Mechanistic analysis of carbon–carbon bond formation by deoxypodophyllotoxin synthase

Deoxypodophyllotoxin contains a core of four fused rings (A to D) with three consecutive chiral centers, the last being created by the attachment of a peripheral trimethoxyphenyl ring (E) to ring C. Previous studies have suggested that the iron(II)- and 2-oxoglutarate–dependent (Fe/2OG) oxygenase, deoxypodophyllotoxin synthase (DPS), catalyzes the oxidative coupling of ring B and ring E to form ring C and complete the tetracyclic core. Despite recent efforts to deploy DPS in the preparation of deoxypodophyllotoxin analogs, the mechanism underlying the regio- and stereoselectivity of this cyclization event has not been elucidated. Herein, we report 1) two structures of DPS in complex with 2OG and (±)-yatein, 2) in vitro analysis of enzymatic reactivity with substrate analogs, and 3) model reactions addressing DPS’s catalytic mechanism. The results disfavor a prior proposal of on-pathway benzylic hydroxylation. Rather, the DPS-catalyzed cyclization likely proceeds by hydrogen atom abstraction from C7', oxidation of the benzylic radical to a carbocation, Friedel–Crafts-like ring closure, and rearomatization of ring B by C6 deprotonation. This mechanism adds to the known pathways for transformation of the carbon-centered radical in Fe/2OG enzymes and suggests what types of substrate modification are likely tolerable in DPS-catalyzed production of deoxypodophyllotoxin analogs.

A tug of war between filament treadmilling and myosin induced contractility generates actin cortex

In most eukaryotic cells, actin filaments assemble into a shell-like actin cortex under the plasma membrane, controlling cellular morphology, mechanics, and signaling. The actin cortex is highly polymorphic, adopting diverse forms such as the ring-like structures found in podosomes, axonal rings, and immune synapses. The biophysical principles that underlie the formation of actin cortices and their structural plasticity remain unknown. Using a molecular simulation platform, called MEDYAN, we discovered that varying the filament treadmilling rate induces a finite size phase transition in actomyosin network structure. We found that actomyosin networks condense into clusters at low treadmilling rates but form ring-like or cortex-like structures at high treadmilling rates. This mechanism is supported by our corroborating experiments on live T cells, which show that disrupting filament treadmilling induces centripetal collapse of pre-existing actin rings and the formation of clusters. Our analyses suggest that the actin cortex is a preferred state of low mechanical energy, which is, importantly, only reachable at high treadmilling rates.

A tug of war between filament treadmilling and myosin induced contractility generates actin cortex

In most eukaryotic cells, actin filaments assemble into a shell-like actin cortex under the plasma membrane, controlling cellular morphology, mechanics, and signaling. The actin cortex is highly polymorphic, adopting diverse forms such as the ring-like structures found in podosomes, axonal rings, and immune synapses. The biophysical principles that underlie the formation of actin cortices and their structural plasticity remain unknown. Using a molecular simulation platform, called MEDYAN, we discovered that varying the filament treadmilling rate induces a finite size phase transition in actomyosin network structure. We found that actomyosin networks condense into clusters at low treadmilling rates but form ring-like or cortex-like structures at high treadmilling rates. This mechanism is supported by our corroborating experiments on live T cells, which show that disrupting filament treadmilling induces centripetal collapse of pre-existing actin rings and the formation of clusters. Our analyses suggest that the actin cortex is a preferred state of low mechanical energy, which is, importantly, only reachable at high treadmilling rates.

The structure of carbon nanotubes in a polymer matrix

We carried out an analytical structural analysis of interfacial effects and differences in the reinforcing ability of carbon nanotubes for polydicyclopentadiene/carbon nanotube nanocomposites with elastomeric and glassy matrices. In general, it showed that the reinforcing (strengthening) element of the structure of polymer nanocomposites is a combination of the nanofiller and interfacial regions. In the polymer matrix of the nanocomposite, carbon nanotubes form ring-like structures. Their radius depends heavily on the volume content of the nanofiller. Therefore, the structural reinforcing element of polymer/carbon nanotube nanocomposites can be considered as ring-like formations of carbon nanotubes coated with an interfacial layer. Their structure and properties differ from the characteristics of the bulk polymer matrix.According to this definition, the effective radius of the ring-like formations increases by the thickness of the interfacial layer. In turn, the level of interfacial adhesion between the polymer matrix and the nanofiller is uniquely determined by the radius of the specified carbon nanotube formations. For the considered nanocomposites, the elastomeric matrix has a higher degree of reinforcement compared to the glassy matrix, due to the thicker interfacial layer. It was shown that the ring-like nanotube formations could be successfully modelled as a structural analogue of macromolecular coils of branched polymers. This makes it possible to assess the effective (true) level of anisotropy of this nanofiller in the polymer matrixof the nanocomposite. When the nanofiller content is constant, this level, characterised by the aspect ratio of the nanotubes, uniquely determines the degree of reinforcement of the nanocomposites

Concise Total Synthesis of (+)-Aphanorphine

A concise total synthesis of (+)-aphanorphine is described. The key features of the strategy include a Pd-catalyzed intermolecular trimethylenemethane [3+2]-cycloaddition to form ring C and a Co-catalyzed radical cyclization through a hydrogen-atom transfer to close ring B. The synthesis was completed in six steps.

The subnormal structure of classical-like groups over commutative rings

Let 𝑛 be an integer greater than or equal to 3, and let (R,\Delta) be a Hermitian form ring, where 𝑅 is commutative. We prove that if 𝐻 is a subgroup of the odd-dimensional unitary group \operatorname{U}_{2n+1}(R,\Delta) normalised by a relative elementary subgroup \operatorname{EU}_{2n+1}((R,\Delta),(I,\Omega)), then there is an odd form ideal (J,\Sigma) such that\operatorname{EU}_{2n+1}((R,\Delta),(JI^{k},\Omega_{\mathrm{min}}^{JI^{k}}\dotplus\Sigma\circ I^{k}))\leq H\leq\operatorname{CU}_{2n+1}((R,\Delta),(J,\Sigma)),where k=12 if n=3 respectively k=10 if n\geq 4. As a consequence of this result, we obtain a sandwich theorem for subnormal subgroups of odd-dimensional unitary groups.

An Alternating Quark Sequence Subnucleonic Structure of Stable Light Nuclei H-1 Through C-13

The proposed structures of stable nuclei of H-1 through C-13 incorporate an alternating up and down quark sequence (AQS) of equally spaced quarks around regular geometries. AQS nuclear models represent quark positions in the same way molecular ball and stick models represent the relative positions of atoms. In AQS, the ball identifies the center of quark mass and the stick length is constant and equal to the most recent radius of the proton (0.8414 fm). AQS radius predictions use current quark masses, and predictions for H-1 to C-13 demonstrate 99.3% average agreement (SD 4%) and statistical correlation of ρ = 0.96, p<0.001, with accepted RMS charge radii. These results compare favorably to a close-packed nucleons model and a spherical nucleus model. A set of AQS parameters is included. Light nuclei tend to form ring structures corresponding to regular polyhedra, the smallest of which is the dodecagon structure of helium-4. Opposite quarks link nucleons to maintain a continuous sequence of alternating equally spaced quarks. Quark sequences may overlap so that protons overlap with neutrons. The more regular polyhedron structures of light nuclei yield better AQS radius predictions, whereas larger nuclei tend to be less regular and are thus less predictable (with the exception of the double overlapping octadecagon structure for the 36 quarks of C-12). The relative certainty in the accepted radius of helium-4, and its geometric relationship to the proton radius, allow a geometric solution to the “proton puzzle” yielding an AQS prediction for the proton radius of 0.8673±0.0014 fm.

An Alternating Quark Sequence Subnucleonic Structure of Stable Light Nuclei H-1 Through Li-7

The proposed structures of stable nuclei of H-1 through Li-7 incorporate an alternating up and down quark sequence (AQS) of equally spaced quarks around regular geometries. AQS nuclear models represent quark positions in the same way molecular ball and stick models represent the relative positions of atoms. In AQS, the ball identifies the center of quark mass and the stick length is constant and equal to the most recent radius of the proton (0.8414 fm). AQS radius predictions use accepted quark masses where necessary, and predictions demonstrate 99.3% average agreement (SD 4%) and statistical correlation of ρ = 0.96, p<0.001, with accepted RMS charge radii. These results compare favorably to a close-packed nucleons model and a spherical nucleus model. A set of AQS parameters is included. Light nuclei tend to form ring structures corresponding to regular polyhedra, the smallest of which is the dodecagon structure of helium-4. Opposite quarks link nucleons to maintain a continuous sequence of alternating equally spaced quarks. Quark sequences may overlap so that protons overlap with neutrons. The more regular polyhedron structures of light nuclei yield better AQS radius predictions, whereas larger nuclei tend to be less regular and are thus less predictable (with the exception of the double overlapping octadecagon structure for the 36 quarks of C-12). The relative certainty in the accepted radius of helium-4, and its geometric relationship to the proton radius, allow a geometric solution to the “proton puzzle” yielding an AQS prediction for the proton radius of 0.8673±0.0014 fm.

Synthesis and Molecular Docking Studies of Novel Triazole Derivatives as Antioxidant Agents

A series of 1,2,4-triazole and 1,2,4- thiadiazole derivatives were prepared starting from ethyl 4-(3-methyl-5-oxo-1,5-dihydro-4H-1,2,4-triazol-4-yl)benzoate. Firstly, both ethyl ester groups were simultaneously transformed into hydrazide groups, then into thiosemicarbazide groups using both microwave- assisted and conventional methods. The latter products were interacted with NaOH and H2SO4 to form ring assemblies containing two 1,2,4-triazole and 1,3,4-thiadiazole fragments, respectively. Antioxidant activities of the synthesized compounds were determined with CUPRAC, ABTS, and DPPH assays. Most of the compounds showed significant antioxidant activity and especially, compound 3 exhibited very good SC50 value for DPPH method and compound 3, 4a, 5a exhibited very high scavenging activity to the ABTS method. In addition, the in silico analysis was carried out with the synthesized derivatives to understand the mode of interaction with superoxide dismutase (SOD) and human tyrosine kinase using docking protocols in order to find out the most active antioxidant drug having high inhibitory activity in cancer.

Structure and conformational cycle of a bacteriophage-encoded chaperonin

Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionary distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionary more ancient chaperonin prior to acquisition of the encapsulation mechanism.