition site and may participate in cellular adhesion, it is considered a promising small peptide for medicinal applications. This successful approach paves the way for investigating larger and more complex biomolecules.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Mechanistic Insights into Peptide Binding and Deactivation of an Adhesion G Protein-Coupled Receptor

Adhesion G protein-coupled receptors (ADGRGs) play critical roles in the reproductive, neurological, cardiovascular, and endocrine systems. In particular, ADGRG2 plays a significant role in Ewing sarcoma cell proliferation, parathyroid cell function, and male fertility. In 2022, a cryo-EM structure was reported for the active ADGRG2 bound by an optimized peptide agonist IP15 and the Gs protein. The IP15 peptide agonist was also modified to antagonists 4PH-E and 4PH-D with mutations of the 4PH residue to Glu and Asp, respectively. However, experimental structures of inactive antagonist-bound ADGRs remain to be resolved, and the activation mechanism of ADGRs such as ADGRG2 is poorly understood. Here, we applied Gaussian accelerated molecular dynamics (GaMD) simulations to probe conformational dynamics of the agonist- and antagonist-bound ADGRG2. By performing GaMD simulations, we were able to identify important low-energy conformations of ADGRG2 in the active, intermediate, and inactive states, as well as explore the binding conformations of each peptide. Moreover, our simulations revealed critical peptide-receptor residue interactions during the deactivation of ADGRG2. In conclusion, through GaMD simulations, we uncovered mechanistic insights into peptide (agonist and antagonist) binding and deactivation of the ADGRG2. These findings will potentially facilitate rational design of new peptide modulators of ADGRG2 and other ADGRs.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Variable dimension automatic synthesis programs (VASP)

Variable dimension FORTRAN 4 version of the Automatic Synthesis Program (ASP) compensates for limitations within the program itself. Improvements are versatile programming language, convenient input/output format, new subprograms, variable dimensioning, and efficient storage.

White, J. S.↗
NASA NTRS1973

Recently published protein sequences. III

A listing of polypeptide sequences announced in published papers in 1972 and 1973 is given. The listing contains twenty one new sequencies which were selected by using the distinction of Asn, Asp, Gln, and Glu from Asx and Glx, and the absence of unsequenced peptides as criteria.

Jukes, T. H.↗
NASA NTRS1974

Chemical evolution. XXI - The amino acids released on hydrolysis of HCN oligomers

Major amino acids released by hydrolysis of acidic and basic HCN oligomers are identified by chromatography as Gly, Asp, and diaminosuccinic acid. Smaller amounts of Ala, Ile and alpha-aminoisobutyric acid are also detected. The amino acids released did not change appreciably when the hydrolysis medium was changed from neutral to acidic or basic. The presence of both meso and d, l-diaminosuccinic acids was established by paper chromatography and on an amino acid analyzer.

Ferris, J. P.↗
NASA NTRS1976

Linear and nonlinear analysis of orbital telescope/space shuttle dynamics and control

Work completed on the design and study of an annular suspension and pointing (ASP) system for the space shuttle was presented. This system makes use of a magnetically suspended vernier pointing assembly. The following objectives were pursued in this study: (1) development of a detailed mathematical model of the Space Shuttle/ASP system, (2) design of control laws in order to obtain the desired pointing performance, and (3) prediction of the statistical pointing accuracies in the presence of stochastic disturbances such as crew-motion, and sensor and actuator noise. The first two of these objectives are documented in this report.

Roberts, A. S., Jr.↗
NASA NTRS1976

Spacelab science missions of the 1980's

The objectives and instrumentation of Spacelab missions planned for the 1980s are discussed. Initial flights will be multidisciplinary, serving to verify the performance of Spacelab subsystems and to demonstrate the capability of Spacelab to carry out broad-ranging research in a variety of fields. Further missions will use highly specialized payloads. Among these are the Atmospheres, Magnetospheres and Plasmas (AMPS) Payload, the Astronomy Spacelab Payload (ASP), including solar physics, stellar astronomy and high energy astrophysics variants, and the Spacelab Infrared Telescope Facility. The growing inventory of instruments developed for these missions will then be available for use in different combinations to meet the needs of individual mission objectives proposed by the international scientific community.

Chappell, C. R.↗