Enzymatic Dissociation of DNA-Histone Condensates in an Electrophoretic Setting: Modulating DNA Patterning and Hydrogel Viscoelasticity

Development of an energy-driven self-assembly process is a matter of interest for understanding and mimicking diverse ranges of biological and environmental patterns in a synthetic system. In this article, first we demonstrate transient and temporally controlled self-assembly of a DNA-histone condensate where trypsin (already present in the system) hydrolyzes histone, resulting in disassembly. Upon performing this dynamic self-assembly process in a gel matrix under an electric field, we observe diverse kinds of DNA patterning across the gel matrix depending on the amount of trypsin, incubation time of the reaction mixture, and gel porosity. Notably, here, the micrometer-sized DNA-histone condensate does not move through the gel and only free DNA can pass; therefore, transport and accumulation of DNA at different zones depend on the release rate of DNA by trypsin. Furthermore, we show that the viscoelasticity of the native gel increases in the presence of DNA and a pattern over gel viscoelasticity at different zones can be achieved by tuning the amount of enzyme, i.e., the dissociation rate of the DNA-histone condensate. We believe enabling spatiotemporally controlled DNA patterning by applying an electric field will be potentially important in designing different kinds of spatiotemporally distinct dynamic materials.

Inhibitory effect of nucleotides on acetylcholine esterase activity and its microflow-based actuation in blood plasma

The inhibitory effect of nucleotides on the catalytic activity of acetylcholine esterase (AChE) was rationalized and similar inhibition trend was observed when analyzing the macroscopic fluid flow generated by surface...

Macromolecular Crowding Effect on the Activity of Liposome-Bound Alkaline Phosphatase: A Paradoxical Inhibitory Action

The cytoplasm of a cell is extremely crowded, with 20-30% being large biomolecules. This crowding enforces a significant amount of the physical and chemical barrier around biomolecules, so understanding any biomolecular event within the cellular system is challenging. Unsurprisingly, enzymes show a diverse kind of catalytic behavior inside a crowded environment and thus have remained an area of active interest in the last few decades. The situation can become even more complex and exciting in the case of understanding the behavior of a membrane-bound enzyme (almost 25-30% of enzymes are membrane-bound) in such a crowded environment that until now has remained unexplored. Herein, we have particularly investigated how a membrane-bound enzyme (using liposome-bound alkaline phosphatase) can behave in a crowded environment comprising polymer molecule-like poly(ethylene glycol) (PEG) of different weights (PEG400, PEG4000, and PEG9000) and Ficoll 400. We have compared the activity using a polymer microbead conjugated enzyme and have found that liposome-bound alkaline phosphatase had much higher activity in crowded environments, showing the importance and superiority of soft-deformable particles (i.e., vesicles) over hard spheres in macro-molecularly crowded media. Interstingly, we have found a paradoxical behavior of inhibitors in terms of both their extent and pathway of inhibitory action. For instance, phosphates, known as competitive inhibitors in buffer, behave as uncompetitive inhibitors in liposome-bound enzymes in crowded media with an ∼5-fold less inhibitory effect, whereas phenyl alanine (an uncompetitive inhibitor in buffer) did not show any inhibitory potential when the enzyme was membrane-bound and in crowded media containing PEG9000 (30 wt %). Overall, this demonstration elucidates aspects of membrane-bound enzymes in crowded media in terms of both catalytic behavior and inhibitory actions and can lead to further studies of the understanding of enzymatic behavior in such complex crowded environments having a dampening effect in regular diffusive transport.

Intelligent writable material based on a supramolecular self-assembly gel

A simple dual acylhydrazone-functionalized gelator (G1) has been designed and synthesized, and it was found to form a supramolecular organogel (G1-gel) in a mixed solvent of DMF-H2O. The gelator solution shows brilliant blue light upon mixing with Mg2+; this blue light can be erased by saliva or CO32-. Owing to this characteristic, a smart erasable writable material was prepared.

Superior Proton-Transfer Catalytic Promiscuity of Cytochrome c in Self-Organized Media

Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid-base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6-7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.