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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A Structurally Diverse Compound Screening Library to Identify Substrates for Diamine, Polyamine, and Related Acetyltransferases

Spermidine/spermine N-acetyltransferases (SSATs) and other types of polyamine acetyltransferases (PAATs) acetylate diamines and/or polyamines. These enzymes are evolutionarily related and belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily, yet we lack a fundamental understanding of their substrate specificity and/or promiscuity toward different compounds. Many of these enzymes are known or are predicted to acetylate polyamines, but in the cell there are other types of compounds that contain moieties derived from polyamines that may be the native substrates for these enzymes. To learn more about the identity of substrates that are acetylated, we selected and screened 17 different GNAT enzymes for activity toward a set of structurally diverse compounds that contained different types of amine moieties (e.g., aminopropyl, aminobutyl, etc.). These compounds included diamines, triamines, and polyamines containing primary amino groups, and they had structural diversity with variation of the chain length and presence or absence of internal amino groups and other functional groups. We found 12 of the 17 enzymes acetylated at least one of the compounds. Some enzymes were selective toward acetylating only one compound while others exhibited substrate promiscuity toward numerous compounds. Our experimental results ultimately allowed us to pinpoint specific substrates that could be further investigated to more fully understand substrate specificity versus promiscuity of GNAT enzymes and the role of acetylated small molecules in cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues

We report the structural analysis of highly drug-resistant human immunodeficiency virus protease (PR) variant PR S17 , rationally selected by machine learning, in complex with substrate analogues. Crystal structures were solved of inhibitor-free inactive PR S17 -D25N, wild-type PR/CA-p2 complex, and PR S17 in complex with substrate analogues, CA-p2 and p2-NC. Peptide analogues p2-NC and CA-p2 exhibit inhibition constants of 514 and 22 nM, respectively, for PR S17 or approximately 3-fold better than for PR. CA-p2 is a better inhibitor of PR S17 than are clinical inhibitors ( K i = 50–8390 nM) except for amprenavir ( K i = 11 nM). G48V resistance mutation induces curled flap tips in PR S17 -D25N structure. The inner P2–P2' residues of substrate analogues in PR S17 complexes maintain similar conformations to those of wild-type complex, while significant conformational changes are observed in the peripheral residues P3, P4' of CA-p2 and P3, P4, and P3' of p2-NC. The loss of β-branched side chain by V82S mutation initiates a shift in 80’s loop and reshapes the S3/S3' subsite, which enhances substrate binding with new hydrogen bonds and van der Waals interactions that are absent in the wild-type structures. The steric hindrance caused by G48V mutation in the flap of PR S17 contributes to altered binding interactions of P3 Arg, P4' norleucine of CA-p2, and P4 and P3' of p2-NC with the addition of new hydrogen bonds and van der Waals contacts. The enhanced interaction of PR S17 with substrate analogues agrees with their relative inhibition, suggesting that this mutant improves substrate binding while decreasing affinity for clinical inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach

Mo-dependent nitrogenase catalyzes the biological reduction of N 2 to 2NH 3 at the FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N 2 , to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized sub-microsecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel not previously reported. The viability of the proposed channel was tested by examining the free energy of passage of N 2 from the surface through the channel to FeMo-cofactor, with discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Molecular Insight into Substrate Recognition and Catalysis of Baeyer-Villiger Monooxygenase MtmOIV, the Key Frame-Modifying Enzyme in the Biosynthesis of Anticancer Agent Mithramycin

Baeyer–Villiger monooxygenases (BVMOs) have been shown to play key roles for the biosynthesis of important natural products. MtmOIV, a homodimeric FAD- and NADPH-dependent BVMO, catalyzes the key frame-modifying steps of the mithramycin biosynthetic pathway, including an oxidative C–C bond cleavage, by converting its natural substrate premithramycin B into mithramycin DK, the immediate precursor of mithramycin. The drastically improved protein structure of MtmOIV along with the high-resolution structure of MtmOIV in complex with its natural substrate premithramycin B are reported here, revealing previously undetected key residues that are important for substrate recognition and catalysis. Kinetic analyses of selected mutants allowed us to probe the substrate binding pocket of MtmOIV and also to discover the putative NADPH binding site. This is the first substrate-bound structure of MtmOIV providing new insights into substrate recognition and catalysis, which paves the way for the future design of a tailored enzyme for the chemo-enzymatic preparation of novel mithramycin analogues.

Bosserman, Mary A.↗
DOE OSTI2015

Influence of Substrate Temperature on the Transformation Front Velocities That Determine Thermal Stability of Vapor-Deposited Glasses

Stable organic glasses prepared by physical vapor deposition transform into the supercooled liquid via propagating fronts of molecular mobility, a mechanism different from that exhibited by glasses prepared by cooling the liquid. In this paper, we show that spectroscopic ellipsometry can directly observe this front-based mechanism in real time and explore how the velocity of the front depends upon the substrate temperature during deposition. For the model glass former indomethacin, we detect surface-initiated mobility fronts in glasses formed at substrate temperatures between 0.68T g and 0.94T g . At each of two annealing temperatures, the substrate temperature during deposition can change the transformation front velocity by a factor of 6, and these changes are imperfectly correlated with the density of the glass. We also observe substrate-initiated fronts at some substrate temperatures. By connecting with theoretical work, we are able to infer the relative mobilities of stable glasses prepared at different substrate temperatures. Finally, an understanding of the transformation behavior of vapor-deposited glasses may be relevant for extending the lifetime of organic semiconducting devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A substrate-driven allosteric switch that enhances PDI catalytic activity

Protein disulfide isomerase (PDI) is an oxidoreductase essential for folding proteins in the endoplasmic reticulum. The domain structure of PDI is a–b–b'–x–a', wherein the thioredoxin-like a and a' domains mediate disulfide bond shuffling and b and b' domains are substrate binding. The b' and a' domains are connected via the x-linker, a 19-amino-acid flexible peptide. Here we identify a class of compounds, termed bepristats, that target the substrate-binding pocket of b'. Bepristats reversibly block substrate binding and inhibit platelet aggregation and thrombus formation in vivo . Ligation of the substrate-binding pocket by bepristats paradoxically enhances catalytic activity of a and a' by displacing the x-linker, which acts as an allosteric switch to augment reductase activity in the catalytic domains. This substrate-driven allosteric switch is also activated by peptides and proteins and is present in other thiol isomerases. Our results demonstrate a mechanism whereby binding of a substrate to thiol isomerases enhances catalytic activity of remote domains.

Science & Technology - Other Topics↗
DOE OSTI2019

Scaling growth rates for perovskite oxide virtual substrates on silicon

Abstract The availability of native substrates is a cornerstone in the development of microelectronic technologies relying on epitaxial films. If native substrates are not available, virtual substrates - crystalline buffer layers epitaxially grown on a structurally dissimilar substrate - offer a solution. Realizing commercially viable virtual substrates requires the growth of high-quality films at high growth rates for large-scale production. We report the stoichiometric growth of SrTiO 3 exceeding 600 nm hr −1 . This tenfold increase in growth rate compared to SrTiO 3 grown on silicon by conventional methods is enabled by a self-regulated growth window accessible in hybrid molecular beam epitaxy. Overcoming the materials integration challenge for complex oxides on silicon using virtual substrates opens a path to develop new electronic devices in the More than Moore era and silicon integrated quantum computation hardware.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases

Testis-restricted melanoma antigen (MAGE) proteins are frequently hijacked in cancer and play a critical role in tumorigenesis. MAGEs assemble with E3 ubiquitin ligases and function as substrate adaptors that direct the ubiquitination of novel targets, including key tumor suppressors. However, how MAGEs recognize their targets is unknown and has impeded the development of MAGE-directed therapeutics. Here, we report the structural basis for substrate recognition by MAGE ubiquitin ligases. Biochemical analysis of the degron motif recognized by MAGE-A11 and the crystal structure of MAGE-A11 bound to the PCF11 substrate uncovered a conserved substrate binding cleft (SBC) in MAGEs. Mutation of the SBC disrupted substrate recognition by MAGEs and blocked MAGE-A11 oncogenic activity. A chemical screen for inhibitors of MAGE-A11:substrate interaction identified 4-Aminoquinolines as potent inhibitors of MAGE-A11 that show selective cytotoxicity. These findings provide important insights into the large family of MAGE ubiquitin ligases and identify approaches for developing cancer-specific therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Cracking in polymer substrates for flexible electronic devices and its mitigation

Mechanical reliability plays a critical role in determining the durability of flexible electronic devices because of the significant mechanical stresses they experience during manufacturing and operation. Many such devices are built on sheets comprising stiff transparent-conducting oxide (TCO) electrode films on compliant polymer substrates, and it is generally assumed that the high-toughness polymer substrates do not crack. Contrary to this assumption, here we show extensive cracking in the polymer substrates during bending of a variety of TCO/polymer sheets, and a device example — flexible perovskite solar cells. Such substrate cracking, which compromises the overall mechanical integrity of the entire device, is driven by the amplified stress-intensity factor caused by the elastic mismatch at the film/substrate interface. To mitigate this substrate cracking, an interlayer-engineering approach is designed and experimentally demonstrated. This approach is potentially applicable to myriad flexible electronic devices, with stiff films on compliant substrates, for improving their durability and reliability.

42 ENGINEERING↗
DOE OSTI2014

Effect of Dispersion on Surface Interactions of Cobalt(II) Octaethylporphyrin Monolayer on Au(111) and HOPG(0001) Substrates: a Comparative First Principles Study

A density functional theory study of a cobalt(II) octaethylporphyrin (CoOEP) monolayer on Au(111) and HOPG(0001) surfaces was performed under periodic boundary conditions. Calculations with and without dispersion corrections are performed and the effect of van der Waals forces on the interface properties is analyzed. Calculations have determined that the CoOEP molecule tends to bind at the 3-fold and the 6-fold center sites on Au(111) and HOPG(0001), respectively. Geometric optimizations at the center binding sites have indicated that the porphyrin molecules (in the monolayer) lie flat on both substrates. Calculations also reveal that the CoOEP monolayer binds slightly more strongly to Au(111) than to HOPG(0001). Charge density difference plots disclose that charge is redistributed mostly around the porphyrin plane and the first layer of the substrates. Dispersion interactions cause a larger substrate to molecule charge pushback on Au(111) than on HOPG. CoOEP adsorption tends to lower the work functions of either substrate, qualitatively agreeing with the experimental photoelectron spectroscopic data. Comparison of the density of states (DOS) of the isolated CoOEP molecule with that on gold and HOPG substrates showed significant band shifts around the Fermi energy due to intermolecular orbital hybridization. Simulated STM images were plotted with the Tersoff–Hamann approach using the local density of states, which also agree with the experimental results. This study elucidates the role of dispersion for better describing porphyrin–substrate interactions. A DFT based overview of geometric, adsorption and electronic properties of a porphyrin monolayer on conductive surfaces is presented.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2021

Effects of growth substrate on the nucleation of monolayer MoTe 2

The discovery and characterization of two-dimensional (2D) materials beyond graphene has increased dramatically over the past decade with increasingly fine control over the growth dynamics of these materials. MoTe 2 represents a model material for studying phase change properties of 2D materials due to small energy differences between its 2H semiconducting phase and 1T' semimetallic phase. Although some substrates are demonstrated to be better than others for the wafer-scale growth of high quality MoTe 2 films, substrate effects on the nucleation and growth of MoTe 2 are still not well understood. Here, we grow monolayer MoTe 2 by converting MoO x thin films deposited on three different substrates: sapphire Al 2 O 3 (0001), amorphous SiO 2 , and amorphous AlO x , and examine the early stages of the conversion reaction to elucidate the substrate effects on the nucleation of MoTe 2 . We observe that the chemical composition of the substrate is more important than the surface topography and crystallinity of the substrate, with high quality monolayer 2H MoTe 2 formed on both Al 2 O 3 (0001) and AlO x in contrast to mixed phase 2H/1T' MoTe 2 formed on SiO 2 , as determined by Raman spectroscopy, X-ray photoelectron spectroscopy, and atomic force microscopy.

36 MATERIALS SCIENCE↗
DOE OSTI2024

GeSn-on-GaAs with photoconductive carrier lifetime >400 ns: role of substrate orientation and atomistic simulation

Group IV GeSn quantum material finds application in electronics and silicon-compatible photonics. Synthesizing these materials with low defect density and high carrier lifetime is a potential challenge due to lattice mismatch induced defects and tin segregation at higher growth temperature. Recent advancements in the growth of these GeSn materials on Si, Ge, GaAs, and with substrate orientations, demonstrated different properties using epitaxial and chemical deposition methods. This article addresses the effect of GaAs substrate orientation and misorientation on the materials’ properties and carrier lifetimes in epitaxial Ge 0.94 Sn 0.06 layers. With starting GaAs substrates of (100)/2°, (100)/6°, (110) and (111)A orientations, Ge 0.94 Sn 0.06 epitaxial layers were grown with an intermediate Ge buffer layer by molecular beam epitaxy and analyzed by several analytical tools. X-ray analysis displayed good crystalline quality, and Raman spectroscopy measurements showed blue shifts in phonon wavenumber due to biaxial compressive strain in Ge 0.94 Sn 0.06 epilayers. Cross-sectional transmission electron microscopy analysis confirmed the defect-free heterointerface of Ge 0.94 Sn 0.06 /Ge/GaAs heterostructure. Minority carrier lifetimes of the unintentionally doped n-type Ge 0.94 Sn 0.06 epilayers displayed photoconductive carrier lifetimes of >400 ns on (100)/6°, 319 ns on (100)/2°, and 434 ns on (110) GaAs substrate at 1500 nm excitation wavelength. On the other hand, Ge 0.94 Sn 0.06 layer showed poor carrier lifetime on (111)A GaAs substrate. The observed differences in carrier lifetimes were correlated with the formation energy of the Ge on (100)/6° and (100)/2° GaAs heterointerface using Stillinger–Weber interatomic potential model-based atomistic simulation with different heterointerfacial bonding by Synopsys QuantumATK tool. Total energy computation of 6280-atom Ge/GaAs supercell on (100)/6° leads to lower formation energy than (100)/2°, making it more thermodynamically stable. Hence, the growth of the GeSn/III–V material system using misoriented (100) substrates that are more thermodynamically stable will enhance the performances of optoelectronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

InGaP solar cell on Ge-on-Si virtual substrate for novel solar power conversion

InGaP single-junction solar cells are grown on lattice-matched Ge-on-Si virtual substrates using metal-organic chemical vapor deposition. Optoelectronic simulation results indicate that the optimal collection length for InGaP single-junction solar cells with a carrier lifetime range of 2–5 ns is wider than approximately 1 μ m. Electron beam-induced current measurements reveal that the threading dislocation density (TDD) of InGaP solar cells fabricated on Ge and Ge-on-Si substrates is in the range of 10 4 –3 × 10 7 cm -2 . We demonstrate that the open circuit voltage ( V oc ) of InGaP solar cells is not significantly influenced by TDDs less than 2 × 10 6 cm -2 . Fabricated InGaP solar cells grown on a Ge-on-Si virtual substrate and a Ge substrate exhibit V oc in the range of 0.96 to 1.43 V under an equivalent illumination in the range of ~0.5 Sun. Finally, the estimated efficiency of the InGaP solar cell fabricated on the Ge-on-Si virtual substrate (Ge substrate) at room temperature for the limited incident spectrum spanning the photon energy range of 1.9–2.4 eV varies from 16.6% to 34.3%.

14 SOLAR ENERGY↗
DOE OSTI2021

The effect of substrate temperature on the critical velocity in microparticle impact bonding

A number of nascent coating and micromanufacturing processes involve particles sprayed at a high velocity, which impact a substrate, deform, and adhere. Successful bonding between the particles and the substrate requires impact velocities higher than the so-called critical adhesion velocity. This critical velocity is influenced by the temperature of the substrate, a variable that we isolate in this work by conducting single-particle impacts on a variable-temperature substrate for three systems (Al–Al, Sn–Sn, and Ti–Ti) with particles individually selected within a narrow size distribution. Our results quantitatively connect the increase in substrate temperature to a significant lowering of the critical velocity, which we attribute to the lower dynamic strength of the thermally softened substrate. The data are generally consistent with expectations for bonding being controlled by a hydrodynamic process of jetting upon impact.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Synthesis and transport properties of epitaxial Bi (111) films on GaAs (111) substrates

In recent decades, the growth of ultrathin epitaxial bismuth (Bi) films on various substrates has garnered interest due to their unique electronic properties. We report upon the growth and electrical transport properties of epitaxial Bi (111) films in the thickness range of 5–32 nm deposited directly on GaAs (111) substrates, without a buffer layer. The quality of Bi films is found to depend on conditions for substrate treatment using Ar + ion-milling and annealing. Substrates milled at low ion beam currents display poor surface reconstruction after annealing, which hinders the growth of high-quality films. In contrast, substrates milled under optimized conditions led to reconstructed surfaces upon annealing, resulting in epitaxial Bi films with predominantly single-domain orientation. Although epitaxial films formed in both cases, transport measurements indicated significantly higher conductivity for films grown on optimally treated substrates. Measurements at low temperatures suggest that the transport properties are dominated by a surface state with high mobility electrons. Magneto-transport measurements suggest that conductivity and mobility improve progressively with increasing film thickness. For the thinnest 5 nm film, a hole-like state emerges, presumably as the electron-like state is gapped out. These results provide a robust methodology for growing high-quality epitaxial Bi films on GaAs (111) and offer insights into their unique transport properties and our ability to tune them.

Atomic force microscopy↗
DOE OSTI2016

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tolerance for the otherwise uncharacterized TruF family. We determined the structures of the Tyr-prenylating enzyme PagF, in complex with an isoprenoid donor analog and a panel of linear and macrocyclic peptide substrates. Unexpectedly, the structures reveal a truncated barrel fold, wherein binding of large peptide substrates is necessary to complete a solvent-exposed hydrophobic pocket to form the catalytically competent active site. Kinetic, mutational, chemical, and computational analyses revealed the structural basis of selectivity, showing a small motif within peptide substrates that is sufficient for recognition by the enzyme. Attaching this 2-residue motif to two random peptides results in their isoprenylation by PagF, demonstrating utility as a general biocatalytic platform for modifications on any peptide substrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural determinants and cellular environment define processed actin as the sole substrate of the N-terminal acetyltransferase NAA80

N-terminal (Nt) acetylation is a major protein modification catalyzed by N-terminal acetyltransferases (NATs). Methionine acidic N termini, including actin, are cotranslationally Nt acetylated by NatB in all eukaryotes, but animal actins containing acidic N termini, are additionally posttranslationally Nt acetylated by NAA80. Actin Nt acetylation was found to regulate cytoskeletal dynamics and motility, thus making NAA80 a potential target for cell migration regulation. In this work, we developed potent and selective bisubstrate inhibitors for NAA80 and determined the crystal structure of NAA80 in complex with such an inhibitor, revealing that NAA80 adopts a fold similar to other NAT enzymes but with a more open substrate binding region. Furthermore, in contrast to most other NATs, the substrate specificity of NAA80 is mainly derived through interactions between the enzyme and the acidic amino acids at positions 2 and 3 of the actin substrate and not residues 1 and 2. A yeast model revealed that ectopic expression of NAA80 in a strain lacking NatB activity partially restored Nt acetylation of NatB substrates, including yeast actin. Thus, NAA80 holds intrinsic capacity to posttranslationally Nt acetylate NatB-type substrates in vivo. In sum, the presence of a dominant cotranslational NatB in all eukaryotes, the specific posttranslational actin methionine removal in animals, and finally, the unique structural features of NAA80 leave only the processed actins as in vivo substrates of NAA80. Together, this study reveals the molecular and cellular basis of NAA80 Nt acetylation and provides a scaffold for development of inhibitors for the regulation of cytoskeletal properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis

The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased K m values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the p K a of the catalytic residue (p K ES1 ) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. In this paper, we propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗