Biophysica, Volume 4, Issue 4 (December 2024) – 18 articles

Microplastics (MPs) are widespread environmental pollutants that have drawn significant attention due to their possible health risks to humans and animals, as well as their extensive presence in ecosystems. Recent growing evidence highlights a remarkable relationship between MPs and extracellular vesicles (EVs), nanoscale particles involved in intercellular communication. The purpose of this review was to investigate how the relationships between MPs and EVs can affect cellular functions and how this interaction could impact environmental conditions leading to broader ecological risks. The interaction patterns and bioactivity of both MPs and EVs are strongly influenced by biophysical characteristics such as hydrophobicity, surface charge, and particle size, which have received particular attention from the scientific community. Recent studies indicate that MPs affect EV distribution and their capacity to function appropriately in biological systems. Additionally, MPs can modify the molecular cargo of EVs, which may result in alterations of cell signaling pathways. Understanding the interactions between MPs and EVs could provide important opportunities to comprehend their potential effects on human health and environmental systems, especially when it comes to cancer development, endocrine, metabolic, and inflammatory disorders, and ecological disruptions. This review emphasizes the necessity of multidisciplinary research to clarify the molecular and biophysical mechanisms regulating the interaction between MPs and EVs. Full article

Targeted Auger emitters are being considered as a cancer treatment owing to the high linear energy transfer of Auger electrons. When targeted to cancers, this allows for a highly efficient treatment with a low risk of damage to surrounding healthy tissue. The purpose of this study was to determine the most DNA-damaging Auger emitters from a range of radionuclides, some of which are clinically utilised. A Monte Carlo method-based software (Geant4-DNA version 10.7) was used to determine the energy deposition and number of DNA double-strand breaks from Auger (and internal conversion) electrons imposed on a tetranucleosome. The Auger emitters, ¹¹⁹Sb and ¹⁰³Pd, have similar or slightly greater damaging properties compared to ¹²³I, ¹¹¹In, and ⁸⁹Zr. ^193mPt demonstrated the greatest therapeutic potency. Whilst ¹²⁵I was highly damaging, its relatively long half-life (60 days) makes it less desirable for clinical use. Geant4-DNA modelling identified the radionuclide ^193mPt as being highly favourable for use in radiotherapy. Full article

Cellular heterogeneity, an inherent feature of biological systems, plays a critical role in processes such as development, immune response, and disease progression. Human mesenchymal stem cells (hMSCs) exemplify this heterogeneity due to their multi-lineage differentiation potential. However, their inherent variability complicates clinical use, and there is no universally accepted method for detecting and quantifying cell population heterogeneity. Dielectrophoresis (DEP) has emerged as a powerful electrokinetic technique for characterizing and manipulating cells based on their dielectric properties, offering label-free analysis capabilities. Quantitative information from the DEP spectrum, such as transient slope, measure cells’ transition between negative and positive DEP behaviors. In this study, we employed DEP to estimate transient slope of various cell populations, including relatively homogeneous HEK-293 cells, heterogeneous hMSCs, and cancer cells (PC3 and DU145). Our analysis encompassed hMSCs derived from bone marrow, adipose, and umbilical cord tissue, to capture tissue-specific heterogeneity. Transient slope was assessed using two methods, involving linear trendline fitting to different low-frequency regions of the DEP spectrum. We found that transient slope serves as a reliable indicator of cell population heterogeneity, with more heterogeneous populations exhibiting lower transient slopes and higher standard deviations. Validation using cell morphology, size, and stemness further supported the utility of transient slope as a heterogeneity metric. This label-free approach holds promise for advancing cell sorting, biomanufacturing, and personalized medicine. Full article

Cyclodextrins (CDs) are natural cyclic oligosaccharides with the ability to form inclusion complexes with various organic substances. In this paper, we investigate the potential of CD complex formation to enhance the antibacterial activity and antioxidant properties of poorly soluble bioactive agents, such as chalcones, chromenes, stilbenoids and xanthylium derivatives, serving as potential adjuvants, in comparison with standard antiseptics. The interaction of these bioactive agents with the hydrophobic pocket of methyl-β-cyclodextrin (MCD) was confirmed using spectroscopic methods such as UV-vis, FTIR, ¹H and ¹³C NMR, mass-spectrometry. CD-based delivery system allows for combining multiple active agents, improving solubility, antibacterial efficacy by enhancing penetration into target bacterial cells (E. coli selectivity demonstrated via confocal microscopy). Novel compounds of chalcones and stilbenoids derivatives additionally enhance efficacy by inhibiting bacterial efflux pumps, increasing membrane permeability, and inhibiting bacterial enzymes, and showed a synergy when used in combination with metronidazole. The intricate relationship between the structural characteristics and functional properties of chalcones and stilbenoids in terms of their antibacterial and antioxidative capabilities is revealed. The substituents within aromatic rings significantly influence this activity, where position of electron-donating methoxy groups playing a crucial role. Among chalcones, stilbenoids, ana xanthyliums, the compounds caring a benzodioxol ring, analogous to natural bioactive compounds like apiol, dillapiol, and myristicin, emerge as prominent antibacterial activity. To explore the possibility to create theranostic formulations, we used fluorescent markers to visualize target cells, antiseptics to provide antibacterial activity, and bioactive agents as chalcones acting as adjuvants. Additionally, new antioxidant compounds were found such as Xanthylium derivative (R351) and chromene derivative: 1-methyl-3-(2-amino-3-cyano-7-methoxychromene-4-yl)-pyridinium methanesulfate: the pronounced antioxidant properties of these substances are observed comparable to quercetin in the efficiency. Rhodamine 6G, gentian violet, and Congo Red exhibit good antioxidant properties, although their activity is an order of magnitude lower than that of quercetin. However, they have remarkable potential due to their multifaceted nature, including the ability to visualize target cells. The most effective theranostic formulation is the combination of the antibiotic (metronidazole) + dye/fluorophore (methylene blue/rhodamine 6G) for visualization of target cells + adjuvant (chalcones or xanthylium derivatives) for antiinflammation effect. This synergistic combination, results in a promising theranostic formulation for treating bacterial infections, with enhanced efficiency, selectivity and minimizing side effects. Full article

The effect of sodium alginate on the denaturation and aggregation behavior of bovine serum albumin and hen egg-white lysozyme was studied. Large amounts of polysaccharide increase the thermal stability of albumin due to the weak binding interactions. At the same time, sodium alginate can reduce the quantity of amyloid fibrils formed by albumin under denaturing conditions, which is a consequence of the stabilization of the native protein form by glycan binding. In the case of lysozyme, the polysaccharide has no influence on the thermal stability of the protein in 2 M guanidinium hydrochloride. However, the inhibition of fibril formation with an increase in the lag time was observed, which is explained by the binding of sodium alginate to lysozyme fibrils, but not to the protein monomer. The molecular nature of the binding interactions between alginate and the studied proteins was elucidated using molecular docking and known experimental structures of glycan–protein complexes. Full article

Cells compartmentalize biochemical processes using physical barriers in the form of membranes. Eukaryotes have a wide diversity of membrane-based compartments that can be used in this context, with the main ones being the extracellular membrane, which separates the inside from the outside of the cell, and the nuclear membrane, which separates the nucleus from the cytoplasm. The nuclear membrane not only isolates and protects the DNA and the transcription and replication processes from the other processes that are occurring in the cytoplasm but also has an active role in the regulation of cellular signaling. The TGF-$\beta$ pathway is one of the most important and conserved signaling cascades, and it achieves compartmentalization using a well-tuned balance between the import and export rates of the active and inactive forms of key proteins. Thus, compartmentalization serves as an additional regulatory mechanism, physically isolating transcription factors from their targets, influencing the dynamics and strength of signal transduction. This contribution focuses on this biophysical layer of regulation, using the TGF-$\beta$ pathway to illustrate the molecular mechanisms underlying this process, as well as the biological consequences of this compartmentalization. We also introduce a simplified mathematical formulation for studying the dynamics of this process using a generalized approach. Full article

The interactions and structural organization of water molecules play a crucial role in a wide range of physical, chemical, and biological processes. The ability of water to form hydrogen bonds (H-bonds) underpins its unique properties and enables it to respond dynamically to various environmental factors. These interactions at the molecular level may affect vital processes like protein folding, enzyme activity, and cellular organization. The presence of solutes and spatial constraints can alter the H-bonding network of water, and these effects are ubiquitous in the biological environment. In this study, we analyzed the fluorescence of 2-acetyl-6-(dimethylamino)naphthalene (ACDAN) fluorescence emission in water solutions containing kosmotropic and chaotropic salts and in agar hydrogels. Recently, this dye has proven invaluable in studying water network structure and dynamics, as its fluorescence signal changes based on the local dielectric environment, revealing variations in the dipolar relaxation of water. Our results show that ACDAN spectral response correlates with the degree of water ordering, providing important insights into solute–water interactions and water dynamics in free and confined environments. Full article

Tissue spheroids are self-organised 3D cellular aggregates that serve as a versatile platform in tissue engineering. While numerous high-throughput methods exist to characterise the cellular function of tissue spheroids, equivalent techniques for the mechanical characterisation are still lacking. In this review, we focus on tissue fusion— a simple, fast, and inexpensive method to characterise the rheology of tissue spheroids. We begin by discussing the implications of tissue rheology in development and disease, followed by a detailed explanation of how the phenomenon of arrested coalescence can be used to explore the rheology of tissue spheroids. Finally, we present different theoretical models that, when combined with experimental data, allow us to extract rheological information. Full article

Vertex models have become essential tools for understanding tissue morphogenesis by simulating the mechanical and geometric properties of cells in various biological systems. These models represent cells as polygons or polyhedra, capturing cellular interactions such as adhesion, tension, and force generation. This review explores the ongoing evolution of computational vertex models, highlighting their application to complex tissue dynamics, including organoid development, wound healing, and cancer metastasis. We examine different energy formulations used in vertex models, which account for mechanical forces such as surface tension, volume conservation, and intercellular adhesion. Additionally, this review discusses the challenges of expanding traditional 2D models to 3D structures, which require the inclusion of factors like mechanical polarisation and topological transitions. We also introduce recent advancements in modelling techniques that allow for more flexible and dynamic cell shapes, addressing limitations in earlier frameworks. Mechanochemical feedback and its role in tissue behaviour are explored, along with cutting-edge approaches like self-propelled Voronoi models. Finally, the review highlights the importance of parameter inference in these models, particularly through Bayesian methods, to improve accuracy and predictive power. By integrating these new insights, vertex models continue to provide powerful frameworks for exploring the complexities of tissue morphogenesis. Full article

The variable heavy chain fragments derived from camelid antibodies, called VHHs or nanobodies, have recently shown promise as high-affinity reagents. They offer higher stability compared to conventional antibodies and fragments thereof. Furthermore, their smaller size (~15–20 kDa) allows better targeting of molecules localized inside the cell and in crowded environments, like tissues and protein aggregates. Despite these advantages, nanobody clones screened using phage display can suffer from poor soluble expression, which we hypothesized is due to the presence of hydrophobic hotspots on their surface. In this work, we propose a novel, computationally guided workflow for screening and production of nanobody binders for optimized expression. After an initial round of phage display screens against our target (K-Ras), we modeled the lead candidates to generate spatial aggregation propensity (SAP) maps to highlight the hydrophobic hotspots with single amino acid resolution, which were subsequently used to guide mutagenesis of the binders for soluble expression. We followed two approaches to perform point hydrophilic mutations: (i) performing point hydrophilic mutations in the hydrophobic hotspots; (ii) combining point mutation resulting from a round of random mutagenesis that show favorable SAP scores. Both approaches led to a remarkable increase in soluble expression, which allowed production and characterization of their binding to their target (K-Ras) on soluble ELISA and biolayer interferometry. We observed that the latter approach resulted in clones with stronger binding affinity compared to the former approach. Our results emphasize the need to perform a round of random mutagenesis to identify point mutations, which can then be used in an in silico guided pipeline to identify the right combination of mutations for high soluble expression. Full article

Chemokine ligands play a pivotal role in immune response by mediating cell migration and coordinating cellular processes through interactions with chemokine receptors. Understanding their sequence and structural integrity is crucial for elucidating their biological functions and potential therapeutic applications. In this study, we investigate the dimer interface between two distinct homodimer topologies: CXC and CC homodimers. Despite nearly identical monomeric structures, the rigid CXC interface is characterized by interactions between the N-loop/β-sheet regions, while the more flexible CC interface involves interactions through the unstructured N-terminal regions. Our structural and biophysical analyses indicate no significant differences in the free energy of folding (2–8 kcal/mol) and binding (10–14 kcal/mol) between the two homodimer topologies, showing that their free energy is primarily driven by sequence. We hypothesize that the biological signal is driven by the malleability of the dimer, depending on the binding interface. Understanding these structural dynamics opens new possibilities for designing chemokine-based therapeutics to modulate immune responses in diseases such as cancer, inflammation, and autoimmune disorders. Full article

We revisit the seminal model of glycolysis first proposed by Sel’kov more than fifty years ago. We investigate the onset of instabilities in biological systems described by the Sel’kov model in order to determine the conditions of the model parameters that lead to bifurcations. We analyze the glycolysis reaction under the circumstances when the diffusivity of both ATP and ADP reactants are taken into account. We estimate the critical value of the model’s single compact dimensionless parameter, which is responsible for the onset of reaction instability and the system’s symmetry breaking. It appears that it leads to spatial inhomogeneities of reactants, leading to the formation of standing waves instead of a homogeneous distribution of ATP molecules. The consequences of this model and its results are discussed in the context of the Warburg effect, which signifies a transition from oxidative phosphorylation to glycolysis that is correlated with the initiation and progression of cancer. Our analysis may lead to the selection of therapeutic interventions in order to prevent the symmetry-breaking phenomenon described in our work. Full article

Various medical treatments aim to counteract the impact of oxidants on mammalian cells. One such antioxidant is Epigallocatechin-3-gallate (EGCG), an active ingredient in green tea, which has demonstrated protective effects against cellular oxidants like camptothecin (CAMPT). This study examines how EGCG mitigates CAMPT’s effects on UMR cells, focusing on cell proliferation and biophysical parameters. UMR cells were treated with different CAMPT concentrations and incubated for 72 h. Subsequently, cell proliferation and viability were assessed. In a separate experiment, UMR cells were co-treated with CAMPT and varying EGCG concentrations to evaluate EGCG’s ability to mitigate CAMPT’s oxidative effect. Electric Cell–Substrate Impedance Sensing (ECIS) technology was also used to assess the biophysical parameters of CAMPT-treated UMR cells, including cell monolayer resistance, cell spreading, and cell attachment. The results showed a concentration-dependent decrease in cell proliferation for CAMPT-treated UMR cells. However, co-treatment with EGCG reversed CAMPT’s oxidative effects in a concentration-dependent manner. ECIS technology revealed a decrease in biophysical parameters when UMR cells were treated with CAMPT alone. Statistical analysis indicated significant differences with p-values < 0.05. This study suggests that EGCG effectively protects UMR cells from oxidative stress and highlights its potential role in mitigating oxidative stress in mammalian cells. Additionally, the use of ECIS technology validates its application in corroborating the biological effects of CAMPT and EGCG on UMR cells. Full article

Mammalian target of rapamycin complex 1 (mTORC1) is an important and promising alternative biological target for the treatment of different types of cancer including breast, lung and renal cell carcinoma. This study contributed to the development of mathematical models highlighting the quantitative structure-activity relationship of a series of piperazine derivatives reported as mTORC1 inhibitors. Various molecular descriptors were calculated using Gaussian 09, Chemsketch, and ChemOffice software. The density funcional theory (DFT) method at the level B3LYP/6-31G+(d, p) was applied to determine the structural, electronic and energetic parameters associated with the studied molecules. The predictive ability of the built models, which is obtained by two methods (MLR and MNLR), showed that the built models are statistically significant. The QSAR modeling results revealed that the six molecular descriptors of lowest unoccupied molecular orbital energy (ELUMO), electrophilicity index (ω), molar refractivity (MR), aqueous solubility (Log S), topological polar surface area (PSA), and refractive index (n) significantly correlated to the biological inhibitory activity of piperazine derivatives. Using QSAR models and in silico pharmacokinetic profiles predictions, five new candidate compounds are selected as potential inhibitors against cancer. Full article

No one can dismiss the fundamental role played by water in several important biochemical processes, including the folding of globular proteins. The so-called hydrophobic effect is the theoretical construct to rationalize how water molecules stabilize the folded state. However, over the years, analyses have been published that lead to the conclusion that water destabilizes the folded state. The aim of the present work is to state that the gain in translational entropy of water molecules (due to the decrease in water-accessible surface area associated with folding) is the driving force behind protein folding. Full article

Tefluthrin (Tef) is categorized as a type-I pyrethroid insecticide, telmisartan (Tel) functions as an angiotensin II receptor blocker, and KB-R7943 has been identified as an inhibitor of the Na⁺-Ca²⁺ exchange process. However, the influence of these compounds on the amplitude and gating properties of voltage-gated Na⁺ current (I_Na) in neurons associated with pain signaling remains unclear. In cultured dorsal root ganglion (DRG) neurons, whole-cell current recordings revealed that Tef or Tel increased the peak amplitude of I_Na, concomitant with an elevation in the time constant of I_Na inactivation, particularly in the slow component. Conversely, exposure to KB-R7943 resulted in a depression in I_Na, coupled with a decrease in the slow component of the inactivation time constant of I_Na. Theoretical simulations and bifurcation analyses were performed on a modeled interneuron in the spinal dorsal horn. The occurrence of I_Na inactivation accentuated the subthreshold oscillations (SO) in the membrane potential. With an increase in applied current, SO became more pronounced, accompanied by the emergence of high-frequency spiking (HS) with a frequency of approximately 150 Hz. Moreover, an elevation in I_Na conductance further intensified both SO and HF. Consequently, through experimental and in silico studies, this work reflects that Tef, Tel, or KB-R7943 significantly impacts the magnitude and gating properties of I_Na in neurons associated with pain signaling. The alterations in I_Na magnitude and gating in these neurons suggest a close relationship with pain transmission. Full article

In certain clinical applications, pulsating currents are applied to specific body regions for therapeutic purposes. In this paper, we analyze the resulting thermal field to determine the optimal amplitude, period, and duration of these stimuli, ensuring that the temperature in the targeted tissue remains below the necrosis threshold. Full article

Coming in a variety of forms, melanin is one of the most abundant, stable, diverse, and evolutionarily ancient pigments found in living things in nature. These pigments often serve protective functions, typically well-adapted to their specific roles. One such protective function is metal chelation and cation exchange, which help regulate and buffer metal concentrations within cells. By binding to certain metals, melanin can acquire magnetic properties. Because of this, it may play a role in magnetic effects and possibly in the response of organisms to external magnetic fields and magnetic sensing. While there is melanin in plants, microbes, fungi, and invertebrates, certain types of melanin are specifically associated with the retina in vertebrates, including migrating bird and fish species. In this review, we examine studies focusing on the properties of melanin in these parts of the body and their possible association with magnetic sensing, and generally, magnetic sensing in the retina. Full article