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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression

Synthetic biology tools for regulating gene expression have many useful biotechnology and therapeutic applications. Most tools developed for this purpose control gene expression at the level of transcription, and relatively few methods are available for regulating gene expression at the translational level. Here, we design and engineer split orthogonal aminoacyl-tRNA synthetases (o-aaRS) as unique tools to control gene translation in bacteria and mammalian cells. Using chemically induced dimerization domains, we developed split o-aaRSs that mediate gene expression by conditionally suppressing stop codons in the presence of the small molecules rapamycin and abscisic acid. Furthermore, by activating o-aaRSs, these molecular switches induce stop codon suppression, and in their absence stop codon suppression is turned off. We demonstrate, in Escherichia coli and in human cells, that split o-aaRSs function as genetically encoded AND gates where stop codon suppression is controlled by two distinct molecular inputs. In addition, we show that split o-aaRSs can be used as versatile biosensors to detect therapeutically relevant protein–protein interactions, including those involved in cancer, and those that mediate severe acute respiratory syndrome-coronavirus-2 infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural insights into redox signal transduction mechanisms in the control of nitrogen fixation by the NifLA system

NifL is a conformationally dynamic flavoprotein responsible for regulating the activity of the σ 54 -dependent activator NifA to control the transcription of nitrogen fixation (nif) genes in response to intracellular oxygen, cellular energy, or nitrogen availability. The NifL-NifA two-component system is the master regulatory system for nitrogen fixation. NifL serves as a sensory protein, undergoing signal-dependent conformational changes that modulate its interaction with NifA, forming the NifL–NifA complex, which inhibits NifA activity in conditions unsuitable for nitrogen fixation. While NifL-NifA regulation is well understood, these conformationally flexible proteins have eluded previous attempts at structure determination. In work described here, we advance a structural model of the NifL dimer supported by a combination of scattering techniques and mass spectrometry (MS)-coupled structural analyses that report on the average structure in solution. Using a combination of small angle X-ray scattering-derived electron density maps and MS-coupled surface labeling, we investigate the conformational dynamics responsible for NifL oxygen and energy responses. Our results reveal conformational differences in the structure of NifL under reduced and oxidized conditions that provide the basis for a model for modulating NifLA complex formation in the regulation of nitrogen fixation in response to oxygen in the model diazotroph,Azotobacter vinelandii.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy

Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.

Science & Technology - Other Topics↗
DOE OSTI2024

Classical vs. quantum plasmon-induced molecular transformations at metallic nanojunctions

Chemical transformations near plasmonic metals have attracted increasing attention in the past few years. Specifically, reactions occurring within plasmonic nanojunctions that can be detected via surface and tip-enhanced Raman (SER and TER) scattering were the focus of numerous reports. In this context, even though the transition between localized and nonlocal (quantum) plasmons at nanojunctions is documented, its implications on plasmonic chemistry remain poorly understood. We explore the latter through AFM-TER-current measurements. We use two molecules: i) 4-mercaptobenzonitrile (MBN) that reports on the (non)local fields and ii) 4-nitrothiophenol (NTP) that features defined signatures of its neutral/anionic forms and dimer product, 4,4′-dimercaptoazobenzene (DMAB). The transition from classical to quantum plasmons is established through our optical measurements: It is marked by molecular charging and optical rectification. Simultaneously recorded force and current measurements support our assignments. In the case of NTP, we observe the parent and DMAB product beneath the probe in the classical regime. Further reducing the gap leads to the collapse of DMAB to form NTP anions. The process is reversible: Anions subsequently recombine into DMAB. Our results have significant implications for AFM-based TER measurements and their analysis, beyond the scope of this work. In effect, when precise control over the junction is not possible (e.g., in SER and ambient TER), both classical and quantum plasmons need to be considered in the analysis of plasmonic reactions

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus

Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N 2 O) emissions, although biochemical origins of this N 2 O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH 2 OH) to dioxygen (O 2 ) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N 2 via reaction with NH 2 OH and dimerization with itself to yield N 2 O. These results afford one plausible enzymatic origin for N 2 O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.

Voland, Robert W. (ORCID:0000000201061257)↗
DOE OSTI2025

Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein

Photosynthetic organisms rely on sophisticated photoprotective mechanisms to prevent oxidative damage under high or fluctuating solar illumination. Cyanobacteria, which have evolved a unique, water-soluble light-harvesting complex—the phycobilisome—achieve photoprotection through a photoactivatable quencher called the Orange Carotenoid Protein (OCP). Phycobilisomes are highly symmetric and modular, formed by hierarchical assembly of conserved subunits into diverse geometries ranging from simple bundles to elaborate fan- or bouquet-like macromolecular architectures. Although OCP is known to provide photoprotection across species of cyanobacteria with different phycobilisome structures, it is not known whether or how these structural variations relate to changes in the photoprotective function of OCP. For example, OCP was recently discovered to bind as a dimer at two specific instances of an abundant structural motif on the tricylindrical phycobilisome of Synechocystis sp. PCC 6803, yet these sites are sterically inaccessible on a more common pentacylindrical phycobilisome ( Anabaena sp. PCC 7120). To understand how structural modularity and binding specificity contribute to conservation of OCP binding sites and function across different phycobilisome architectures, here we compare experimentally measured photophysical states accessible to these prototypical tricylindrical and pentacylindrical phycobilisomes, with and without OCP, at the single-molecule level. Together with Monte Carlo simulations of exciton transfer in OCP-quenched phycobilisomes, our results suggest that OCP binds at distinct and specific sites in each type of phycobilisome, yet provides nearly identical quenching strength to both phycobilisomes. Our findings highlight the utility of modular phycobilisome structures in balancing robust conservation of photoprotective function with adaptability of site-specific binding across species.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2020

Structure-based group A streptococcal vaccine design: Helical wheel homology predicts antibody cross-reactivity among streptococcal M protein–derived peptides

Group A streptococcus (Strep A) surface M protein, an α-helical coiled-coil dimer, is a vaccine target and a major determinant of streptococcal virulence. The sequence-variable N-terminal region of the M protein defines the M type and also contains epitopes that promote opsonophagocytic killing of streptococci. Recent reports have reported considerable cross-reactivity among different M types, suggesting the prospect of identifying cross-protective epitopes that would constitute a broadly protective multivalent vaccine against Strep A isolates. In this work, we have used a combination of immunological assays, structural biology, and cheminformatics to construct a recombinant M protein–based vaccine that included six Strep A M peptides that were predicted to elicit antisera that would cross-react with an additional 15 nonvaccine M types of Strep A. Rabbit antisera against this recombinant vaccine cross-reacted with 10 of the 15 nonvaccine M peptides. Two of the five nonvaccine M peptides that did not cross-react shared high sequence identity (≥50%) with the vaccine peptides, implying that high sequence identity alone was insufficient for cross-reactivity among the M peptides. Additional structural analyses revealed that the sequence identity at corresponding polar helical-wheel heptad sites between vaccine and nonvaccine peptides accurately distinguishes cross-reactive from non–cross-reactive peptides. On the basis of these observations, we developed a scoring algorithm based on the sequence identity at polar heptad sites. When applied to all epidemiologically important M types, this algorithm should enable the selection of a minimal number of M peptide–based vaccine candidates that elicit broadly protective immunity against Strep A.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted histone release in the nucleus

Core histones, synthesized and processed in the cytoplasm, must be chaperoned as they are transported into the nucleus for nucleosome assembly. The importin Kap114 transports H2A-H2B into the yeast nucleus, where RanGTP facilitates histone release. Kap114 and H2A-H2B also bind the histone chaperone Nap1, but how Nap1 and Kap114 cooperate in transport and nucleosome assembly remains unclear. Here, biochemical and structural analyses show that Kap114, H2A-H2B, and a Nap1 dimer (Nap12) associate in the absence and presence of RanGTP to form equimolar complexes. A previous study had shown that RanGTP reduces Kap114’s ability to chaperone H2A-H2B, but a new cryo-EM structure of the Nap12•H2A-H2B•Kap114•RanGTP complex explains how both Kap114 and Nap12 interact with H2A-H2B, restoring its chaperoning within the assembly while effectively depositing it into nucleosomes. Together, our results suggest that Kap114 and Nap12 provide a sheltered path that facilitates the transfer of H2A-H2B from Kap114 to Nap12, ultimately directing its specific deposition into nucleosomes.

Fung, Ho Yee Joyce (ORCID:0000000205021957)↗
DOE OSTI2022

The Gutzwiller conjugate gradient minimization method for correlated electron systems

In this report we review our recent work on the Gutzwiller conjugate gradient minimization method, an ab initio approach developed for correlated electron systems. The complete formalism has been outlined that allows for a systematic understanding of the method, followed by a discussion of benchmark studies of dimers, one- and two-dimensional single-band Hubbard models. In the end, we present some preliminary results of multi-band Hubbard models and large-basis calculations of F 2 to illustrate our efforts to further reduce the computational complexity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Benchmarking structural evolution methods for training of machine learned interatomic potentials

When creating training data for machine-learned interatomic potentials (MLIPs), it is common to create initial structures and evolve them using molecular dynamics (MD) to sample a larger configuration space. Here, we benchmark two other modalities of evolving structures, contour exploration (CE) and dimer-method (DM) searches against MD for their ability to produce diverse and robust density functional theory training data sets for MLIPs. We also discuss the generation of initial structures which are either from known structures or from random structures in detail to further formalize the structure-sourcing processes in the future. The polymorph-rich zirconium-oxygen composition space is used as a rigorous benchmark system for comparing the performance of MLIPs trained on structures generated from these structural evolution methods. Using Behler–Parrinello neural networks as our MLIP models, we find that CE and the DM searches are generally superior to MD in terms of spatial descriptor diversity and statistical accuracy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A rotationally invariant approach based on Gutzwiller wave function for correlated electron systems

Here, we introduce a rotationally invariant approach combined with the Gutzwiller conjugate gradient minimization method to study correlated electron systems. In the approach, the Gutzwiller projector is parametrized based on the number of electrons occupying the onsite orbitals instead of the onsite configurations. The approach efficiently groups the onsite orbitals according to their symmetry and greatly reduces the computational complexity, which yields a speedup of $20 \sim 50 \times $ in the minimal basis energy calculation of dimers. The computationally efficient approach promotes more accurate calculations beyond the minimal basis that is inapplicable in the original approach. A large-basis energy calculation of F 2 demonstrates favorable agreements with standard quantum-chemical calculations Bytautas et al (2007 J. Chem. Phys. 127 164317).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Interplay of vibration- and environment-assisted energy transfer

Abstract We study the interplay between two environmental influences on excited state energy transfer in photosynthetic light harvesting complexes, namely, vibrationally assisted energy transfer (VAET) and environment-assisted quantum transport (ENAQT), considering a dimeric chromophore donor–acceptor model as a prototype for larger systems. We demonstrate how the basic features of the excitonic energy transfer are influenced by these two environments, both separately and together, with the environment being fully quantum in the case of VAET and treated in the Haken–Strobl–Reineker classical limit in the case of ENAQT. Our results reveal that in the weak noise regime, the presence of a classical noise source is detrimental to the energy transfer that is resonantly assisted by the exciton-vibration interactions intrinsic to VAET. In the strong noise regime we reproduce all the features of ENAQT, including the turnover into a Zeno regime where energy transfer is suppressed, and VAET is insignificant.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Exploring few and single layer CrPS 4 with near-field infrared spectroscopy

Abstract We combine synchrotron-based near-field infrared spectroscopy and first principles lattice dynamics calculations to explore the vibrational response of CrPS 4 in bulk, few-, and single-layer form. Analysis of the mode pattern reveals a C 2 polar + chiral space group, no symmetry crossover as a function of layer number, and a series of non-monotonic frequency shifts in which modes with significant intralayer character harden on approach to the ultra-thin limit whereas those containing interlayer motion or more complicated displacement patterns soften and show inflection points or steps. This is different from MnPS 3 where phonons shift as 1/size 2 and are sensitive to the three-fold rotation about the metal center that drives the symmetry crossover. We discuss these differences as well as implications for properties such as electric polarization in terms of presence or absence of the P–P dimer and other aspects of local structure, sheet density, and size of the van der Waals gap.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Effect of environmental screening and strain on optoelectronic properties of two-dimensional quantum defects

Point defects in hexagonal boron nitride (hBN) are promising candidates as single-photon emitters (SPEs) in nanophotonics and quantum information applications. The precise control of SPEs requires in-depth understanding of their optoelectronic properties. However, how the surrounding environment of host materials, including the number of layers, substrates, and strain, influences SPEs has not been fully understood. Here, in this work, we study the dielectric screening effect due to the number of layers and substrates, and the strain effect on the optical properties of carbon dimer and nitrogen vacancy defects in hBN from first-principles many-body perturbation theory. We report that environmental screening causes a lowering of the quasiparticle gap and exciton binding energy, leading to nearly constant optical excitation energy and exciton radiative lifetime. We explain the results with an analytical model starting from the Bethe–Salpeter equation Hamiltonian with Wannier basis. We also show that optical properties of quantum defects are largely tunable by strain with highly anisotropic response, in good agreement with experimental measurements. Our work clarifies the effect of environmental screening and strain on optoelectronic properties of quantum defects in two-dimensional insulators, facilitating future applications of SPEs and spin qubits in low-dimensional systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Investigating the limits of superconductivity in UTe 2

Abstract Spin-triplet bulk superconductors are a promising route to topological superconductivity, and UTe 2 is a recently discovered contender. The superconducting properties of UTe 2 , however, vary substantially as a function of the synthetic route, and even nonsuperconducting single crystals have been reported. To understand the driving mechanism suppressing superconductivity, we investigate UTe 2 single crystals grown close to the nonsuperconducting boundary (growth temperature ∼710 ∘ C) through a combination of thermodynamic and x-ray diffraction measurements. Specific heat measurements reveal a sharp decrease in the superconducting volume and a concomitant increase in the residual specific heat coefficient close to the nonsuperconducting boundary. Notably, these crystals are inhomogeneous and show an apparent double transition in specific heat measurements, similar to samples grown at much higher temperatures (∼1000 ∘ C). Our single crystal x-ray diffraction measurements reveal that there are two important tuning parameters: uranium vacancies and the atomic displacement along the c axis, which shows a twofold increase in samples with a reduced superconducting volume. Our results highlight the key role of local disorder along the uranium-uranium dimers and suggest that the apparent double superconducting transition is more likely to emerge close to the superconducting limits of UTe 2 .

Weiland, A. (ORCID:0000000171983559)↗
DOE OSTI2021

Osmosensing by WNK Kinases

With No Lysine (K) WNK kinases regulate electro-neutral cotransporters that are controlled by osmotic stress and chloride. We showed previously that autophosphorylation of WNK1 is inhibited by chloride, raising the possibility that WNKs are activated by osmotic stress. Here we demonstrate that unphosphorylated WNK isoforms 3 and 1 autophosphorylate in response to osmotic pressure in vitro, applied with the crowding agent polyethylene glycol (PEG)400 or osmolyte ethylene glycol (EG), and that this activation is opposed by chloride. Small angle x-ray scattering of WNK3 in the presence and absence of PEG400, static light scattering in EG, and crystallography of WNK1 were used to understand the mechanism. Osmosensing in WNK3 and WNK1 appears to occur through a conformational equilibrium between an inactive, unphosphorylated, chloride-binding dimer and an autophosphorylation-competent monomer. An improved structure of the inactive kinase domain of WNK1, and a comparison with the structure of a monophosphorylated form of WNK1, suggests that large cavities, greater hydration, and specific bound water may participate in the osmosensing mechanism. Our prior work showed that osmolytes have effects on the structure of phosphorylated WNK1, suggestive of multiple stages of osmotic regulation in WNKs.

59 BASIC BIOLOGICAL SCIENCES↗