Structural studies of antitumor compounds that target the RING domain of MDM2
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Terrell, James Ross↗
SEARCH · Engineering Papers
Results for “structural rings”
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A DNA packaging motor inchworms along one strand allowing it to adapt to alternative double-helical structures
Abstract Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism. Here, we investigate the operation of ring motors that transport ordered, helical substrates, such as the bacteriophage ϕ29 dsDNA packaging motor. This pentameric motor alternates between an ATP loading dwell and a hydrolysis burst wherein it packages one turn of DNA in four steps. When challenged with DNA-RNA hybrids and dsRNA, the motor matches its burst to the shorter helical pitches, keeping three power strokes invariant while shortening the fourth. Intermittently, the motor loses grip on the RNA-containing substrates, indicating that it makes optimal load-bearing contacts with dsDNA. To rationalize these observations, we propose a helical inchworm translocation mechanism in which, during each cycle, the motor increasingly adopts a lock-washer structure during the ATP loading dwell and successively regains its planar form with each power stroke during the burst.
59 BASIC BIOLOGICAL SCIENCES↗
Consequences of Pore Polarity and Solvent Structure on Epoxide Ring-Opening in Lewis and Brønsted Acid Zeolites
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhanced chloroplast FtsZ-ring constriction by the ARC6–ARC3 module in Arabidopsis
Chloroplast division, a process tightly linked to the energy demands of plants, is initiated by the formation of the stromal filamenting temperature-sensitive Z (FtsZ) ring. The Z ring is highly dynamic, and its constriction provides the essential force for chloroplast division. However, the regulatory mechanisms governing Z-ring dynamics and constriction remain poorly understood. Here, we report that the chloroplast inner envelope membrane (IEM) protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS6 (ARC6) interacts with the chloroplast stromal protein ARC3, and this interaction is negatively regulated by the conserved J-like domain of ARC6. ARC3 is found both distributed throughout the stroma and localized to a ring-like structure at the chloroplast division site. We demonstrate that ARC6 recruits ARC3 to the division site to form a ring-like structure, likely through direct interaction. This ARC6–ARC3 interaction enables ARC3 to bind FtsZs. Furthermore, we show that the ARC6–ARC3 complex significantly promotes the dynamics of chloroplast Z rings reconstituted in a heterologous system. Finally, the constriction of these reconstituted Z rings is markedly enhanced by ARC6–ARC3. Our findings reveal a regulatory mechanism that governs Z-ring dynamics and constriction, shedding light on the molecular mechanisms underlying chloroplast division.
Science & Technology - Other Topics↗
Bond Length Alternation and Internal Dynamics in Model Aromatic Substituents of Lignin
In this report broadband microwave spectra were recorded over the 2-18 GHz frequency range for a series of four model aromatic components of lignin; namely, guaiacol (ortho-methoxy phenol, G), syringol (2,6-dimethoxy phenol, S), 4-methyl guaiacol (MG), and 4-vinyl guaiacol (VG), under jet-cooled conditions in the gas phase. Using a combination of 13 C isotopic data and electronic structure calculations, distortions of the phenyl ring by the substituents on the ring are identified. In all four molecules, the r C(1)-C(6) bond between the two substituted C-atoms lengthens, leading to clear bond alternation that reflects an increase in the phenyl ring resonance structure with double bonds at r C(1)-C(2) , r C(3)-C(4) and r C(5)-C(6) . Syringol, with its symmetric methoxy substituents, possesses a microwave spectrum with tunneling doublets in the a-type transitions associated with H-atom tunneling. These splittings were fit to determine a barrier to hindered rotation of the OH group of 1975 cm -1 , a value nearly 50% greater than that in phenol, due to the presence of the intramolecular OH…OCH 3 H-bonds at the two equivalent planar geometries. In 4-methyl guaiacol, methyl rotor splittings are observed and used to confirm and refine an earlier measurement of the three-fold barrier V 3 = 67 cm -1 . Finally, 4-vinyl guaiacol shows transitions due to two conformers differing in the relative orientations of the vinyl and OH groups.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ring Size Effects on the Structures of Sandwich Compounds with a Stoichiometry of C 12 H 12 M (M = Ti–Ni)
Ring size effects on geometries and electronic structures were investigated for the (C n H n )M(C m H m ) (n = 4, 5, or 6; m = 8, 7, or 6; m + n = 12; M = Ti–Ni) systems using density functional theory. The lowest-energy C 12 H 12 M structures for the early transition metals titanium, vanadium, and chromium are the experimentally known singlet (η 5 -C 5 H 5 )Ti(η 7 -C 7 H 7 ), doublet (η 5 -C 5 H 5 )V(η 7 -C 7 H 7 ), and singlet (η 6 -C 6 H 6 ) 2 Cr, respectively. The likewise experimentally known singlet (η 6 -C 6 H 6 ) 2 Ti, doublet (η 6 -C 6 H 6 ) 2 V, and singlet (η 5 -C 5 H 5 )Cr(η 7 -C 7 H 7 ) are the secondlowest- energy structures with only a small energy difference between the two vanadium structures. For the later transition metals, dibenzenemetal complexes are the lowest-energy C 12 H 12 M species with two fully bonded hexahapto benzene rings in the lowest-energy manganese and iron derivatives and one hexahapto and one dihapto benzene ring in the lowest-energy cobalt and nickel derivatives. The lowest-energy (C 5 H 5 )M(C 7 H 7 ) structures for the later transition metals iron, cobalt, and nickel have partially bonded nonplanar C 7 H 7 rings with one or two uncomplexed C=C bonds. The (C 4 H 4 )M(C 8 H 8 ) (M = Ti–Ni) structures with the metal sandwiched between four- and eight-membered rings were found to be much higher in energy than their (C 5 H 5 )M(C 7 H 7 ) and (C 6 H 6 ) 2 M isomers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer
Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.
Biochemistry & Molecular Biology↗
Using Data Science Tools to Reveal and Understand Subtle Relationships of Inhibitor Structure in Frontal Ring-Opening Metathesis Polymerization
The rate of frontal ring-opening metathesis polymerization (FROMP) using the Grubbs generation II catalyst is impacted by both the concentration and choice of monomers and inhibitors, usually organophosphorus derivatives. Herein we report a data-science-driven workflow to evaluate how these factors impact both the rate of FROMP and how long the formulation of the mixture is stable (pot life). Using this workflow, we built a classification model using a single-node decision tree to determine how a simple phosphine structural descriptor (V bur-near ) can bin long versus short pot life. Additionally, we applied a nonlinear kernel ridge regression model to predict how the inhibitor and selection/concentration of comonomers impact the FROMP rate. Furthermore, the analysis provides selection criteria for material network structures that span from highly cross-linked thermosets to non-cross-linked thermoplastics as well as degradable and nondegradable materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Lithium calix[4]arenes: structural studies and use in the ring opening polymerization of cyclic esters
We have structurally characterized a number of lithiated calix[4]arenes, where the bridge in the calix[4]arene is thia (–S–, L S H 4 ), sulfinyl (–SO–, L SO H 4 ), sulfonyl (–SO 2 –, L SO2 H 4 ), dimethyleneoxa (–CH 2 OCH 2 –, L COC H 4 ) or methylene (–CH 2 –, LH 4 ). In the case of L 4S H 4 , interaction with LiO t Bu led to the isolation of the complex [Li 8 (L 4S ) 2 (THF) 4 ]·5THF ( 1 ·5THF), whilst similar interaction of L 4SO H 4 led to the isolation of [Li 6 (L 4SO H) 2 (THF) 2 ]·5(THF) ( 2 ·5THF). Interestingly, the mixed sulfinyl/sulfonyl complexes [Li 8 (calix[4]arene(SO)(SO 2 )(SO 1.68 ) 2 ) 2 (THF) 6 ]·8(THF) ( 3 ·8THF) and [Li 5 Na(L SO/3SO2 H) 2 (THF) 5 ]·7.5(THF) ( 4 ·7.5(THF) have also been characterized. Interaction of LiO t Bu with L SO2 H 4 and L COC H 4 afforded [Li 5 L 4SO2 (OH)(THF) 4 ]·2THF ( 5 ·2THF) and [Li 6 (L COC ) 2 (HO t Bu) 2 ]·0.78THF·1.22hexane ( 6 ·0.78THF·1.22hexane), respectively. In the case of LH 4 , reaction with LiO t Bu in THF afforded a monoclinic polymorph [LH 2 Li 2 (thf)(OH 2 ) 2 ]·3THF ( 7 ·3THF) of a known triclinic form of the complex, whilst reaction of the de-butylated analogue of LH 4 , namely de-BuLH 4 , afforded a polymeric chain structure {[Li 5 (de-BuL)(OH)(NCMe) 3 ]·2MeCN} n ( 8 ·2MeCN). For comparative catalytic studies, the complex [Li 6 (L Pr ) 2 (H 2 O) 2 ]·hexane ( 9 hexane), where L Pr2 H 2 = 1,3-di- n -propyloxycalix[4]areneH 2 , was also prepared. The molecular crystal structures of 1–9 are reported, and their ability to act as catalysts for the ring opening (co-)/polymerization (ROP) of the cyclic esters ε-caprolactone, δ-valerolactone, and rac -lactide has been investigated. In most of the cases, complex 6 outperformed the other systems, allowing for higher conversions and/or greated polymer M n .
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A kinematic excess in the annular gap and gas-depleted cavity in the disc around HD 169142
ABSTRACT We present ALMA band 6 images of the 12CO, 13CO, and C18O J = 2-1 line emissions for the circumstellar disc around HD 169142, at ∼8 au spatial resolution. We resolve a central gas-depleted cavity, along with two independent near-symmetric ring-like structures in line emission: a well-defined inner gas ring [∼25 au] and a second relatively fainter and diffuse outer gas ring [∼65 au]. We identify a localized super-Keplerian feature or vertical flow with a magnitude of ∼75 ms−1 in the 12CO map. This feature has the shape of an arc that spans azimuthally across a position angle range of −60° to 45° and radially in between the B1[26au] and B2[59au] dust rings. Through reconstruction of the gas surface density profile, we find that the magnitude of the background perturbations by the pressure support and self-gravity terms are not significant enough to account for the kinematic excess. If of planetary origin, the relative depletion in the gas-density profile would suggest a 1 MJ planet. In contrast, the central cavity displays relatively smooth kinematics, suggesting either a low-mass companion and/or a binary orbit with a minimal vertical velocity component.
79 ASTRONOMY AND ASTROPHYSICS↗
Thermochemical Data for Furan-based Monomer Candidates for Frontal Ring-Opening Metathesis Polymerization (FROMP)
This dataset includes 471 furan-based monomer candidates for frontal ring-opening metathesis polymerization (FROMP) and relevant thermochemistry as calculated with density functional theory (DFT). The monomer candidates were combinatorically enumerated using Diels-Alder reactions of furan derivatives as dienes and four types of dienophiles (alkenes, alkynes, allenes, and benzynes). Common substituents were enumerated for the dienophile classes, and methyl substitution on the diene was explored. We used the SMILES arbitrary target specification (SMARTS) language to produce monomers and ring-opened structures from diene and dienophile precursor SMILES, and we studied the ring-opening reaction using a homodesmotic equation with ethene. RDKit conformers were initially generated from SMILES, then optimized with GFN2-xTB. The two conformers lowest in energy were then optimized with DFT using the wb97x-D3 functional, def2-TZVP basis set, and def2/J auxiliary basis set. Gibbs free energy corrections were obtained through frequency calculations. Structures with imaginary frequencies below -50 cm^{-1} were excluded from this work, and smaller imaginary modes were flipped to be positive for free energy calculations. Modes below 50 cm^{-1} were treated with the modified rigid rotor approximation, and all thermochemical values were calculated at T=200C. The CSV file contains the monomer SMILES, the free energy of reaction for Diels-Alder addition (G_DA_200), and the enthalpy of the ring-opening reaction (H_RO_200). All energies are given in kcal/mol. An interactive HTML is also included to visualize the monomers in this dataset.
Chua, Lauren↗
Aggregation of solutes in bosonic versus fermionic quantum fluids
Quantum fluid droplets made of helium-3 ( 3 He) or helium-4 ( 4 He) isotopes have long been considered as ideal cryogenic nanolabs, enabling unique ultracold chemistry and spectroscopy applications. The droplets were believed to provide a homogeneous environment in which dopant atoms and molecules could move and react almost as in free space but at temperatures close to absolute zero. Here, we report ultrafast x-ray diffraction experiments on xenon-doped 3 He and 4 He nanodroplets, demonstrating that the unavoidable rotational excitation of isolated droplets leads to highly anisotropic and inhomogeneous interactions between the host matrix and enclosed dopants. Superfluid 4 He droplets are laced with quantum vortices that trap the embedded particles, leading to the formation of filament-shaped clusters. In comparison, dopants in 3 He droplets gather in diffuse, ring-shaped structures along the equator. The shapes of droplets carrying filaments or rings are direct evidence that rotational excitation is the root cause for the inhomogeneous dopant distributions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Vortex bursting and associated twist dynamics on helical vortex tubes and vortex rings
The interaction of opposite-signed twist waves on vortex tubes can lead to vortex bursting, a process where the core expands into a double ring-like structure with strong swirling flows. Previous works have studied vortex bursting on rectilinear vortices by axially perturbing the initial core size to generate the twist waves, and observed largely axisymmetric bursting dynamics. In this work, we numerically study bursting on vortical structures with curved centrelines, analysing the interaction between the centreline dynamics, twist wave generation and propagation, and vortex bursting. We focus on axially perturbed helical vortex tubes with small radius-to-pitch ratios up to$0.0625$, as well as vortex rings with a large radius-to-core size ratio$10$, both at a circulation-based Reynolds number$5000$. The results show that though the initial twist wave propagation speeds are relatively unaffected by the curvature and torsion of the centreline, the bursting process is altered significantly compared with rectilinear vortices. The self-induced rotation of the centreline of the helical tube induces a non-axisymmetric distortion of the bursting structure, which rapidly breaks up the vortex core into small-scale helical structures. A similar destabilization of the bursting structure also occurs on vortex rings. The enstrophy increase and accelerated energy decay associated with bursting are predominantly determined by the twist wave strength, rather than the curvature and torsion of the centreline. Combined, our findings imply that bursting could play an important role in transferring and dissipating energy of vortical structures in wakes, and turbulent flows in general.
Mechanics↗
NEMA-Phase Compliant Traffic Signal Controller Module in SUMO
The controller modules in SUMO use a stage-based control structure. A phase is defined as a stage of all allowed movements at a time instance. However, traffic signal controllers used in North America widely use National Electrical Manufacturers Association (NEMA) phase definition. A NEMA phase is defined by a certain flow movement at an intersection. At one time, more than one NEMA phase could happen together as long as they do not conflict with each other. We can visualize the NEMA phases and timings in Ring-and-Barrier structured NEMA diagrams. For one controller, only one phase from a ring can be activated at a time. Phases from different rings could be activated together as long as they are not from the different sides of a barrier. When a controller is operated in fixed-time control mode, we can model the NEMA phase timing as a corresponding stage-based control timing without any issues. When introducing actuation into the signal control, a Ring-and-Barrier structured traffic signal controller can be more flexible than stage-based controller by allowing different possible phase combinations. We made two efforts in modeling Ring-and-Barrier structured controllers in SUMO. One is to translate a NEMA phases timing into SUMO-readable phases and timings as an additional file for SUMO. This translation worked well for fixed-time control. To model actuated control and coordinated actuated control, we augmented the SUMO source code by adding a Ring-and-Barrier structured controller module. This module could implement traffic signal timing from controllers using NEMA phases. We also augmented TraCI to be able to set new NEMA phase timings during simulations. We examined the Ring-and-Barrier structured traffic signal controller module by both visually observing the simulation animations and the simulation records. The developed control module can model the generalized Ring-and-Barrier structured traffic signal timing that is used in North America. SEE: https://github.com/eclipse/sumo/blob/main/src/microsim/traffic_lights/NEMAController.cpp
Wang, Qichao↗
Saturation of Vortex Rings Ejected from Shock-Accelerated Interfaces
Structures evoking vortex rings can be discerned in shock-accelerated flows ranging from astrophysics to inertial confinement fusion. By constructing an analogy between vortex rings produced in conventional propulsion systems and rings generated by a shock impinging upon a high-aspect-ratio protrusion along a material interface, we extend classical, constant-density vortex-ring theory to compressible multifluid flows. Here, we further demonstrate saturation of such vortex rings as the protrusion aspect ratio is increased, thus explaining morphological differences observed in practice.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NSTX-U Machine Core Vacuum Seals Upgrade Design
The vacuum in the National Spherical Torus Experiment Upgrade (NSTX-U) is in the range of 2.66x10⁻⁶ Pa (2x 10⁻⁸ torr). To enhance vacuum seals and lower gas permeation in the NSTX-U and therefore ensuring operation safety and quality, the machine core vacuum seal design has been upgraded using double elastomeric seals and pumped interspaces (guard channels). In NSTX-U machine core, there are six major vacuum seals, including upper and lower vacuum vessel main flanges, upper and lower bellows flanges, and two in the ceramic isolation ring assembly that are mounted to the upper vacuum vessel main flange. The elastomeric seals are commercially available and customized fluorocarbon (Viton) O-rings. To ensure appropriate O-ring compression ratios for the vacuum seal, the O-ring grooves are customized with appropriate tolerances considering specific situations for each seal. In this upgrade, the vacuum in each interspace is designed to reach 13.33 Pa (0.1 torr), thus the overall pressure difference crossing each double O-ring seal is expected to be reduced by at least three orders of magnitude, and accordingly the overall rates of leakage and permeation will be lowered by three orders of magnitude. The corresponding pump-down times for each seal, at room temperature, are estimated at about 60 s. Additionally, the vacuum pumped interspaces will be able to function as a real-time leak monitor.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Synthesis of Poly(bisisoindigo) Using a Metal-Free Aldol Polymerization for Thin-Film Transistor Applications
Typical syntheses of conjugated polymers rely heavily on organometallic reagents and metal-catalyzed cross-coupling reactions. In this paper, we show that an environmentally benign aldol polymerization can be used to synthesize poly(bisisoindigo), an analog of polyisoindigo with a ring-fused structural repeat unit. Owing to its extended conjugation length, poly(bisisoindigo) absorbs across the UV/vis/NIR spectrum, with an absorption tail that reaches 1000 nm. Due to the four electron-deficient lactam units on each repeat unit, poly(bisoindigo) possesses a low-lying LUMO, which lies at -3.94 eV relative to vacuum. Incorporation of the ring-fused monomer unit also lowered the overall torsional strain in the polymer backbone (relative to polyisoindigo), and the polymer was successfully used in prototype unipolar n-channel organic thin-film transistors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗