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DOE OSTI2020

Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface

Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Catalytic upcycling of polyolefins into lubricants

A method of upcycling polymers to useful hydrocarbon materials. A catalyst with nanoparticles on a substrate selectively docks and cleaves longer hydrocarbon chains over shorter hydrocarbon chains. The nanoparticles exhibit an edge to facet ratio to provide for more interactions with the facets.

Celik, Gokhan↗

DOE OSTI2023

Catalytic upcycling of polymers

Delferro, Massimiliano↗

DOE OSTI2010

Fluconazole Binding and Sterol Demethylation in Three CYP51 Isoforms Indicate Differences in Active Site Topology

14{alpha}-Demethylase (CYP51) is a key enzyme in all sterol biosynthetic pathways (animals, fungi, plants, protists, and some bacteria), catalyzing the removal of the C-14 methyl group following cyclization of squalene. Based on mutations found in CYP51 genes from Candida albicans azole-resistant isolates obtained after fluconazole treatment of fungal infections, and using site-directed mutagenesis, we have found that fluconazole binding and substrate metabolism vary among three different CYP51 isoforms: human, fungal, and mycobacterial. In C. albicans, the Y132H mutant from isolates shows no effect on fluconazole binding, whereas the F145L mutant results in a 5-fold increase in its IC{sub 50} for fluconazole, suggesting that F145 (conserved only in fungal 14{alpha}-demethylases) interacts with this azole. In C. albicans, F145L accounts, in part, for the difference in fluconazole sensitivity reported between mammals and fungi, providing a basis for treatment of fungal infections. The C. albicans Y132H and human Y145H CYP51 mutants show essentially no effect on substrate metabolism, but the Mycobacterium tuberculosis F89H CYP51 mutant loses both its substrate binding and metabolism. Because these three residues align in the three isoforms, the results indicate that their active sites contain important structural differences, and further emphasize that fluconazole and substrate binding are uncoupled properties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Structural characterization of intramolecular Hg2+ transfer between flexibly-linked domains of mercuric ion reductase

The enzyme mercuric ion reductase, MerA, is the central component of bacterial mercury resistance encoded by the mer operon. Many MerA proteins possess a metallochaperone-like N-terminal domain, NmerA, that can transfer Hg2+ to the catalytic core (Core) for reduction to Hg0. These domains are tethered to the homodimeric Core by ~30-residue linkers that are subject to proteolysis, which has limited structural and functional characterization of the interactions of these domains. Here, we report purification of homogeneous full-length MerA using a fusion protein construct and combine small-angle X-ray and neutron scattering with molecular dynamics simulation to characterize the structure of constructs that mimic the system before and during handoff of Hg2+ from NmerA to the Core. The radii of gyration, distance distribution functions and Kratky plots derived from the small-angle X-ray scattering data are consistent with full-length MerA adopting elongated conformations resulting from flexibility in the linkers to the NmerA domains. The scattering profiles are best reproduced using an ensemble of linker conformations. This flexible attachment of NmerA may facilitate fast and efficient removal of Hg2+ from diverse protein substrates. Using a specific mutant of MerA allowed determination of the position and relative orientation of NmerA to the Core during Hg2+ handoff. The small buried surface area at the site of interaction suggests molecular recognition may be of less importance for the integrity of metal ion transfers between tethered domains than for transfers between separate proteins in metal trafficking pathways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Plasmonic tuning of gold doped thin films for layers of photovoltaic devices

In order to increase the absorption rates in solar cells, increasing research activities on the plasmonic nanostructures are followed carefully. The plasmonic nanoparticles provides an important enhancement in the trapping of photons in the active layer of the solar cells by means of interaction between incident light and plasmonic nanoparticles. In order to obtain this approach, under of 5×10{sup −4} mbar and 1×10{sup −2} mbar ambient argon gas pressure, gold thin film was deposited on the silicon substrate by applying PLD system. The morphology of thin films obtained was investigated by AFM and SEM considering the effect of Ar gas pressure on the plasma plume. SPR peaks for Au nanoparticles deposited under 5×10{sup −4} mbar and 1×10{sup −2} mbar Ar gas pressure were observed at 756 nm and 658 nm wavelengths respectively. It has been stated that the SPR peak in the infrared is depend on the near field interaction between Au nanoparticles. Furthermore, when the pressure is increased to 1×10{sup −2} mbar Ar, it has been observed that the SPR peak for thin film is shifted towards to shorter wavelengths, and it has also been observed that the intensity of absorption peak is decreased.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2010

Coherent heteroepitaxy of Bi{sub 2}Se{sub 3} on GaAs (111)B

We report the heteroepitaxy of single crystal thin films of Bi{sub 2}Se{sub 3} on the (111)B surface of GaAs by molecular beam epitaxy. We find that Bi{sub 2}Se{sub 3} grows highly c-axis oriented, with an atomically sharp interface with the GaAs substrate. By optimizing the growth of a very thin GaAs buffer layer before growing the Bi{sub 2}Se{sub 3}, we demonstrate the growth of thin films with atomically flat terraces over hundreds of nanometers. Initial time-resolved Kerr rotation measurements herald opportunities for probing coherent spin dynamics at the interface between a candidate topological insulator and a large class of GaAs-based heterostructures.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis

We report multicopper oxidases (MCOs) represent a diverse family of enzymes that catalyze the oxidation of either an organic or a metal substrate with concomitant reduction of dioxygen to water. These enzymes contain variable numbers of cupredoxin domains, two, three or six per subunit, and rely on four copper ions, a single type I copper and three additional copper ions organized in a trinuclear cluster (TNC), with one type II and two type III copper ions, to catalyze the reaction. Here, two crystal structures and the enzymatic characterization of Marinithermus hydrothermalis MCO, a two-domain enzyme, are reported. This enzyme decolorizes Congo Red dye at 70°C in the presence of high halide concentrations and may therefore be useful in the detoxification of industrial waste that contains dyes. In two distinct crystal structures, MhMCO forms the trimers seen in other two-domain MCOs, but differs from these enzymes in that four trimers interact to create a dodecamer. This dodecamer of MhMCO forms a closed ball-like structure and has implications for the sequestration of bound divalent metal ions as well as substrate accessibility. In each subunit of the dodecameric structures, a Trp residue, Trp351, located between the type I and TNC sites exists in two distinct conformations, consistent with a potential role in facilitating electron transfer in the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

54 Mn Radiotracers Demonstrate Continuous Dissolution and Reprecipitation of Vernadite (δ-MnO 2 ) during Interaction with Aqueous Mn(II)

54 Mn radiotracers were used to assess Mn atom exchange between aqueous Mn(II) and vernadite (δ-MnO 2 ) at pH 5.0. Continuous solid–liquid redistribution of 54 Mn atoms occurred, and systems are near isotopic equilibrium after reaction for 3 months. Despite this extensive exchange, X-ray diffraction and X-ray absorption spectroscopy data showed no major changes in vernadite bulk mineralogy. These results demonstrate that the vernadite–Mn(II) interface is dynamic, with the substrate undergoing continuous dissolution and reprecipitation mediated by aqueous Mn(II) without observable impacts on its mineralogy. Interfacial redox reactions between adsorbed Mn(II) and solid-phase Mn(IV) and Mn(III) are proposed as the main drivers of this process. Interaction between aqueous Mn(II) and structural Mn(III) likely involves interfacial electron transfer coupled with Mn atom exchange. Here, the exchange of aqueous Mn(II) and solid-phase Mn(IV) is more complex and is proposed to result from coupled interfacial comproportionation–disproportionation reactions, where electron transfer from adsorbed Mn(II) to lattice Mn(IV) produces transient Mn(III) species that disproportionate to regenerate aqueous Mn(II) and structural Mn(IV). These findings provide further evidence of the importance of Mn(II) (aq) –MnO 2(s) interactions and the attendant production of transient Mn(III) intermediates to the geochemical functioning of phyllomanganates in environments undergoing Mn redox cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Thermally-driven H interaction with HfO{sub 2} films deposited on Ge(100) and Si(100)

In the present work, we investigated the thermally-driven H incorporation in HfO{sub 2} films deposited on Si and Ge substrates. Two regimes for deuterium (D) uptake were identified, attributed to D bonded near the HfO{sub 2}/substrate interface region (at 300 °C) and through the whole HfO{sub 2} layer (400–600 °C). Films deposited on Si presented higher D amounts for all investigated temperatures, as well as, a higher resistance for D desorption. Moreover, HfO{sub 2} films underwent structural changes during annealings, influencing D incorporation. The semiconductor substrate plays a key role in this process.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2012

Characterization of hydrogen-plasma interactions with photoresist, silicon, and silicon nitride surfaces

For the 45 nm technology node and beyond, a major challenge is to achieve reasonably high photoresist ash rates while minimizing the loss of the silicon (Si) substrate and its nitride (Si{sub 3}N{sub 4}). Accordingly, an objective of this work is to characterize the photoresist strip rate under varying conditions of H{sub 2} plasma and the effects of these conditions on Si and Si{sub 3}N{sub 4} etch rates. In addition, we discuss in detail the fundamental mechanisms of the reactions between H atoms and the above substrates and successfully reconcile the process trends obtained with the reaction mechanisms. In this work, photoresist, Si, and Si{sub 3}N{sub 4} films were exposed to downstream pure-H{sub 2} discharges and their removal rates were characterized by ellipsometry as a function of the following parameters: substrate temperature, reactor pressure, H{sub 2} flow rate, and source power. The authors found that the H{sub 2}-based dry ash and Si{sub 3}N{sub 4} etch are both thermally activated reactions, evidenced by the steady increase in etch rate as a function of temperature, with activation energies of {approx}5.0 and {approx}2.7 kcal/mol, respectively. The Si substrate exhibits a rather unique behavior where the etch rate increases initially to a maximum, which occurs at {approx}40 deg. C, and then decreases upon a further increase in temperature. The decrease in the Si etch rate at higher temperatures is attributed to the activation of competing side reactions that consume the chemisorbed H atoms on the Si surface, which then suppresses the Si-etch step. The photoresist and Si{sub 3}N{sub 4} removal rates increase initially with increasing pressure, reaching maxima at {approx}800 and 2000 mTorr, respectively, beyond which the removal rates drop with increasing pressure. The initial increase in removal rate at the low-pressure regime is attributed to the increased atomic-hydrogen density, whereas the decrease in ash rate at the high-pressure regime could be attributed to the recombination of H atoms that could occur by various mechanisms. At temperatures where the reaction rates are relatively fast, the photoresist and Si removal rates both increase continuously with the H{sub 2} flow rate, indicating that both reactions are in the supply-limited regime. For the range of process conditions explored here, we find that the etch rates of Si are generally much higher than those for Si{sub 3}N{sub 4} with Si:Si{sub 3}N{sub 4} etch-rate ratios that vary from 25 to >>520. Based on the process trends obtained here, we have identified a process window--high temperature and intermediate pressure--that attains relatively high photoresist ash rates and low Si and Si{sub 3}N{sub 4} etch rates.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors

Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H 2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H 2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO 2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

A coverage dependent study of the adsorption of pyridine on the (111) coinage metal surfaces

Using density functional theory we explore the adsorption of pyridine (NC 5 H 5 ) on Cu, Ag, and Au(111) surfaces. To study the effect of coverage we run calculations on a 3 × 4 (12 atom), 4 × 4 (16 atom), 5 × 4 (20 atom), and 4 × 6 (24 atom) surface. To examine the role of the van der Waals interaction we use the following vdW inclusive functionals: optB86-vdW, optB88-vdW, optPBE-vdW, revPBE-vdW, rPW86-vdW2, SCAN+rVV10 along with the PBE functional. Regardless of functional, metal, and coverage we find the most energetically stable adsorption site to be a vertical site with the pyridine's N atom directly above a metal atom, which contradicts the available experimental literature. Introducing the vdW interaction lowers the energy gap between the most energetically favorable flat and vertical adsorption configurations. Moving to a higher coverage increases the overall interaction of the pyridine molecule with the surface. We also find that the SCAN+rVV10 functional performs similarly to the optB86b-vdW and optB88-vdW functional. Along with the geometric properties of the substrate/adsorbate system, here we report several electronic properties of the substrate/adsorbate system such as charge transfer from the surface to the molecule, change in the surface's work function, and change in d-band of the atoms in the first layer of the substrate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Modular Assembly of FTO|Chromophore-Catalyst Hierarchical Films Based on Strong Dipole Interactions

Here, we have designed and characterized modular self-assembled hierarchical films containing a molecular catalyst tethered to an anchoring molecule by means of dipole-induced dipole interactions. In order to do so, two new Co III -based molecular catalyst candidates were designed, namely, [Co III L 1 (pyrr) 2 ]ClO 4 (Co1) and [Co III L 2 (pyrr) 2 ]ClO 4 (Co2), where L 1 and L 2 are the respective deprotonated forms of N,N′-[4,5-bis(dodecyloxy)-1,2-phenylene]dipicolinamide and N,N′-[4,5-bis(methoxyethoxy)-1,2-phenylene]dipicolinamide and were characterized by electrochemical, electronic, and film formation properties. Species Co1 and Co2 were deposited onto an anchor molecule such as octylphosphonic acid (OPA) or the chromophoric [Ru II (bpy PO3H ) 2 (bpy C7 )]Cl 2 (Ru) previously attached onto conductive fluorine-doped tin oxide (FTO). Four hierarchical films of the form substrate|anchor-catalyst were obtained, namely, FTO|OPA-Co1, FTO|OPA-Co2, FTO|Ru-Co1, and FTO|Ru-Co2, and the role of dipole-dipole interactions between anchor and catalyst modules was assessed. These newly synthesized hierarchical films were characterized by a host of surface-specific methods that include X-ray photoelectron spectroscopy, ellipsometry, X-ray fluorescence, and water contact angle, thus enabling an unprecedented level of analysis. Compared to the weak C-H van der Waals interactions exhibited by Co1, the presence of alkoxy chains in Co2 ensures stronger dipole-dipole interactions with the alkyl chain of the anchors due to O···H formation. The persistence of their redox properties, which include metal oxidation, and directionality of electron transport were probed suggesting direct relevance to catalytic processes such as water oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA

FANCD2 and FANCI function together in the Fanconi anemia network of deoxyribonucleic acid (DNA) crosslink repair. These proteins form the dimeric ID2 complex that binds DNA and becomes monoubiquitinated upon exposure of cells to DNA crosslinking agents. The monoubiquitinated ID2 complex is thought to facilitate DNA repair via recruitment of specific nucleases, translesion DNA polymerases and the homologous recombination machinery. Using the ubiquitin conjugating enzyme (E2) UBE2T and ubiquitin ligase (E3) FANCL, monoubiquitination of human FANCD2 and FANCI was examined. The ID2 complex is a poor substrate for monoubiquitination, consistent with the published crystal structure showing the solvent inaccessibility of the target lysines. Importantly, FANCD2 monoubiquitination within the ID2 complex is strongly stimulated by duplex or branched DNA, but unstructured singlestranded DNA or chromatinized DNA is ineffective. Interaction of FANCL with the ID2 complex is indispensable for its E3 ligase efficacy. Interestingly, mutations in FANCI that impair its DNA binding activity compromise DNA-stimulated FANCD2 monoubiquitination. Moreover, we demonstrate that in the absence of FANCD2, DNA also stimulates FANCI monoubiquitination, but in a FANCL-independent manner. These results implicate the role of a proper DNA ligand in FANCD2 and FANCI monoubiquitination, and reveal regulatory mechanisms that are dependent on protein–protein and protein–DNA interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded DNA

The origin-binding domain (OBD) of simian virus 40 (SV40) large T-antigen (T-Ag) is essential for many of T-Ag's interactions with DNA. Nevertheless, many important issues related to DNA binding, for example, how single-stranded DNA (ssDNA) transits along the T-Ag OBD, have yet to be established. Therefore, X-ray crystallography was used to determine the costructure of the T-Ag OBD bound to DNA substrates such as the single-stranded region of a forked oligonucleotide. A second structure of the T-Ag OBD crystallized in the presence of poly(dT){sub 12} is also reported. To test the conclusions derived from these structures, residues identified as being involved in binding to ssDNA by crystallography or by an earlier nuclear magnetic resonance study were mutated, and their binding to DNA was characterized via fluorescence anisotropy. In addition, these mutations were introduced into full-length T-Ag, and these mutants were tested for their ability to support replication. When considered in terms of additional homology-based sequence alignments, our studies refine our understanding of how the T-Ag OBDs encoded by the polyomavirus family interact with ssDNA, a critical step during the initiation of DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Structural mechanism of Escherichia coli cyanase

Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5–1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. Further, in the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.

59 BASIC BIOLOGICAL SCIENCES↗