Effect of Polymer Network Architecture on Adsorption Kinetics at Liquid–Liquid Interfaces: A Comparison Between Poly(NIPAM-co-AA) Copolymer Microgels and Interpenetrating Network Microgels Galina A. Komarova, Elena Yu. Kozhunova, Rustam A. Gumerov, Igor I. Potemkin, Irina R. Nasimova Gels, 2025 Understanding the adsorption features of polymer microgels with different chemical compositions and structures is crucial in studying the mechanisms of respective emulsion stabilization. Specifically, the use of stimuli-responsive particles can introduce new properties and broaden the application range of such complex systems. Recently, we demonstrated that emulsions stabilized by microgels composed of interpenetrating networks (IPNs) of poly-N-isopropylacrylamide (PNIPAM) and polyacrylic acid (PAA) exhibit higher colloidal stability upon heating compared to PNIPAM homopolymer and other relevant PNIPAM-based copolymer counterparts. In the present work, using pendant drop tensiometry, we studied the evolution of water–tetradecane interfacial tension during the adsorption of PNIPAM-PAA IPN particles, comparing them with single-network P-(NIPAM-co-AA) and PNIPAM microgels. The results showed that, despite having the same chemical composition, copolymer particles exhibit completely different adsorption behavior in comparison to other microgel architectures. The observed disparity can be attributed to the nonuniform distribution of charged acrylic acid groups within the P-(NIPAM-co-AA) network obtained through precipitation polymerization. Oppositely, the presence of IPN architecture provides a uniform distribution of different monomers inside respective microgels. Additionally, hydrogen bonding between PNIPAM and PAA subchains appears to reduce the electrostatic energy barrier, enhancing the ability of IPN particles to successfully cover the liquid interface. Overall, our findings confirm the efficiency of using PNIPAM-PAA IPN microgels for the preparation of oil-in-water emulsions and their stability, even when the temperature rises above the lower critical solution temperature of PNIPAM.
Molecular dynamics simulations of nucleosomes are coming of age Anastasiia S. Fedulova, Grigoriy A. Armeev, Tatiana A. Romanova, Lovepreet Singh‐Palchevskaia, Nikita A. Kosarim, et al. Wiley Interdisciplinary Reviews Computational Molecular Science, 2024 Understanding the function of eukaryotic genomes, including the human genome, is undoubtedly one of the major scientific challenges of the 21st century. The cornerstone of eukaryotic genome organization is nucleosomes—elementary building blocks of chromatin about 10 nm in size that wrap DNA around an octamer of histone proteins. Nucleosomes are integral players in all genomic processes, including transcription, DNA replication and repair. They mediate genome regulation at the epigenetic level, bridging the discrete nature of the genetic information encoded in DNA with the analog physical nature of the intermolecular interactions required to access that information. Due to their relatively large size and dynamic nature, nucleosomes are difficult objects for experimental characterization. Molecular dynamics (MD) simulations have emerged over the years as a useful tool to complement experimental studies. Particularly in recent years, advances in computing power, refinement of MD force fields and codes have opened up new frontiers in terms of simulation timescales and quality for nucleosomes and related systems. It has become possible to elucidate in atomistic detail their functional dynamics modes such as DNA unwrapping and sliding, to characterize the effects of epigenetic modifications, DNA and protein sequence variation on nucleosome structure and stability, to describe the mechanisms governing nucleosome interactions with chromatin‐associated proteins and the formation of supranucleosome structures. In this review, we systematically analyzed all‐atom MD simulation studies of nucleosomes and related structures published since 2018 and discussed their relevance in the context of older studies, experimental data, and related coarse‐grained and multiscale studies.This article is categorized under: Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Biochemistry and Biophysics
Peculiarities of Emulsions Stabilized by Stimuli-Responsive Interpenetrating Polymeric Network Microgels Galina A. Komarova, Rustam A. Gumerov, Vladimir Yu. Rudyak, Elena Yu. Kozhunova, Igor I. Potemkin, et al. Langmuir, 2024 Emulsions have become a crucial product form in various industries in modern times. Expanding the class of substances used to stabilize emulsions can improve their stability or introduce new properties. Particularly, the use of stimuli-responsive microgels makes it possible to create "smart" emulsions whose stability can be controlled by changing any of the specified stimuli. Thus, finding new ways to stabilize emulsions may broaden their application. In this work, for the first time, we applied microgels based on interpenetrating polymeric networks (IPNs) of poly(N-isopropylacrylamide) (PNIPAM) and poly(acrylic acid) (PAA) as stabilizing agents for "oil-in-water" emulsions. We have demonstrated that emulsions stabilized by such soft particles can remain colloidally stable for an extended period, even after being heated up to 40 °C, which is above the lower critical solution temperature (LCST) of PNIPAM. On the contrary, the emulsions stabilized by PNIPAM homopolymer microgels were broken upon heating. To understand the stabilization mechanism of the emulsions, mesoscopic computer simulations were performed to study the IPN microgels at the liquid-liquid interface. The simulations demonstrated that when the first subnetwork (PNIPAM) collapses, the particle adopts a flattened core-shell morphology with a highly swollen PAA-rich shell and a collapsed PNIPAM-rich core. Unlike its PNIPAM homopolymer counterpart, the IPN microgel maintains its three-dimensional shape, which provides stability to the microgel-based emulsions over a wide range of temperatures. Our combined findings could be useful in developing new approaches to emulsions' storage, biphasic catalysis, and lubrication of mechanisms in various operating and climatic conditions.
Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study Pavel D. Oleinikov, Anastasiia S. Fedulova, Grigoriy A. Armeev, Nikita A. Motorin, Lovepreet Singh-Palchevskaia, et al. International Journal of Molecular Sciences, 2023 In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide–nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.
Swift Janitor: Efficient Absorption of a Minor Component from the Mixtures of Immiscible Liquids by Thermoresponsive Macroscopic and Microscopic Hydrogels Elena Yu. Kozhunova, Galina A. Komarova, Mikhail V. Anakhov, Rustam A. Gumerov, Igor I. Potemkin ACS Applied Materials and Interfaces, 2022 Polymer hydrogels are known to be efficient absorbents of various aqueous solutions. Along with the hydrophilicity of the polymer network, the presence of specific functional groups is required for the absorption of respective solutes. Alternatively, a selective uptake can be realized without any specific attraction of solutes to the network, which is shown in this paper. By combining experimental and simulation approaches, we demonstrated that thermoresponsive poly(N-isopropylacrylamide) gels and microgels in compositionally strongly asymmetric water/1-octanol mixtures selectively uptake the minor (1-octanol) component. Initially swollen in water, the gels substitute water by the organic solvent upon the addition of its small fraction into aqueous solution. In turn, for microgels, it was shown that the single particles could absorb the amount of the organic liquid more than two times higher than their mass while preserving the colloidal stability. At the same time, the accumulation of 1-octanol in the networks "switches off" the temperature response. The mesoscopic computer simulations revealed a physical reason and molecular picture of the phenomenon. Absorption of the minor component by the gels is caused by the decrease in water/1-octanol interfacial tension due to the formation of the dense polymer layer at the interface. The simulations allowed tracking the evolution of the size and the internal structure of the single microgels with changing 1-octanol concentration.
Behavior of PNIPAM Microgels in Different Organic Solvents Galina A. Komarova, Elena Yu. Kozhunova, Igor I. Potemkin Molecules, 2022 In this research, we studied, in detail, the behavior of common PNIPAM microgels, obtained through surfactant-free precipitation polymerization, in a number of organic solvents. We showed that many of the selected solvents serve as good solvents for the PNIPAM microgels and that the size and architecture of the microgels depend on the solvent chosen. Expanding the range of solvents used for PNIPAM microgel incubation greatly enhances the possible routes for microparticle functionalization and modification, as well as the encapsulation of water-insoluble species. In this demonstration, we successfully encapsulated water-insoluble Sudan III dye in PNIPAM microgels and prepared the aqueous dispersions of such composite-colored microparticles.
Antiseptic Materials on the Base of Polymer Interpenetrating Networks Microgels and Benzalkonium Chloride Elena Yu. Kozhunova, Galina A. Komarova, Oxana V. Vyshivannaya, Irina R. Nasimova, Anastasia E. Kuvarina, et al. International Journal of Molecular Sciences, 2022 Polymer microgels, including those based on interpenetrating networks (IPNs), are currently vastly studied, and their practical applications are a matter of thriving research. In this work, we show the perspective for the use of polyelectrolyte IPN microgels either as scavengers or carriers of antiseptic substances. Here, we report that poly-N-isopropylacrylamide/polyacrylic acid IPN microgels can efficiently absorb the common bactericidal and virucidal compound benzalkonium chloride. The particles can form a stable aqueous colloidal suspension or be used as building blocks for soft free-standing films. Both materials showed antiseptic efficacy on the examples of Bacillus subtilis and S. aureus, which was approximately equal to the commercial antibiotic. Such polymer biocides can be used as liquid disinfectants, stable surface coatings, or parts of biomedical devices and can enhance the versatility of the possible practical applications of polymer microgels.
