Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor
Abstract not provided
Olson, Linda J.↗
SEARCH · Engineering Papers
Results for “molecular modelling”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Au 3 -to-Ag 3 coordinate-covalent bonding and other supramolecular interactions with covalent bonding strength
An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(m-Pz-(i-C 3 H7) 2 )] 3 ∙[Ag(m-Tz-(n-C 3 F 7 ) 2 )] 3 (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction – representing the 1st crystallographically-verified M 3 @M' 3 stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M–M' (Au / Ag), metal–π, π–π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol -1 between the two trimer moieties – a large value for intermolecular interactions between adjacent d 10 centres (nearly doubling the value for a recently claimed Au(I) / Cu(I) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) – which becomes 87 kcal mol -1 with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked M 3 @M' 3 product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M' frontier molecular orbitals in such polar-covalent M–M' bonds in this family of molecules. The Au / Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H 3 N: → Ag in [Ag(NH 3 ) 2 ] + , as demonstrated herein quantitatively. Solidstate and molecular modeling illustrate electron flow from the p-basic gold trimer to the p-acidic silver trimer with augmented contributions from ligand-to-ligand’ (LL'CT) and metal-to-ligand (MLCT) charge transfer.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Synthesis and exceptional operational durability of polyaniline-inspired conductive ladder polymers
Ladder-type structures can impart exceptional stability to polymeric electronic materials. This article introduces a new class of conductive polymers featuring a fully ladder-type backbone. A judicious molecular design strategy enables the synthesis of a low-defect ladder polymer, which can be efficiently oxidized and acid-doped to achieve its conductive state. The structural elucidation of this polymer and the characterization of its open-shell nature are facilitated with the assistance of studies on small molecular models. An autonomous robotic system is used to optimize the conductivity of the polymer thin film, achieving over 7 mS cm −1 . Impressively, this polymer demonstrates unparalleled stability in strong acid and under harsh UV-irradiation, significantly surpassing commercial benchmarks like PEDOT:PSS and polyaniline. Moreover, it displays superior durability across numerous redox cycles as the active material in an electrochromic device and as the pseudocapacitive material in a supercapacitor device. This work provides structural design guidance for durable conductive polymers for long-term device operation.
36 MATERIALS SCIENCE↗
Ambient mechanosynthesis of flexible two-dimensional covalent organic frameworks
We present the first ambient mechanosynthesis of 16 flexible covalent organic frameworks (COFs) within an hour. Notably, one representative COF exhibited a high iodine uptake capacity of ∼4.3 g g −1 from aqueous solutions and 5.97 g g −1 from vapor. Flexible two-dimensional covalent organic frameworks (2D COFs) constructed from nonplanar building blocks represent an emerging paradigm in COF design. Nevertheless, the prevailing solvothermal synthesis suffers from low time efficiency, environmental unfriendliness, and cumbersome protocols. Here, we address these challenges by developing the first ambient mechanosynthesis of a diverse library of flexible 2D COFs. Sixteen distinct triazine-cored Schiff-base COFs, including five as-yet-unreported ones, were rapidly synthesized via ball milling using 2,4,6-tris(4-aminophenoxy)-1,3,5-triazine (TPT-NH 2 ) and 2,4,6-tris(4-formylphenoxy)-1,3,5-triazine (TPT-CHO) as building blocks. Notably, the representative COF, MC-flexible-COF-1, was synthesized in as little as one hour under mechanosynthesis conditions, whereas it remained unattainable via the traditional solvothermal method, despite prolonged heating and extensive solvent screening. The highly dynamic nature of the imine linkage was unequivocally demonstrated through mechanochemical “scrambling” experiments using molecular model compounds. Furthermore, MC-flexible-COF-1 exhibited a high iodine uptake capacity of ∼4.30 g g −1 from aqueous solutions and 5.97 g g −1 from the vapor phase. This work underscores the immense potential of mechanochemistry as a powerful and sustainable tool for the rapid synthesis of advanced 2D COFs, including those inaccessible via conventional solution-based methods.
Nailwal, Yogendra↗
Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions
This article reviews recent molecular simulation studies of "collective" properties of aqueous electrolyte solutions, specifically free energies and activity coefficients, solubilities, nucleation rates of crystals, and transport coefficients. These are important fundamental properties for biology and geoscience, but also relevant for many technological applications. Their determination from molecular-scale calculations requires large systems and long sampling times, as well as specialized sampling algorithms. As a result, such properties have not typically been taken into account during optimization of force field parameters; thus, they provide stringent tests for the transferability and range of applicability of proposed molecular models. There has been significant progress on simulation algorithms to enable the determination of these properties with good statistical uncertainties. Comparisons of simulation results to experimental data reveal deficiencies shared by many commonly used models. Moreover, there appear to exist specific tradeoffs within existing modeling frameworks, so that good prediction of some properties is linked to poor prediction for specific other properties. For example, non-polarizable models that utilize full charges on the ions generally fail to predict accurately both activity coefficients and solubilities; the concentration dependence of viscosity and diffusivity for these models is also incorrect. Scaled-charge models improve the dynamic properties and could also perform well for solubilities, but fail in the prediction of nucleation rates. Even models that do well at room temperature for some properties generally fail to capture their experimentally observed temperature dependence. Finally, the main conclusion from the present review is that qualitatively new physics will need to be incorporated in future models of electrolyte solutions to allow description of collective properties for broad ranges of concentrations, temperatures, and solvent conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Evaluation of two-particle properties within finite-temperature self-consistent one-particle Green’s function methods: Theory and application to GW and GF2
One-particle Green’s function methods can model molecular and solid spectra at zero or non-zero temperatures. One-particle Green’s functions directly provide electronic energies and one-particle properties, such as dipole moment. However, the evaluation of two-particle properties, such as $\langle$S 2 $\rangle$ and $\langle$N 2 $\rangle$, can be challenging because they require a solution of the computationally expensive Bethe–Salpeter equation to find two-particle Green’s functions. We demonstrate that the solution of the Bethe–Salpeter equation can be completely avoided. Applying the thermodynamic Hellmann–Feynman theorem to self-consistent one-particle Green’s function methods, we derive expressions for two-particle density matrices in a general case and provide explicit expressions for GF2 and GW methods. Such density matrices can be decomposed into an antisymmetrized product of correlated one-electron density matrices and the two-particle electronic cumulant of the density matrix. Cumulant expressions reveal a deviation from ensemble representability for GW, explaining its known deficiencies. We analyze the temperature dependence of $\langle$S 2 $\rangle$ and $\langle$N 2 $\rangle$ for a set of small closed-shell systems. Interestingly, both GF2 and GW show a non-zero spin contamination and a non-zero fluctuation of the number of particles for closed-shell systems at the zero-temperature limit.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Experimental and theoretical examination of shock-compressed copper through the fcc to bcc to melt phase transitions
Recent studies show a face-centered cubic (fcc) to body-centered cubic (bcc) transformation along the shock Hugoniot for several metals (i.e., Cu, Au, and Ag). Here, we combine laser-shock compression of Cu foils on nanosecond timescales with in situ x-ray diffraction (XRD) to examine the microstructural changes with stress. We study the fcc phase and the phase transition from fcc to bcc (pressures greater than 180 GPa). Textural analysis of the azimuthal intensities from the XRD images is consistent with transformation into the bcc phase through the Pitsch-distortion mechanism. We use embedded atom model molecular dynamics simulations to determine the stability of the bcc phase in pressure–temperature space. Finally, our results indicate that the bcc phase is stabilized only at high temperatures and remains stable at pressures greater than 500 GPa.
36 MATERIALS SCIENCE↗
Accelerating the density-functional tight-binding method using graphical processing units
Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Herein two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1–6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1–2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The contribution of Compton ionization to ultrafast x-ray scattering
We investigate the role of Compton ionization in ultrafast non-resonant x-ray scattering using a molecular model system, which includes the ionization continuum via an orthonormalized plane wave ansatz. Elastic and inelastic components of the scattering signal, as well as coherent-mixed scattering that arises from electron dynamics, are calculated. By virtue of a near-quantitative distinction between scattering related to electronic transitions into bound and continuum states, we demonstrate how Compton ionization contributes to the coherent-mixed component. Analogous to inelastic scattering, the contribution to the coherent-mixed signal is significant and particularly manifests at intermediate and high-momentum transfers. Strikingly, for molecules with inversion symmetry, the exclusion of bound or continuum transitions may lead to the prediction of spurious coherent-mixed signals. We conclude that qualitative and quantitative accuracies of predicted scattering signals on detectors without energy resolution require that elements of the two-electron density operator are used. This approach inherently accounts for all accessible electronic transitions, including ionization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗