Biophysica

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

This study investigates the formation and impact of Endogenous Quasi-Pathogens (EQPs) within cellular environments, focusing on the role of Endogenous Smart Medicine (ESM) as a therapeutic intervention. This work elucidates how induced vibrations facilitate new molecular and atomic connections between adjacent cells, leading to endobiotic bond formation and significantly altered DNA behavior. These vibrations, which dominate cellular processes, induce both temporary and permanent changes in cellular dynamics. The resulting increase in extracellular impedance triggers the emergence of new EQP sources, potentially initiating divergent pathological cycles. Cells experiencing moderate impedance changes are classified as benign, while those with substantial alterations are considered malignant. This study highlights the medical diagnostic implications of EQPs and positions ESM as a precise method for modulating cellular impedance, reducing the effects of EQPs, and potentially treating diseases where disruptions in cellular dynamics and stiffness are critical. Additionally, the integration of ChronoBit Storage (CBS) within ESM introduces a novel energy management mechanism, enhancing therapeutic precision by synchronizing energy distribution with cellular needs. The ChronoVital Index (CVI), a temporal model for assessing time dynamics across biological systems from individual cells to whole organs further refines this approach. By advancing the CVI and CBS, this research paves the way for more sophisticated therapeutic strategies, offering promising applications in the fields of disease management and cellular restoration within the framework of Endogenous Smart Medicine. Full article

Experiments to measure a single molecule/particle, i.e., an individual molecule/particle, at room temperature or under physiological conditions without immobilization—for example, on a surface or without significant hydrodynamic flow—have so far failed. This failure has given impetus to the underlying theory of Brownian molecular motion towards its stochastics due to diffusion. Quantifying the thermodynamic jitter of molecules/particles inspires many and forms the theoretical basis of single-molecule/single-particle biophysics and biochemistry. For the first time, our simulation results for a live cell (cytoplasm) show that the tracks of individual single molecules are localized in Brownian motion, while there is fanning out in fractal diffusion (anomalous diffusion). Full article

This study presents a quantum well model using the transfer matrix technique to analyze the charge transfer characteristics of nanostructure sequences in both DNA and superlattices. The unconfined state, or unbound state, above the quantum well is used to investigate carrier behaviors in a semiconductor nanostructure. These analytical approaches can be extended to enhance the understanding of charge transfer in DNA nanostructures with periodic and aperiodic sequences. Experimental validation was conducted through photoreflectance spectroscopy on nanostructures within the semiconductor superlattices. Furthermore, the study’s findings were compared with earlier research by Li et al. on the thermoelectric effect and its dependence on molecular length and sequences in single DNA molecules. The results showed agreement, offering novel insights into charge transfer and transport in DNA nanostructures across various sequence types. Full article

Bone minerals may be more complex than the prevailing opinion suggests. Understanding its biomaterial properties in health and disease may address fundamental geo/biomorphological ambiguities recurrent within its calcified cancellous hierarchy of macro-, micro-, and nano-skeletal networks. (i) There is evidence that the outer mineral macroskeleton of interconnected trabeculae (150 µm diameter) is modulated according to axes of tensile stress by permeating arrays of periosteal Sharpey’s fibres (collagen type III/VI, 5–25 µm thick) studded with tenascin organiser protein. (ii) Its substructural mineral microskeleton is a reticulation of bridged and deformable calcium phosphate/carbonate microspheres (about 1 µm diameter). These organically enshrouded (e.g., bone sialoprotein, osteocalcin, osteopontin) objects, configured by the adhesive organiser protein fibronectin and tempered by trace elements (e.g., Si, Mg, Fe, Al), display differential histochemistry (e.g., acid phosphatase, carbonic anhydrase) and anomalous traits (tetracycline binding, gram-positive microbial staining and nucleic acid staining affinity). The calcified microspheres are intracellular fabrications of osteocyte cohorts developed within “switched on” Golgi cisternae prior to aggregation at the extracellular calcification front in chains and looped assemblies. (iii) Within each microsphere, a less dense centre is encircled by a mineral nanoskeleton of beaded filaments (5 nm in diameter) transmutable in electron density, with a trait for lateral fusion into ladder-like struts, stays and senescent fenestrated plates, constituting domains of microparticle slip and crystal fracture. The evidence suggests a bone mineral biosystem of integrated complexity within which a particulate assemblage at the animate: inanimate calcification front resembles a colonial construct of prokaryote-like, Golgi-fabricated objects calcified with phosphate and harbouring a resident biochemistry. A self-contained “Petrified Microbiome” is proposed to be orchestrated according to a biodynamic primordial paradigm. Full article

Aqueous two-phase systems (ATPSs) are formed when two nonionic polymers, or a single polymer and salt, are mixed in water above a specific concentration, resulting in the emergence of phase separation and the formation of two immiscible aqueous phases. The solvent properties of the aqueous media within the phases of ATPSs rely on the specific composition of the co-solutes and the arrangement of the hydrogen bond network within each phase. Here, we investigate the anion effect of various sodium salts on the enhancement or destabilization of polyethylene glycol (PEG)–salt ATPS formation. Relatively small changes in ATPS ionic composition were shown to result in significant changes in solute partitioning. Additionally, we previously established that the arrangement of hydrogen bonds within the coexisting phases of ATPSs is different, as evidenced by Attenuated Total Reflection—Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. The hydrogen bond arrangement was shown to abruptly change at concentrations below the threshold of macroscopic phase separation in the ATPSs. Using dynamic light scattering (DLS), we observed a correlation between these abrupt changes in H-bond arrangement and the detection of agglomerate formation in both polymer–polymer and polymer–salt systems. Full article

Herein, we propose an analytical approach based on intermolecular fluorescent resonant energy transfer (FRET) pairs for the visualization of specific enzyme activity in model biomembranes and in living cells. Cell visualizations with fluorescent confocal laser microscopy usually rely on fluorescent probes, such as Fluorescein isothiocyanate (FITC), Alexa488, Tetramethylrhodamine isothiocyanate (TRITC) and many others. However, for more specific tasks, such as the detection of certain enzymatic activity inside the living cell, the toolbox is quite limited. In the case of enzyme-hydrolases for example, the choice is limited to organic molecules comprising a fluorescent dye (typically, 4-methylumbelliferone (MUmb) or 7-amino-4-methylcoumarin (AMC) derivatives) and a fluorescence quencher, bound via an enzyme-sensitive linker—so that when the linker is degraded, the fluorescent signal increases. Unfortunately, both MUmb and AMC are quenched and have a relatively low quantum yield in cells, and their excitation and emission ranges overlap with that of intracellular fluorophores, often producing a strong background noise. R6G, on the other hand, has excellent quantum yield apart from intracellular fluorophores, but there are no efficient quenchers that could be chemically linked to R6G. Herein, we show that R6G is able to form intermolecular FRET pairs with MUmb or AMC, with the latter serving as fluorescence donors. This yields a combination of R6G’s excellent fluorescence properties with a possibility to use an enzyme-sensitive linker in MUTMAC or AMC derivatives. This phenomenon was initially discovered in a model system, reversed micelles, where the donor, the acceptor, and the enzyme are forced to be in close proximity to each other, so that proximity could serve as an explanation for the intermolecular FRET effect. Surprisingly enough, the phenomenon has been reproduced in living cells. Moreover, we were able to create working intermolecular donor–acceptor FRET pairs for several different enzymes, including chymotrypsin, phosphatase, and asparaginase. This appears counterintuitive, as besides the overlap of the emission spectra of the donor and the absorption spectra of the acceptor, there are other criteria for the FRET effect, including the convergence of two fluorophores at a distance of about 1–10 nm, and the orientation of their dipoles at a certain angle, which is difficult to imagine in a bulk system like a living cell. We hypothesize that FRET-enabling donor–acceptor interaction may be taking place at the inner surface of the lipid bilayer, to which both donor and acceptor molecules would likely have an affinity. This hypothesis would require a more detailed investigation. Therefore, we have shown that the method suggested has good potential in the visualization of enzyme functioning inside living cells, which is often a challenging task. Shifting of the fluorescence signal to the long-wavelength region would increase the signal selectivity, making it easily distinguishable from autofluorescence. Full article

The production of public goods is a necessary condition for the survival of the species, but it comes at the expense of individual growth. In a prototype bacterial colony, we model the role of quorum sensing as a resource redistribution mechanism. Two types of bacterial colonies are analyzed, one made up of a single strain and one made up of two different strains. Based on a recent series of experimental data present in the literature, we analyze two types of strains with different extinction times: strains that consume available resources very quickly, therefore becoming extinct quickly, and strains that consume resources slowly and die due to aging. We show that the proposed quorum sensing model describes the main experimental result that coexistence may favor the survival of both strains. Furthermore, the production of public goods is maximized when both types of individuals have the maximum proliferation output. Finally, we highlight the role played by so-called dormant cells in the duration of survival time. These cells are of particular interest because their ability to counteract different types of stress (e.g., the use of antibiotics) still constitutes a challenge. Full article

In this study, we examine the cooperative effect between vitamins C and E that mitigates oxidative stress by using experimental and computational methods. We performed superoxide scavenging experiments on each vitamin individually and their combination using rotating ring–disk electrode voltammetry. The results indicate that vitamins E and C together produce more effective scavenging of superoxide as evaluated by a steeper slope in the efficiency graph, −7.2 × 10⁴, compared to that of vitamin E alone, −1.8 × 10³, or vitamin C alone, −1.3 × 10⁴. Density Functional Theory calculations agree with our experimental results, and we describe a mechanism for the antioxidant action of individual vitamins E and C, plus the synergistic action when both vitamins interact. This process involves the restoration of vitamin E by vitamin C and includes π-π interactions between superoxide and scavengers. The overall result produces an increase in scavenging superoxide radicals when both vitamins act together. Full article

The thermodynamics of protein–ligand interactions seems to be associated with a narrow range of Gibbs free energy. As a consequence, a linear enthalpy–entropy relationship showing an apparent enthalpy–entropy compensation (EEC) is frequently associated with protein–ligand interactions. When looking for the most negative values of ∆H to gain affinity, the entropy compensation gives rise to a barely noticeable increase in affinity, therefore negatively affecting the design and discovery of new and more efficient drugs capable of binding protein targets with a higher affinity. Originally attributed to experimental errors, compensation between ∆H and T∆S values is an observable fact, although its molecular origin has remained obscure and controversial. The thermodynamic parameters of a protein–ligand interaction can be interpreted in terms of the changes in molecular weak interactions as well as in vibrational, rotational, and translational energy levels. However, a molecular explanation to an EEC rendering a linear enthalpy–entropy relationship is still lacking. Herein, we show the results of a data search of ∆G values of 3025 protein–ligand interactions and 2558 “in vivo” ligand concentrations from the Protein Data Bank database and the Metabolome Database (2020). These results suggest that the EEC may be plausibly explained as a consequence of the narrow range of ∆G associated with protein–ligand interactions. The Gaussian distribution of the ∆G values matches very well with that of ligands. These results suggest the hypothesis that the set of ∆G values for the protein–ligand interactions is the result of the evolution of proteins. The conformation versatility of present proteins and the exchange of thousands (even millions) of minute amounts of energy with the environment may have functioned as a homeostatic mechanism to make the ∆G of proteins adaptive to changes in the availability of ligands and therefore achieve the maximum regulatory capacity of the protein function. Finally, plausible strategies to avoid the EEC consequences are suggested. Full article

Animal skin patterns are increasingly explained using the Turing pattern model proposed by Alan Turing. The Turing model, a self-organizing model, can produce spotted or striped patterns. However, several animal patterns exist that do not correspond to these patterns. For example, the body patterns of the ornamental carp Nishiki goi produced in Japan vary randomly among individuals. Therefore, predicting the pattern of offspring is difficult based on the parent fish. Such a randomly formed pattern could be explained using a majority voting model. This model is a type of cellular automaton model that counts the surrounding states and transitions to high-number states. Nevertheless, the utility of these two models in explaining fish patterns remains unclear. Interestingly, the patterns generated by these two models can be detected among very closely related species. It is difficult to think that completely different epidermal formation mechanisms are used among species of the same family. Therefore, there may be a basic model that can produce both patterns. Herein, the Turing pattern and majority voting method are represented using cellular automata, and the possibility of integrating these two methods is examined. This integrated model is equivalent to both models when the parameters are adjusted. Although this integrated model is extremely simple, it can produce more varied patterns than either one of the individual models. However, further research is warranted to determine whether this model is consistent with the mechanisms involved in the formation of animal fish patterns from a biological perspective. Full article

We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores the bottom-up assembly of regulatory networks, introducing as many components and interactions as possible to capture the oscillatory nature of the clock. The reduction phase deals with functional decomposition, distilling complex models to their essential dynamical repertoire. Current challenges in this field, including the integration of spatial considerations and environmental influences like light and temperature, are also discussed. The review emphasizes the ongoing need for models that balance molecular detail with practical simplicity. Full article

The adsorption behavior of recombinant cage-shaped proteins with carbon nanotube (CNT)-binding peptides on carbon surfaces was quantitatively and dynamically analyzed using a highly stable quartz crystal microbalance (QCM). Two types of CNT-binding peptide aptamers obtained by the phage display method were attached to the N- and C-termini of the Dps (DNA-binding protein derived from starved cells) to produce carbonaceous material-binding Dps. The carbon adsorption ability of the mutant Dps was studied by QCM measurement using a carbon-coated QCM sensor. The produced peptide aptamer-modified Dps showed higher affinity than a wild Dps and also showed higher adsorption capacity than a previously used Dps with carbon nanohorn-binding peptides. The newly obtained peptide aptamers were proven to provide Dps with high adsorption affinity on carbon surfaces. Furthermore, the aptamer modified to the N-terminus of the Dps subunit showed more efficient adsorption than the aptamers attached to the C-terminus of the Dp, and the linker was found to improve the adsorption ability. Full article

Laurus nobilis, sometimes referred to as laurel, has been used for medicinal and culinary purposes for a very long time. The main subjects of this study are the phytochemical composition, mineralogical profile, and potential antioxidant properties of Laurus nobilis in Tangier, Northern Morocco. For phytochemical analysis of methanolic extracts, high-performance liquid chromatography (HPLC-UV-MS) was used, and Fourier transformation infrared spectroscopy (FT-IR) was used to identify each individual component. Minerals were studied by inductively coupled plasma atomic emission spectroscopy (ICP-AES) and wavelength dispersive X-ray fluorescence (WD-XRF). Total tannin, flavonoid, and phenolic amounts were quantified using aqueous and methanolic extracts. The antioxidant properties were assessed using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) assays. Research has revealed a complex array of phytochemicals, including tannins, flavonoids, and phenolic acids. Mineral analysis has revealed the existence of vital components that are beneficial to health. Comparing the methanolic extract to the water extract, it demonstrated higher levels of phenols, flavonoids, and tannins as well as stronger antioxidant activity, indicating greater health benefits. This comprehensive study highlights the importance of Laurus nobilis from Northern Morocco as a reliable botanic resource with potential pharmaceutical, nutritional, and cosmetic uses. Full article