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DOE OSTI2023

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins

A challenge for design of protein–small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria

How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Triepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis

Monensin A is a prototypical natural polyether polyketide antibiotic. It acts by binding a metal cation and facilitating its transport across the cell membrane. Biosynthesis of monensin A involves construction of a polyene polyketide backbone, subsequent epoxidation of the alkenes, and, lastly, formation of cyclic ethers via epoxide-opening cyclization. MonCI, a flavin-dependent monooxygenase, is thought to transform all three alkenes in the intermediate polyketide premonensin A into epoxides. Our crystallographic study has revealed that MonCI’s exquisite stereocontrol is due to the preorganization of the active site residues which allows only one specific face of the alkene to approach the reactive C(4a)-hydroperoxyflavin moiety. Furthermore, MonCI has an unusually large substrate-binding cavity that can accommodate premonensin A in an extended or folded conformation which allows any of the three alkenes to be placed next to C(4a)-hydroperoxyflavin. Importantly, MonCI, with its ability to perform multiple epoxidations on the same substrate in a stereospecific manner, demonstrates the extraordinary versatility of the flavin-dependent monooxygenase family of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Peculiarities of planar shockwave interaction with air–water interface and solid target

We present the results of the research on underwater electrical explosion of planar copper wire arrays, accompanied by the generation of a planar shock, using the synchrotron-based phase-contrast radiography imaging capabilities of the ID19 beamline at the European Synchrotron Radiation Facility. It is shown that the interaction of a strong shock with an air–water interface leads to additional acceleration of the wire expansion due to a rarefaction wave along with the emergence of micro-jets. In the case of a target placed above the array, we observed the formation of a cavity between the array and the target due to the interaction of two rarefaction waves. Furthermore, the results of two-dimensional hydrodynamic simulations of the wire explosion and the interaction of the generated shock with the water–air and water-target interfaces showed good agreement with experimental results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS2011

Heliocentric Distance of Coronal Mass Ejections at the Time of Energetic Particle Release: Revisiting the Ground Level Enhancement Events of Solar Cycle 23

Using the kinematics of coronal mass ejections (CMEs), onset time of soft X-ray flares, and the finite size of the pre-eruption CME structure, we derive the heliocentric distan~e at which the energetic particles during the ground level enhancement (GLE) events of Solar Cycle 23. We find that the GLE particles are released when the CMEs reach an average heliocentric distance of approx.3.25 solar radii (Rs). From this we infer that the shocks accelerating the particles are located at similar heights. Type II radio burst observations indicate that the CMEs are at much lower distances (average approx.1.4 Rs) when the CME-driven shock first forms. The shock seems to travel approx.1.8 Rs over a period of approox.30 min on the average before releasing the GLE particles. In deriving these results, we made three assumptions that have observational support: (i) the CME lift off occurs from an initial distance of about 1.25 Rs; (ii) the flare onset and CME onset are one and the same because these are two different manifestations of the same eruption; and (iii) the CME has positive acceleration from the onset to the first appearance in the coronagraphic field of view (2.5 to 6 Rs). Observations of coronal cavities in eclipse pictures and in coronagraphic images justify the assumption (i). The close relationship between the flare reconnection magnetic flux and the azimuthal flux of interplanetary magnetic clouds justify assumption (ii) consistent with the standard model (CSHKP) of solar eruption. Coronagraphic observations made close to the solar surface indicate a large positive acceleration of CMEs to a heliocentric distance of approx.3 Rs before they start slowing down due to the drag force. The inferred acceleration (approx.1.5 km/s/s) is consistent with reported values in the literature.

Gopalswamy, Natchimuthuk↗

DOE OSTI2022

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins

The human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15mg/L and has a melting temperature of 71.9°C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

X-ray FEL linear accelerator design via start-to-end global optimization

An X-ray Free Electron Laser (FEL) prefers using an electron beam with low emittance, small energy spread, and a high core current to generate coherent radiation through an undulator. In order to attain such a high brightness beam, the linear accelerator beam dynamics design generally involves separate photoinjector optimization and linac optimization. In this paper, we propose a new beam dynamics design strategy based on global optimization with fast start-to-end simulations from the photocathode to the end of the accelerator. The new start-to-end model significantly reduces the simulation time and makes the global optimization practical. The global optimization method avoids the need to choose a single solution based on bunch length at the injector exit for the linac optimization and helps find the solution with unfavorable bunch length at the injector exit but better phase space distribution that can result in better final electron beam phase space distribution at the entrance of the undulator. Here, using the start-to-end global optimization, we showed in an application example, with a 100 pC beam that good transverse emittance and over kilo-Ampere final core current can be attained using a photoinjector that consists of a VHF gun and boosting RF cavities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Unusual zwitterionic catalytic site of SARS–CoV-2 main protease revealed by neutron crystallography

The main protease (3CL M pro ) from SARS–CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL M pro possesses an unusual catalytic dyad composed of Cys 145 and His 41 residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL M pro , which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease. We observe that the catalytic site natively adopts a zwitterionic reactive form in which Cys 145 is in the negatively charged thiolate state and His 41 is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged. The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen-bonding networks in the active-site cavity and at the dimer interface. The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature. Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

The Story of 5d Metallocorroles: From Metal–Ligand Misfits to New Building Blocks for Cancer Phototherapeutics

Porphyrin chemistry is Shakespearean: over a century of study has not withered the field’s apparently infinite variety. Heme proteins continually astonish us with novel molecular mechanisms, while new porphyrin analogues bowl us over with unprecedented optical, electronic, and metal-binding properties. Within the latter domain, corroles occupy a special place, exhibiting a unique and rich coordination chemistry. The 5d metallocorroles are arguably the icing on that cake. New Zealand chemist Penny Brothers has used the word “misfit” to describe the interactions of boron, a small atom with a predilection for tetrahedral coordination, and porphyrins, classic square-planar ligands. Steve Jobs lionized misfits as those who see things differently and push humanity forward. Both perspectives have inspired us. The 5d metallocorroles are misfits in that they encapsulate a large 5d transition metal ion within the tight cavity of a contracted porphyrin ligand. Given the steric mismatch inherent in their structures, the syntheses of some 5d metallocorroles are understandably capricious, proceeding under highly specific conditions and affording poor yields. Three broad approaches may be distinguished. (a) In the metal–alkyl approach, a free-base corrole is exposed to an alkyllithium and the resulting lithio-corrole is treated with an early transition metal chloride; a variant of the method eschews alkyllithium and deploys a transition metal–alkyl instead, resulting in elimination of the alkyl group as an alkane and insertion of the metal into the corrole. This approach is useful for inserting transition metals from groups 4, 5, and, to some extent, 6, as well as lanthanides and actinides. (b) In our laboratory, we have often deployed a low-valent organometallic approach for the middle transition elements (groups 6, 7, 8, and 9). The reagents are low-valent metal–carbonyl or −olefin complexes, which lose one or more carbon ligands at high temperature, affording coordinatively unsaturated, sticky metal fragments that are trapped by the corrole nitrogens. (c) Finally, a metal acetate approach provides the method of choice for gold and platinum insertion (groups 10 and 11). This Account provides a first-hand perspective of the three approaches, focusing on the last two, which were largely developed in our laboratory. In general, the products were characterized with X-ray crystallography, electrochemistry, and a variety of spectroscopic methods. The physicochemical data, supplemented by relativistic DFT calculations, have provided fascinating insights into periodic trends and relativistic effects. An unexpected feature of many 5d metallocorroles, given their misfit character, is their remarkable stability under thermal, chemical, and photochemical stimulation. Many of them also exhibit long triplet lifetimes on the order of 100 μs and effectively sensitize singlet oxygen formation. Many exhibit phosphorescence in the near-infrared under ambient conditions. Furthermore, water-soluble ReO and Au corroles exhibit impressive photocytotoxicity against multiple cancer cell lines, promising potential applications as cancer phototherapeutics. We thus envision a bright future for the compounds as rugged building blocks for new generations of therapeutic and diagnostic (theranostic) agents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Revealing mechanisms of processing defect mitigation in laser powder bed fusion via shaped beams using high-speed X-ray imaging

The laser powder bed fusion (LPBF) process utilizing a focused Gaussian-shaped beam faces challenges, including pore formation, melt pool fluctuation and liquid spattering. While beam shaping technology has been explored as a potential approach for defect mitigation, the beam-matter interaction dynamics during melting with shaped beams remain unclear. Here, we report the direct observation of ring-shaped beam-matter interaction dynamics, including pore formation, melt pool fluctuation and liquid spattering, and unveil defect mitigation mechanisms in ring-shaped beam laser powder bed fusion process. Here, we find that, by spatially manipulating incident laser rays, the ring-shaped beam controls keyhole morphology, thereby managing the distribution of the reflected rays. This manipulation can effectively eliminate the formation of an unstable cavity at the keyhole tip, stabilizing the keyhole and mitigating keyhole pores. This enhanced keyhole stability effectively reduces the melt pool fluctuation, the formation of liquid breakup induced spatters and liquid droplet colliding induced large spatters in the laser powder bed fusion process. Additionally, the high-energy forefront of the ring-shaped beam effectively melts the powder bed, reducing agglomeration liquid spatter in the laser powder bed fusion process. The discovered defect mitigation mechanisms may guide the design of beam shaping strategies for simultaneously increasing the quality and productivity of metal additive manufacturing.

Beam shaping↗

DOE OSTI2024

Phase stability and microstructure of neutron-irradiated substoichiometric yttrium dihydrides

The impact of the neutron-displacement damage on phase stability and microstructure of substoichiometric yttrium dihydrides (YH x , x <2) were investigated to assess their use as solid moderator in high-temperature nuclear reactors. YH x specimens were, thus, subjected to neutron irradiations in the range of 0.1–2 displacements per yttrium atom (dpa-Y) in the temperature range of 536–878°C at the Oak Ridge National Laboratory's (ORNL's) High Flux Isotope Reactor (HFIR). YH x specimens were initially prepared at stoichiometry (H/Y) ratios of 1.69 and 1.83. HFIR-irradiated specimens were characterized by variety of techniques to investigate H retention characteristics including dimensional analysis, optical microscopy, scanning electron microscopy electron back scatter diffraction (EBSD), transmission electron microscopy, thermal desorption spectroscopy (TDS), and high-energy x-ray diffraction (HE-XRD) characterizations. Overall, YH x exhibited notable structural and phase stability under short-term neutron-irradiation, except for the samples with significant silicon carbide (SiC) interaction at high doses and temperatures. Basic dimensional and mass measurements were misleading for accurate assessment of H retention, as confirmed by EBSD phase maps, XRD line profiles, and TDS signals. Thus, it was discussed that a robust H retention metric is needed to assess irradiated hydrides. Further, nanoscale cavities were observed as a result of the neutron irradiation in all samples. Although no clear impact of dose and irradiation temperature was determined, the initial H/Y ratio had an impact on the cavity number density where low H/Y specimens had high-resistance to cavity formation. The Y-vacancy cluster formation at the collision stage of the displacement cascade and their stabilization by H were considered to be the likely underlying mechanisms for the observed cavity microstructure.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Multiport High-pressure Fluid Cell (MHPFC) for Photon and Electron Beams

A multiport high-pressure fluid cell was developed based on an engineered thin film membrane solution with a reinforced frame of boron-doped silicon, optimized to withstand better pressure with an increase of 17.6% in average burst pressure over similar membranes without frame. The novel cells (patent pending) have 8 microfluidic ports, two intra-cavity electrodes and two pressure sensors on a 8 mm x 8 mm Si chip. The prototypes resisted up to 60 bar with 50-nm-thick silicon nitride membranes of size 70 nm x 70 nm. The cells can be used for testing reactions in fluids in medium-high pressure (up to 300 bar) using X-rays (primary application), electron beams, IR or visible light. Improvements in the pressure sensing setup and customization for applications are supposed to follow.

36 MATERIALS SCIENCE↗

NASA NTRS1984

A Model of the Soft X-ray Background as a Blast Wave Viewed from Inside

The suggestion that the soft X-ray background arises in part from the Sun which is inside a large supernova blastwave was examined by models of spherical blastwaves. The models can produce quantitative fits to both surface brightnesses and energy band ratios when t = 10 to the 5th power E sub o = 5 x 10 to the 50th power ergs, and n sub approx. 0.004 cm to the -3 power. The models are generalized by varying the relative importance of factors such as thermal conduction, Coulomb heating of electrons, and external pressure; and to allow the explosions to occur in preexisting cavities with steep density gradients, or by examination of the effects of large obstructions or other anisotrophies in the ambient medium.

Edgar, R. J.↗

NASA NTRS1992

Heating of H II regions with application to the Galactic center

The heating and thermal equilibrium of photoionized gas is reviewed. Photon-heating mechanisms (UV photoionization heating, grain photoelectric heating, and X-ray heating) either fail to provide the required heating rates or else require that the ionization state of the gas is very high. Specific application to the Galactic center observations show that the total heating power required to maintain the gas at the derived temperatures, using the observed emission measure in the bar and the temperature distribution derived from the radio recombination lines, is about 7 x 10 exp 6 solar luminosities, comparable to the bolometric luminosity of the central source as measured by the FIR flux from grains. Thus, the cooling emission from this hot gas, if LTE-derived temperatures are correct, would supply a major fraction of the bolometric and ionizing luminosity inferred from the ionized gas in the central 1 pc cavity and the dust and neutral gas in the surrounding torus.

Maloney, Philip R.↗

NASA NTRS2008

High Variability in Vela X-1: Giant Flares and Off States

Aims. We investigate the spectral and temporal behavior of the high mass X-ray binary Vela X-1 during a phase of high activity, with special focus on the observed giant flares and off states. Methods. INTEGRAL observed Vela X-1 in a long almost uninterrupted observation for two weeks in 2003 Nov/Dec. The data were analyzed with OSA 7.0 and FTOOLS 6.2. We derive the pulse period, light curves, spectra, hardness ratios, hardness intensity diagrams, and study the eclipse. Results. In addition to an already high activity level, Vela X-1 exhibited several very intense flares, the brightest ones reaching a maximum intensity of more than 5 Crab in the 20-40 keV band and several off states where the source is no longer detected by INTEGRAL. We determine the pulse period to be 283.5320 +/- 0.0002 s which is stable throughout the whole observation. Analyzing the eclipses resulted in an improvement of the ephemeris. Spectral analysis of the flares shows that there seem to be two types of flares: relatively brief flares which can be extremely intense, and show spectral softening, contrary to high intensity states which are longer and show no softening. Conclusions. Both flares and off states are interpreted as being due to a strongly structured wind of the optical companion. When Vela X-1 encounters a cavity with strongly reduced density, the flux will drop triggering the onset of the propeller effect which inhibits further accretion, thus giving rise to off states. The required drop of the density of the material to trigger the propeller effect in Vela X-1 is of the same order as predicted by theoretical papers on the densities in the OB star winds. The same structured wind can give rise to the giant flares when Vela X-1 encounters a dense blob in the wind.

Kreykenbohm, Ingo↗

NASA NTRS2013

Modeling Contamination Migration on the Chandra X-ray Observatory II

During its first 14 years of operation, the cold (about ‐60degC) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X‐ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low‐energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition may have changed, perhaps partially related to changes in the operating temperature of the ACIS housing. This evolution of the accumulation of the molecular contamination has motivated further analysis of contamination migration on the Chandra X‐ray Observatory, particularly within and near the ACIS cavity. To this end, the current study employs a higher‐fidelity geometric model of the ACIS cavity, detailed thermal modeling based upon monitored temperature data, and an accordingly refined model of the molecular transport.

O'Dell, Stephen L.↗

NASA NTRS2013

Modeling Contamination Migration on the Chandra X-ray Observatory II

O'Dell, Steve↗

NASA NTRS2013

Modeling Contamination Migration on the Chandra X-ray Observatory - II

During its first 14 years of operation, the cold (about -60C) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X-ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low-energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition have changed. This evolution has motivated further analysis of contamination migration within and near the ACIS cavity. To this end, the current study employs a higher-fidelity geometric model of the ACIS cavity, detailed thermal modeling based upon temperature data, and a refined model of the molecular transport.

O'Dell, Stephen L.↗