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DOE OSTI2025

Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues

This study employed structural information from cocrystals of rufomycin 4 (1a) and caseinolytic protein C1 (ClpC1)-NTD-wt to guide design and semisynthesis of rufomycin analogues, evaluate their antituberculosis (TB) biological profiles, and establish structure–activity relationships (SAR). Covering three regions of interest (ROIs, A–C) as modification sites, 14 of the 30 semisynthetic analogues (2–31) showed similar or improved MICs relative to the main natural precursors, rufomycins 4/6 (1a/b). Compounds 5 and 27 exhibited up to 10-fold enhanced potency against Mycobacterium tuberculosis (Mtb) in vitro, with MIC values of 1.9 and 1.4 nM, respectively. Evaluation of ClpC1-binding properties used existing ClpC1-NTD complexes with rufomycin 4 (PDB: 6cn8) and ecumicin (PDB: 6pbs) as references. The newly reported X-ray ClpC1-NTD cocrystal structure of 11 (syn. But4-Cl) revealed significant conformational effects involving the side chains of certain amino acids of the heptapeptide and confirmed the importance of ROIs A–C for medicinal chemistry efforts. Observed interactions of the N-terminal tail of ClpC1 with the rufomycin analogues vs ecumicin explains their different modes of inactivating the ClpC1/P1/P2 homeostatic machinery. Collectively, the observations inform further SAR optimization strategies for the rufomycin class of antibiotics and complement our understanding of their mode of action.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase

The O-linked β-N-acetyl glucosamine (O-GlcNAc) modification dynamically regulates the functions of numerous proteins. A single human enzyme O-linked β-N-acetyl glucosaminase (O-GlcNAcase or OGA) hydrolyzes this modification. To date, it remains largely unknown how OGA recognizes various substrates. Here we report the structures of OGA in complex with each of four distinct glycopeptide substrates that contain a single O-GlcNAc modification on a serine or threonine residue. Intriguingly, these glycopeptides bind in a bidirectional yet conserved conformation within the substrate-binding cleft of OGA. This study provides fundamental insights into a general principle that confers the substrate binding adaptability and specificity to OGA in O-GlcNAc regulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO – , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. Finally, these features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1994

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

Review↗

DOE OSTI2021

Correlated oxide Dirac semimetal in the extreme quantum limit

Quantum materials (QMs) with strong correlation and nontrivial topology are indispensable to next-generation information and computing technologies. Exploitation of topological band structure is an ideal starting point to realize correlated topological QMs. Here, we report that strain-induced symmetry modification in correlated oxide SrNbO 3 thin films creates an emerging topological band structure. Dirac electrons in strained SrNbO 3 films reveal ultrahigh mobility (μ max ≈ 100,000 cm 2 /Vs), exceptionally small effective mass (m* ~ 0.04m e ), and nonzero Berry phase. Strained SrNbO 3 films reach the extreme quantum limit, exhibiting a sign of fractional occupation of Landau levels and giant mass enhancement. Our results suggest that symmetry-modified SrNbO 3 is a rare example of correlated oxide Dirac semimetals, in which strong correlation of Dirac electrons leads to the realization of a novel correlated topological QM.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding

As an adaptation for survival during infection, Mycobacterium tuberculosis becomes dormant, reducing its metabolism and growth. Two types of citrate synthases have been identified in Mycobacterium tuberculosis, GltA2 and CitA. Previous work shows that overexpression of CitA, the secondary citrate synthase, stimulates the growth of Mycobacterium tuberculosis under hypoxic conditions without showing accumulation of triacylglycerols and makes mycobacteria more sensitive to antibiotics, suggesting that CitA may play a role as a metabolic switch during infection and may be an interesting TB drug target. To assess the druggability and possible mechanisms of targeting CitA with small-molecule compounds, the CitA crystal structure was solved to 2.1 Å by X-ray crystallography. The solved structure shows that CitA lacks an NADH binding site that would afford allosteric regulation, which is atypical of most citrate synthases. However, a pyruvate molecule is observed within the analogous domain, suggesting pyruvate may instead be the allosteric regulator for CitA. Further, the R149 and R153 residues forming the charged portion of the pyruvate binding pocket were mutated to glutamate and methionine, respectively, to assess the effect of mutations on activity. Protein thermal shift assay shows thermal stabilization of CitA in the presence of pyruvate compared to the two CitA variants designed to decrease pyruvate affinity. Solved crystal structures of both variants show no significant structural changes. However, the catalytic efficiency of the R153M variant increases by 2.6-fold. Additionally, we show that covalent modification of C143 of CitA by Ebselen completely arrests enzyme activity. Similar inhibition is observed using two spirocyclic Michael acceptor containing compounds, which inhibit CitA with IC app 50 values of 6.6 and 10.9 μM. A crystal structure of CitA modified by Ebselen was solved, but significant structural changes were lacking. Considering that covalent modification of C143 inactivates CitA and the proximity of C143 to the pyruvate binding site, this suggests that structural and/or chemical changes in this sub-domain are responsible for regulating CitA enzymatic activity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1

The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or ‘PUS’ enzymes include those that rely on guide RNA molecules and others that function as ‘stand-alone’ enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Theory of two-meson photo- and electroproduction off the nucleon

Using the reaction γN → ππN as the paradigmatic topological framework, a field-theoretical description of the electromagnetic production of two pseudoscalar mesons off the nucleon is derived and applied to photo- and electroproduction processes, assuming only one-photon exchange for the latter. The dynamics of all explicit three-point interaction mechanisms of the ππN system is accounted for by the Faddeev-type ordering structure of the Alt-Grassberger-Sandhas equations. The modifications necessary for incorporating n-meson vertices for n ≥ 4 are discussed. The formulation is valid for hadronic two-point and three-point functions dressed by arbitrary (even nonlinear) internal mechanisms provided all associated electromagnetic currents are constructed to satisfy their respective (generalized) Ward-Takahashi identities. Coupling the photon to the Faddeev structure of the underlying hadronic two-pion production mechanisms results in a natural expansion of the full two-pion photoproduction current $M$$^{μ}_{ππ}$ in terms of multiple dressed loops involving two-body subsystem scattering amplitudes of the ππN system that preserves gauge invariance as a matter of course order by order in the number of (dressed) loops. A closed-form expression is presented for the entire gauge-invariant current $M$$^{μ}_{ππ}$ with complete three-body dynamics. Individually gauge-invariant truncations of the full dynamics most relevant for practical applications at the no-loop, one-loop, and two-loop levels are discussed in detail. An approximation scheme to the full two-meson amplitude for calculational purposes is also presented. It approximates, systematically, the full amplitude to any desired order of expansion in the underlying hadronic two-body amplitude. Furthermore, it allows for the approximate incorporation of all neglected higher-order mechanisms in terms of a locally gauge-invariant phenomenological remainder current.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS2011

High-Temperature Smart Structures for Engine Noise Reduction and Performance Enhancement

One of key NASA goals is to develop and integrate noise reduction technology to enable unrestricted air transportation service to all communities. One of the technical priorities of this activity has been to account for and reduce noise via propulsion/airframe interactions, identifying advanced concepts to be integrated with the airframe to mitigate these noise-producing mechanisms. An adaptive geometry chevron using embedded smart structures technology offers the possibility of maximizing engine performance while retaining and possibly enhancing the favorable noise characteristics of current designs. New high-temperature shape memory alloy (HTSMA) materials technology enables the devices to operate in both low-temperature (fan) and high-temperature (core) exhaust flows. Chevron-equipped engines have demonstrated reduced noise in testing and operational use. It is desirable to have the noise benefits of chevrons in takeoff/landing conditions, but have them deployed into a minimum drag position for cruise flight. The central feature of the innovation was building on rapidly maturing HTSMA technology to implement a next-generation aircraft noise mitigation system centered on adaptive chevron flow control surfaces. In general, SMA-actuated devices have the potential to enhance the demonstrated noise reduction effectiveness of chevron systems while eliminating the associated performance penalty. The use of structurally integrated smart devices will minimize the mechanical and subsystem complexity of this implementation. The central innovations of the effort entail the modification of prior chevron designs to include a small cut that relaxes structural stiffness without compromising the desired flow characteristics over the surface; the reorientation of SMA actuation devices to apply forces to deflect the chevron tip, exploiting this relaxed stiffness; and the use of high-temperature SMA (HTSMA) materials to enable operation in the demanding core chevron environment. The overall conclusion of these design studies was that the cut chevron concept is a critical enabling step in bringing the variable geometry core chevron within reach. The presence of the cut may be aerodynamically undesirable in some respects, but it is present only when the chevron is not immersed in the core jet exhaust. When deployed, the gap closes as the chevron tip enters the high-speed, high-temperature core stream. Aeroacoustic testing and flow visualization support the contention that this cut is inconsequential to chevron performance.

Quackenbush, Todd R.↗

DOE OSTI2018

Interplay of local structure, charge, and spin in bilayered manganese perovskites

Chemical doping is a reliable method of modification of the electronic properties of transition metal compounds. In manganese perovskites, it leads to charge transfer and peculiar ordering phenomena. However, depending on the interplay of the local crystal structure and electronic properties, synthesis of stable compounds in the entire doping range is often impossible. In this paper, we show results of high-energy resolution x-ray absorption and emission spectroscopies on a ${\mathrm{La}}_{2{-}2x}{\mathrm{Sr}}_{1+2x}{\mathrm{Mn}}_{2}{\mathrm{O}}_{7}$ family of bilayered manganites in a broad doping range $(0.5{\le}x{\le}1)$. We established a relation between local Mn charge and Mn-O distances as a function of doping. Finally, based on a comparison of such relation with other manganites, we suggest why stable structures cannot be realized for certain doping levels of bilayered compounds.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria

Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

PDB↗

NASA NTRS1992

Development of the quasi-procedural method for use in aircraft configuration optimization

The performance of the quasi-procedural analysis system in optimization tasks is investigated. In particular, the quasi-procedural method is applied to the complete mission optimization of a medium-sized transport aircraft using a vortex-lattice aerodynamic model and finite element structural analysis of the wing and the tail. Some modifications and improvements to the system, required in order to complete this task, are described. The performance of the system is compared with that of the standard procedural system, and it is shown that the quasi-procedural approach reduces the analysis required to reach the optimum. The overall cost is shown to be strongly dependent on the analysis architecture and data structure.

Gage, P.↗

DOE OSTI2019

Electronic Structure of LiCoO 2 Surfaces and Effect of Al Substitution

The surface properties of LiCoO 2 nanoplatelets, and their chemical modifications with Al 3+ , were studied using combined experimental and theoretical approaches. Our model shows that the electronic structures of several LiCoO 2 surface facets are significantly different from those of bulk LiCoO 2 , due to altered spin states of surface Co 3+ atoms. O K -edge X-ray absorption revealed a prominent splitting of the Co 3d -O 2p states, which is attributed to the presence of intermediate-state and/or high-spin-state Co 3+ . at the surface. In particular, the nonpolar (104) surface with intermediate-spin-state Co 3+ exhibits a strong two-dimensional character of splitting in these states, whereas the polar (001) surface with low-spin-state Co 3+ has a similar electronic structure to bulk LiCoO 2 . Here, partial substitution of Co 3+ by Al 3+ through the formation of core-shell architectures increases the ratio of low-spin-state Co3+, resulting in a distinct change in the intensity ratio of the split Co 3d -O 2p states, as revealed by spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1976

Spectroscopic analysis of solar and cosmic X-ray spectra. I - The nature of cosmic X-ray spectra and proposed analytical techniques

X-ray spectroscopic techniques developed in the study of the temperature and density structure of the solar corona are reviewed as introduction to a discussion of the modifications in these techniques which will be required for the study of cosmic X-ray sources. The structure of the interstellar medium - the presence of interstellar grains, the presence of molecules, the ionization structure - are considered in relation to the X-ray opacity of the interstellar medium. The expected spectral structure of individual cosmic X-ray sources is reviewed with emphasis on galactic supernova remnants and galactic binary X-ray sources.

Walker, A. B. C., Jr.↗

DOE OSTI2025

Evolution of Mass Spectrometers for High m / z Biological Ion Formation, Transmission, Analysis and Detection: A Personal Perspective

Mass spectrometry (MS) has become an essential tool in virtually all academic, pharmaceutical, and biopharmaceutical analytical laboratories. The specialized and bespoke area of MS research and application of high m / z ion (> m / z 6000 and high mass, >150 kDa) formation, transmission, analysis, and detection is a relatively new area of focus for MS that has seen dramatic acceleration in interest over the last two decades. Herein we delve into this exciting aspect of MS, discussing how MS instrumentation has been refined and evolved for native-MS analysis. We cover the early groundbreaking experiments showing high m / z ion formation, transmission, and preservation of protein structure in the gas phase. Additionally, we discuss specific instrument optimizations and modifications that have advanced high m / z ion generation, transmission, analysis, and detection, contributing to the research area known as gas-phase structural biology. Native-MS sample introduction methods, emerging technologies, and future perspectives are also examined. Finally, we share personal opinions, observations, and experiences that are new to the community or previously unpublished.

collisions↗

NASA NTRS1993

Nonlinear random response prediction using MSC/NASTRAN

An equivalent linearization technique was incorporated into MSC/NASTRAN to predict the nonlinear random response of structures by means of Direct Matrix Abstract Programming (DMAP) modifications and inclusion of the nonlinear differential stiffness module inside the iteration loop. An iterative process was used to determine the rms displacements. Numerical results obtained for validation on simple plates and beams are in good agreement with existing solutions in both the linear and linearized regions. The versatility of the implementation will enable the analyst to determine the nonlinear random responses for complex structures under combined loads. The thermo-acoustic response of a hexagonal thermal protection system panel is used to highlight some of the features of the program.

Robinson, J. H.↗

DOE OSTI2022

Enhancing Lifetime and Reducing Costs for Fish Diversion Netting Structures (Abstract)

This effort will focus on technology transfer and commercialization of antifouling coatings with an enthusiastic and engaged industrial team. Environmental requirements and operational demands call for a nontoxic coating/paint to prevent fouling on fish passage guidance netting at hydropower facilities. For example, one netting customer estimated the capital cost for compliance at $\$12$ million to $\$15$ million. This project will build partnerships between PNNL and private companies to optimize, demonstrate, mature, and commercialize a novel PNNL-developed technology that addresses this critical coating need of the hydropower industry. This effort will support modification of existing coatings for application to flexible netting structures. Industrial partners include commercial coating development specialist (Lorama), hydrophobic material manufacturer and paint developer (Dry Surface Technologies), aquatic applications specialists (Prometheus Innovations and River Connectivity Systems), and hydropower netting producer (Pacific Netting Products). Engagement with the U.S. Army Corps of Engineers (USACE) and Bureau of Reclamation (BOR), two hydropower operators, throughout the project will provide expertise and field test sites that will provide crucial proof of real-world performance data (additional details provided in Teaming section). Taylor Shellfish Farms will provide organisms and fouling expertise as well as a perspective of potential broader impacts for the blue economy. Sample netting will demonstrate performance in a range of environments for key hydropower applications. PNNL will work with industrial partners to overcome commercialization barriers as well as resolving any manufacturing or regulatory issues. This Phase 1 effort is focused on technology optimization for application to fish passage guidance netting and technology validation as verified by independent testing (through USACE, BOR, Taylor Shellfish and Prometheus Innovations). Through this effort, SLIC will be demonstrated for netting applications at technology readiness level (TRL) 5. The field test data will allow optimization of SLIC formulation and performance which is key to enabling technology transfer of a mature proven technology to industry and production of a viable commercial product specifically focused for hydropower needs.

13 HYDRO ENERGY↗

NASA NTRS1992

Control of leading-edge vortices on a delta wing

The unsteady flow structure of leading-edge vortices on a delta wing has been investigated using new types of experimental techniques, in order to provide insight into the consequences of various forms of active control. These investigations involve global control of the entire wing and local control applied at crucial locations on or adjacent to the wing. Transient control having long and short time-scales, relative to the convective time-scale C/U(sub infinity), allows substantial modification of the unsteady and time-mean flow structure. Global control at long time-scale involves pitching the wing at rates an order of magnitude lower than the convective time-scale C/U(sub infinity), but at large amplitudes. The functional form of the pitching maneuver exerts a predominant influence on the trajectory of the feeding sheet, the instantaneous vorticity distribution, and the instantaneous location of vortex breakdown. Global control at short time-scales of the order of the inherent frequency of the shear layer separating from the leading-edge and the natural frequency of vortex breakdown shows that 'resonant' response of the excited shear layer-vortex breakdown system is attainable. The spectral content of the induced disturbance is preserved not only across the entire core of the vortex, but also along the axis of the vortex into the region of vortex breakdown. This unsteady modification results in time-mean alteration of the axial and swirl velocity fields and the location of vortex breakdown. Localized control at long and short time-scales involves application of various transient forms of suction and blowing using small probes upstream and downstream of the location of vortex breakdown, as well as distributed suction and blowing along the leading-edge of the wing applied in a direction tangential to the feeding sheet. These local control techniques can result in substantial alteration of the location of vortex breakdown; in some cases, it is possible to accomplish this without net mass addition to the flow field.

Magness, C.↗