H2A.Z deposition by SWR1C involves multiple ATP-dependent steps

The histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial, priming step that occurs after ATP addition that likely involves transient DNA unwrapping from the nucleosome. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, the rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate the timely and accurate deposition of H2A.Z at key genomic locations.

Bio-inspired Chemical Space Exploration of Terpenoids

Many computational methods are used to expand the open-ended border of chemical spaces. Natural products and their derivatives are an important source for drug discovery, and some algorithms are devoted to rapidly generating pseudo-natural products, while their accessibility and chemical interpretation were often ignored or underestimated, thus hampering experimental synthesis in practice. Herein, a bio-inspired strategy (named TeroGen) is proposed, in which the cyclization and decoration stage of terpenoid biosynthesis were mimicked by meta-dynamics simulations and deep learning models respectively, to explore their chemical space. In the protocol of TeroGen, the synthetic accessibility is validated by reaction energetics (reaction barrier and reaction heat) based on the GFN2-xTB methods. Chemical interpretation is an intrinsic feature as the reaction pathway is bioinspired and triggered by the RMSD-PP method in conjunction with an encoder-decoder architecture. This is quite distinct from conventional library/fragment-based or rule-based strategies, by using TeroGen, new reaction routes are feasibly explored to increase the structural diversity. For example, only a rather limited number of sesterterpenoids in our training set is included in this work, but our TeroGen would predict more than 30000 sesterterpenoids and map out the reaction network with super efficiency, ten times as many as the known sesterterpenoids (less than 2500). In sum, TeroGen not only greatly expands the chemical space of terpenoids but also provides various plausible biosynthetic pathways, which are crucial clues for heterologous biosynthesis, bio-mimic and chemical synthesis of complicated terpenoids.

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5′-phosphate–dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid–base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.

A Bond Bundle Case Study of Diels-Alder Catalysis Using Oriented Electric Fields

Bond bundles are chemical bonding regions, analogous to Bader atoms, uniquely defined according to the topology of the gradient bundle condensed charge density, itself obtained by a process of infinitesimal partitioning of the three-dimensional charge density into differential zero-flux surface bounded regions. Here we use bond bundle analysis to investigate the response of the charge density to an oriented electric field in general, and the catalytic effect of such a field on Diels-Alder reactions in particular, which in this case is found to catalyze by allowing the transition state valance bond bundle configuration to be achieved earlier along the reaction pathway. Using precise numerical values, we arrive at the conclusion that chemical reactions and electric field catalysis can be understood in terms of intra-atomic charge density redistribution, i.e., that charge shifts within more so than between atoms account for the making and breaking of bonds.

Water Formation Reaction under Interfacial Confinement: Al0.25Si0.75O2 on O-Ru(0001)

Confined nanosized spaces at the interface between a metal and a seemingly inert material, such as a silicate, have recently been shown to influence the chemistry at the metal surface. In prior work, we observed that a bilayer (BL) silica on Ru(0001) can change the reaction pathway of the water formation reaction (WFR) near room temperature when compared to the bare metal. In this work, we looked at the effect of doping the silicate with Al, resulting in a stoichiometry of Al0.25Si0.75O2. We investigated the kinetics of WFR at elevated H2 pressures and various temperatures under interfacial confinement using ambient pressure X-ray photoelectron spectroscopy. The apparent activation energy was lower than that on bare Ru(0001) but higher than that on the BL-silica/Ru(0001). The apparent reaction order with respect to H2 was also determined. The increased residence time of water at the surface, resulting from the presence of the BL-aluminosilicate (and its subsequent electrostatic stabilization), favors the so-called disproportionation reaction pathway (*H2O + *O ↔ 2 *OH), but with a higher energy barrier than for pure BL-silica.

New insights in polydopamine formation via surface adsorption

Polydopamine is a biomimetic self-adherent polymer, which can be easily deposited on a wide variety of materials. Despite the rapidly increasing interest in polydopamine-based coatings, the polymerization mechanism and the key intermediate species formed during the deposition process are still controversial. Herein, we report a systematic investigation of polydopamine formation on halloysite nanotubes; the negative charge and high surface area of halloysite nanotubes favour the capture of intermediates that are involved in polydopamine formation and decelerate the kinetics of the process, to unravel the various polymerization steps. Data from X-ray photoelectron and solid-state nuclear magnetic resonance spectroscopies demonstrate that in the initial stage of polydopamine deposition, oxidative coupling reaction of the dopaminechrome molecules is the main reaction pathway that leads to formation of polycatecholamine oligomers as an intermediate and the post cyclization of the linear oligomers occurs subsequently. Furthermore, Tris molecules are incorporated into the initially formed oligomers.

Sugar decorated star-shaped (co)polymers with resveratrol-based core – physicochemical and biological properties

Star-shaped glycopolymers due to the attractive combination of the physicochemical, morphological, self-assembly properties along with biological activity have gained increased attention as innovative agents in novel cancer therapies. Unfortunately, the production of these highly desirable biomaterials remains a challenge in modern macromolecular chemistry. The main reason for that is the low polymerizability of ionic glycomonomers originated from their steric congestion and the occurrence of ionic interactions that generally negatively influence the polymerization progress and hinder controllable reaction pathway. In this work, the new ionic sugar monomer was (co)polymerized for the first time via Activator Generated by Electron Transfer Atom Transfer Radical Polymerization (AGET ATRP) using a three-arm resveratrol-based core to obtain star-like (co)polymers. The obtained products were examined in terms of their physicochemical properties and morphology. Aside from the synthesis of these new glycopolymers, also a thorough description of their thermal properties, ability to self-assembly, the formation of stable superstructures was studied in detail. It was found that examined (co)polymers did not show any heterogeneities and phase separation, while their variation of glass transition temperature (Tg) was strictly related to the change in the number of glycomonomer. Also, the stability and shapes of formed superstructures strictly depend on their composition and topology. Finally, we have shown that synthesized carbohydrate-based polymers revealed high antiproliferative activity against several cancer cell lines (i.e., breast, colon, glioma, and lung cancer). The cytotoxic activity was particularly observed for star-shaped polymers that were systematically enhanced with the growing concentration of amine moieties and molecular weight. The results presented herein suggest that synthesized star-shaped glyco(co)polymers are promising as drug or gene carriers in anticancer therapies or anti-tumor agents, depending on their cytotoxicity. Graphical abstract