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At least 235 records · Page 13

Mechanistic roles of metal- and ligand-protonated species in hydrogen evolution with [Cp*Rh] complexes

Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry and often result in the generation of reactive metal hydrides. However, some organometallic species supported by η 5 -pentamethylcyclopentadienyl (Cp*) ligands have recently been shown to undergo ligand-centered protonation by direct proton transfer from acids or tautomerization of metal hydrides, resulting in the generation of complexes bearing the uncommon η 4 -pentamethylcyclopentadiene (Cp*H) ligand. Here, time-resolved pulse radiolysis (PR) and stopped-flow spectroscopic studies have been applied to examine the kinetics and atomistic details involved in the elementary electron- and proton-transfer steps leading to complexes ligated by Cp*H, using Cp*Rh(bpy) as a molecular model (where bpy is 2,2′-bipyridyl). Stopped-flow measurements coupled with infrared and UV-visible detection reveal that the sole product of initial protonation of Cp*Rh(bpy) is [Cp*Rh(H)(bpy)] + , an elusive hydride complex that has been spectroscopically and kinetically characterized here. Tautomerization of the hydride leads to the clean formation of [(Cp*H)Rh(bpy)] + . Variable-temperature and isotopic labeling experiments further confirm this assignment, providing experimental activation parameters and mechanistic insight into metal-mediated hydride-to-proton tautomerism. Spectroscopic monitoring of the second proton transfer event reveals that both the hydride and related Cp*H complex can be involved in further reactivity, showing that [(Cp*H)Rh] is not necessarily an off-cycle intermediate, but, instead, depending on the strength of the acid used to drive catalysis, an active participant in hydrogen evolution. Identification of the mechanistic roles of the protonated intermediates in the catalysis studied here could inform design of optimized catalytic systems supported by noninnocent cyclopentadienyl-type ligands.

08 HYDROGEN↗

Mechanistic insights explain the transforming potential of the T507K substitution in the protein-tyrosine phosphatase SHP2

The protein-tyrosine phosphatase SHP2 is an allosteric enzyme critical for cellular events downstream of growth factor receptors. Mutations in the SHP2 gene have been linked to many different types of human diseases, including developmental disorders, leukemia, and solid tumors. Unlike most SHP2-activating mutations, the T507K substitution in SHP2 is unique in that it exhibits oncogenic Ras-like transforming activity. However, the biochemical basis of how the SHP2/T507K variant elicits transformation remains unclear. By combining kinetic and biophysical methods, X-ray crystallography, and molecular modeling, as well as using cell biology approaches, in this work we uncovered that the T507K substitution alters both SHP2 substrate specificity and its allosteric regulatory mechanism. We found that although SHP2/T507K exists in the closed, autoinhibited conformation similar to the WT enzyme, the interactions between its N-SH2 and protein-tyrosine phosphatase domains are weakened such that SHP2/T507K possesses a higher affinity for the scaffolding protein Grb2-associated binding protein 1 (Gab1). We also discovered that the T507K substitution alters the structure of the SHP2 active site, resulting in a change in SHP2 substrate preference for Sprouty1, a known negative regulator of Ras signaling and a potential tumor suppressor. Our results suggest that SHP2/T507K's shift in substrate specificity coupled with its preferential association of SHP2/T507K with Gab1 enable the mutant SHP2 to more efficiently dephosphorylate Sprouty1 at pTyr-53. This dephosphorylation hyperactivates Ras signaling, which is likely responsible for SHP2/T507K's Ras-like transforming activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A temperature-sensitive FERONIA mutant allele that alters root hair growth

Abstract In plants, root hairs undergo a highly polarized form of cell expansion called tip-growth, in which cell wall deposition is restricted to the root hair apex. In order to identify essential cellular components that might have been missed in earlier genetic screens, we identified conditional temperature-sensitive (ts) root hair mutants by ethyl methanesulfonate mutagenesis in Arabidopsis thaliana. Here, we describe one of these mutants, feronia-temperature sensitive (fer-ts). Mutant fer-ts seedlings were unaffected at normal temperatures (20°C), but failed to form root hairs at elevated temperatures (30°C). Map based-cloning and whole-genome sequencing revealed that fer-ts resulted from a G41S substitution in the extracellular domain of FERONIA (FER). A functional fluorescent fusion of FER containing the fer-ts mutation localized to plasma membranes, but was subject to enhanced protein turnover at elevated temperatures. While tip-growth was rapidly inhibited by addition of rapid alkalinization factor 1 (RALF1) peptides in both wild-type and fer-ts mutants at normal temperatures, root elongation of fer-ts seedlings was resistant to added RALF1 peptide at elevated temperatures. Additionally, at elevated temperatures fer-ts seedlings displayed altered reactive oxygen species (ROS) accumulation upon auxin treatment and phenocopied constitutive fer mutant responses to a variety of plant hormone treatments. Molecular modeling and sequence comparison with other Catharanthus roseus receptor-like kinase 1L (CrRLK1L) receptor family members revealed that the mutated glycine in fer-ts is highly conserved, but is not located within the recently characterized RALF23 and LORELI-LIKE-GLYCOPROTEIN 2 binding domains, perhaps suggesting that fer-ts phenotypes may not be directly due to loss of binding to RALF1 peptides.

Plant Sciences↗

Biexcitons are bound in CsPbBr 3 perovskite nanocrystals

Here, we study the energetics of quasiparticle excitations in CsPbBr 3 perovskite nanocrystals using path integral molecular dynamics simulations. Employing detailed molecular models, we elucidate the interplay of anharmonic lattice degrees of freedom, dielectric confinement, and electronic correlation on exciton and biexciton binding energies of a range of nanocrystal sizes. We find generally good agreement with some experimental observations of binding energies and additionally explain the observed size-dependent Stokes shift. The explicit model calculations are compared with simplified approximations to rationalize the lattice contributions to binding. We find that polaron formation significantly reduces exciton binding energies, whereas these effects are negligible for biexciton interactions. While experimentally the binding energy of biexcitons is uncertain, based on our study, we conclude that biexcitons are bound in CsPbBr 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Major facilitator family transporters specifically enhance caffeyl alcohol uptake during C‐lignin biosynthesis

The mode of transport of lignin monomers to the sites of polymerization in the apoplast remains controversial. C-Lignin is a recently discovered form of lignin found in some seed coats that is composed exclusively of units derived from caffeyl alcohol. RNA-seq and proteome analyses identified a number of transporters co-expressed with C-lignin deposition in the seed coat of Cleome hassleriana. Cloning and influx/efflux analysis assays in yeast identified two low-affinity transporters, ChPLT3 and ChSUC1, that were active with caffeyl alcohol but not with the classical monolignols p-coumaryl, coniferyl, and sinapyl alcohols, consistent with molecular modeling and docking studies. Expression of ChPLT3 in Arabidopsis seedlings enhanced root growth in the presence of caffeyl alcohol, and expression of ChPLT3 and ChSUC1 correlated with lignin C-unit content in hairy roots of Medicago truncatula. We present a model, consistent with phylogenetic and evolutionary considerations, whereby passive caffeyl alcohol transport may be supplemented by hitchhiking on secondary active transporters to ensure the synthesis of C-lignin, and inhibition of synthesis of G-lignin, in the apoplast.

59 BASIC BIOLOGICAL SCIENCES↗

Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies

Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.

59 BASIC BIOLOGICAL SCIENCES↗

A Nitroxide Containing Organic Molecule in a Deep Eutectic Solvent for Flow Battery Applications

The nitroxide radical redox organic molecule, 2-phenyl-4,4,5,5-tetrame- thylimidazoline-1-oxyl-3-oxide (PTIO), was investigated for the first time in a deep eutectic solvent (DES)-like system consisting of a 1:4 molar ratio of choline chloride and ethylene glycol(Ch1EG4) as a redox flow battery electrolyte. PTIO is a single molecule with three oxidation states, and can provide both positive and negative redox couples for a flow battery. A flow battery using the PTIO/Ch1EG4 electrolyte demonstrated nearly 50% roundtrip efficiency with an approximately 1 V open circuit potential. Inefficiencies were primarily due to membrane resistance which can be significantly lowered with increased temperature. While PTIO appears stable over short periods (hours), the oxidized form is not stable in the DES-like electrolyte over longer times. Molecular modeling was performed to investigate the relative stability of PTIO in DES as compared to the previously studied 4-hydroxy-TEMPO (4HT). It was found that the oxoammonium cation 4HT + exhibits a noticeably larger nucleophilic reactive cloud as compared to PTIO + , indicating a higher reactivity. This method to predict stability of the oxoammonium cation shows promise to inform the design and synthesis of promising redox systems based on nitroxide radicals in DES electrolytes to identify new chemistries for large scale energy storage.

25 ENERGY STORAGE↗

Understanding Redox Organic Behavior in Deep Eutectic Solvents: Considerations for Molecular Design

Electrolytes based on deep eutectic solvents (DESs) coupled with redox active organic molecules have shown potential as a versatile and energy dense electrochemical energy storage system. However, progress in these systems has been held back by a lack of understanding of the irregular behavior displayed when redox active organic molecules are transitioned from other solvent systems. In this work, the hydrogen bonding characteristics of a series of redox organic molecules were investigated through infrared spectroscopy and molecular modeling. New understanding of these interactions was then used to explain their electrochemical behavior in a DES electrolyte. A model was used to predict the behavior of new derivatives towards the design of an optimized redox organic-DES system. Hydrogen bonding between the redox molecules and the solvent was found to significantly shift the potential of a redox reaction more positive when a hydrogen bond forms at the redox active site. It was predicted that functionalizing a molecule with electron withdrawing groups to lower the electron density of the redox active functional group lowers the strength of the hydrogen bond and thus alleviates the undesirable potential shift. This hypothesis was demonstrated by the addition of nitro groups to fluorenones.

25 ENERGY STORAGE↗

FlbB forms a distinctive ring essential for periplasmic flagellar assembly and motility in Borrelia burgdorferi

Spirochetes are a widespread group of bacteria with a distinct morphology. Some spirochetes are important human pathogens that utilize periplasmic flagella to achieve motility and host infection. The motors that drive the rotation of periplasmic flagella have a unique spirochete-specific feature, termed the collar, crucial for the flat-wave morphology and motility of the Lyme disease spirochete Borrelia burgdorferi. Here, we deploy cryo-electron tomography and subtomogram averaging to determine high-resolution in-situ structures of the B. burgdorferi flagellar motor. Comparative analysis and molecular modeling of in-situ flagellar motor structures from B. burgdorferi mutants lacking each of the known collar proteins (FlcA, FlcB, FlcC, FlbB, and Bb0236/FlcD) uncover a complex protein network at the base of the collar. Importantly, our data suggest that FlbB forms a novel periplasmic ring around the rotor but also acts as a scaffold supporting collar assembly and subsequent recruitment of stator complexes. The complex protein network based on the FlbB ring effectively bridges the rotor and 16 torque-generating stator complexes in each flagellar motor, thus contributing to the specialized motility and lifestyle of spirochetes in complex environments.

59 BASIC BIOLOGICAL SCIENCES↗

Integrative illustration of a JCVI-syn3A minimal cell

Abstract Data from genomics, proteomics, structural biology and cryo-electron microscopy are integrated into a structural illustration of a cross section through an entire JCVI-syn3.0 minimal cell. The illustration is designed with several goals: to inspire excitement in science, to depict the underlying scientific results accurately, and to be feasible in traditional media. Design choices to achieve these goals include reduction of visual complexity with simplified representations, use of orthographic projection to retain scale relationships, and an approach to color that highlights functional compartments of the cell. Given that this simple cell provides an attractive laboratory for exploring the central processes needed for life, several functional narratives are included in the illustration, including division of the cell and the first depiction of an entire cellular proteome. The illustration lays the foundation for 3D molecular modeling of this cell.

Goodsell, David S.↗

Process Image Analysis using Big Data, Machine Learning, and Computer Vision

The development of algorithms for machine learning and data analysis for the 3013 MIS corrosion surveillance program is a collaborative effort by SRNL, USC and GT. For corrosion detection, LCM image data is extracted from large binary files, with software written to convert the data to physical attributes (i.e. height, color and grayscale values; all as functions of a location in a plane projection). The user interface for the software permits selective downloading of binary data and interrogation of attributes. User input thresholds are used to flag attributes of interest. Machine learning algorithms, developed for this application, are used to determine whether the features are the result of corrosion. To address the fundamental mechanisms of corrosion, machine learning algorithms are being developed to derive interatomic potential force-fields from ab-initio DFT calculations. The goal is to apply molecular modeling on a large enough scale to guide the design of resistant materials.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Phosphorus Recycling from Ribonucleotide Structures by Iron Oxide Minerals

In this research, we combined experimental and molecular modeling to obtain a fundamental understanding required to evaluate and predict the role of three natural iron oxides minerals (ferrihydrite, goethite, and hematite) in recycling phosphorus from organic matter, particularly ribonucleotides.

58 GEOSCIENCES↗

HamLib: A library of Hamiltonians for benchmarking quantum algorithms and hardware

In order to characterize and benchmark computational hardware, software, and algorithms, it is essential to have many problem instances on-hand. This is no less true for quantum computation, where a large collection of real-world problem instances would allow for benchmarking studies that in turn help to improve both algorithms and hardware designs. To this end, here we present a large dataset of qubit-based quantum Hamiltonians. The dataset, called HamLib (for Hamiltonian Library), is freely available online and contains problem sizes ranging from 2 to 1000 qubits. HamLib includes problem instances of the Heisenberg model, Fermi-Hubbard model, Bose-Hubbard model, molecular electronic structure, molecular vibrational structure, MaxCut, Max- k -SAT, Max- k -Cut, QMaxCut, and the traveling salesperson problem. The goals of this effort are (a) to save researchers time by eliminating the need to prepare problem instances and map them to qubit representations, (b) to allow for more thorough tests of new algorithms and hardware, and (c) to allow for reproducibility and standardization across research studies.

97 MATHEMATICS AND COMPUTING↗

Bimetallic Coinage Metal Complexes of Tetradentate ortho Ter arylene Ligands

The synthesis, structural and photophysical properties of five bimetallic coinage metal complexes of three tetradentate charge-transfer (CT) ligands are presented. The ligand structures incorporate donor/acceptor moieties electronically decoupled by ortho connection to a bridging biphenylene group. The M M distances observed in the crystal structures of the bimetallic complexes are shorter than the sum of the Van der Waals radii of the metal ions, suggesting stabilizing interactions between the d10 metal centers. Additionally, short distances between the bridging biphenylene and metal atoms suggest arylene metal interactions. Bimetallic Cu, Ag, and Au complexes of the ligand incorporating a carbazole donor and pyridyl acceptor (N2R22-) show absorption and emission energies that trend with the ionization potential of each metal, indicating metal character in the excited state. These properties contrast with our previously reported mononuclear Zn complex of N2R22-The structural and photophysical properties of five bimetallic d10 coinage metal complexes were presented. The M M distances observed in the crystal structures of the bimetallic complexes are shorter than the sum of the metals’ Van der Waals radii, suggesting attractive interactions between the d10 metal centers. Additionally, short distances between the bridging biphenylene and metal atoms suggest arylene metal interactions. The absorption and emission spectra of the bimetallic complexes redshift based on the oxidation potential of the metal ion. This suggests involvement of metal based orbitals in the excited state transitions of the bimetallic complexes, which was corroborated by molecular modeling. High photoluminescent quantum yields were observed in solution and in rigid media (up to PL = 0.75), and the excited state lifetimes in solution were found to exceed several microseconds.

Shariaty, Darius Allen [University of Southern Cal↗

Nonsynonymous amino acid changes in the α-chain of complement component 5 influence longitudinal susceptibility to Plasmodium falciparum infections and severe malarial anemia in kenyan children

Background: Severe malarial anemia (SMA; Hb < 5.0 g/dl) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission regions such as western Kenya. Methods: We investigated the relationship between two novel complement component 5 (C5) missense mutations [rs17216529:C>T, p(Val145Ile) and rs17610:C>T, p(Ser1310Asn)] and longitudinal outcomes of malaria in a cohort of Kenyan children (under 60 mos, n = 1,546). Molecular modeling was used to investigate the impact of the amino acid transitions on the C5 protein structure. Results: Prediction of the wild-type and mutant C5 protein structures did not reveal major changes to the overall structure. However, based on the position of the variants, subtle differences could impact on the stability of C5b. The influence of the C5 genotypes/haplotypes on the number of malaria and SMA episodes over 36 months was determined by Poisson regression modeling. Genotypic analyses revealed that inheritance of the homozygous mutant (TT) for rs17216529:C>T enhanced the risk for both malaria (incidence rate ratio, IRR = 1.144, 95%CI: 1.059–1.236, p = 0.001) and SMA (IRR = 1.627, 95%CI: 1.201–2.204, p = 0.002). In the haplotypic model, carriers of TC had increased risk of malaria (IRR = 1.068, 95%CI: 1.017–1.122, p = 0.009), while carriers of both wild-type alleles (CC) were protected against SMA (IRR = 0.679, 95%CI: 0.542–0.850, p = 0.001). Conclusion: Collectively, these findings show that the selected C5 missense mutations influence the longitudinal risk of malaria and SMA in immune-naïve children exposed to holoendemic P. falciparum transmission through a mechanism that remains to be defined.

60 APPLIED LIFE SCIENCES↗

The HHV-6B U20 glycoprotein binds ULBP1, masking it from recognition by NKG2D and interfering with natural killer cell activation

Human Herpesvirus 6B (HHV-6B) impedes host immune responses by downregulating class I MHC molecules (MHC-I), hindering antigen presentation to CD8+ T cells. Downregulation of MHC-I disengages inhibitory receptors on natural killer (NK) cells, resulting in activation and killing of the target cell if NK cell activating receptors such as NKG2D have engaged stress ligands upregulated on the target cells. Previous work has shown that HHV-6B downregulates three MHC-like stress ligands MICB, ULBP1, and ULBP3, which are recognized by NKG2D. The U20 glycoprotein of the related virus HHV-6A has been implicated in the downregulation of ULBP1, but the precise mechanism remains undetermined. We set out to investigate the role of HHV-6B U20 in modulating NK cell activity. We used HHV-6B U20 expressed as a recombinant protein or transduced into target cells, as well as HHV-6B infection, to investigate binding interactions with NK cell ligands and receptors and to assess effects on NK cell activation. Small-angle X-ray scattering was used to align molecular models derived from machine-learning approaches. We demonstrate that U20 binds directly to ULBP1 with sub-micromolar affinity. Transduction of U20 decreases NKG2D binding to ULBP1 at the cell surface but does not decrease ULBP1 protein levels, either at the cell surface or in toto. HHV-6B infection and soluble U20 have the same effect. Transduction of U20 blocks NK cell activation in response to cell-surface ULBP1. Structural modeling of the U20 – ULBP1 complex indicates some similarities to the m152-RAE1γ complex.

60 APPLIED LIFE SCIENCES↗

Cryo-EM structure of the diapause chaperone artemin

The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in Artemia cysts during diapause. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 Å resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage but in a different configuration than previously hypothesized with molecular modeling. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and Interactional Analysis of the Flavonoid Pathway Proteins: Chalcone Synthase, Chalcone Isomerase and Chalcone Isomerase-like Protein

Chalcone synthase (CHS) and chalcone isomerase (CHI) catalyze the first two committed steps of the flavonoid pathway that plays a pivotal role in the growth and reproduction of land plants, including UV protection, pigmentation, symbiotic nitrogen fixation, and pathogen resistance. Based on the obtained X-ray crystal structures of CHS, CHI, and chalcone isomerase-like protein (CHIL) from the same monocotyledon, Panicum virgatum, along with the results of the steady-state kinetics, spectroscopic/thermodynamic analyses, intermolecular interactions, and their effect on each catalytic step are proposed. In addition, PvCHI’s unique activity for both naringenin chalcone and isoliquiritigenin was analyzed, and the observed hierarchical activity for those type-I and -II substrates was explained with the intrinsic characteristics of the enzyme and two substrates. The structure of PvCHS complexed with naringenin supports uncompetitive inhibition. PvCHS displays intrinsic catalytic promiscuity, evident from the formation of p-coumaroyltriacetic acid lactone (CTAL) in addition to naringenin chalcone. In the presence of PvCHIL, conversion of p-coumaroyl-CoA to naringenin through PvCHS and PvCHI displayed ~400-fold increased Vmax with reduced formation of CTAL by 70%. Supporting this model, molecular docking, ITC (Isothermal Titration Calorimetry), and FRET (Fluorescence Resonance Energy Transfer) indicated that both PvCHI and PvCHIL interact with PvCHS in a non-competitive manner, indicating the plausible allosteric effect of naringenin on CHS. Significantly, the presence of naringenin increased the affinity between PvCHS and PvCHIL, whereas naringenin chalcone decreased the affinity, indicating a plausible feedback mechanism to minimize spontaneous incorrect stereoisomers. These are the first findings from a three-body system from the same species, indicating the importance of the macromolecular assembly of CHS-CHI-CHIL in determining the amount and type of flavonoids produced in plant cells.

59 BASIC BIOLOGICAL SCIENCES↗