Mean Square Displacement Research Articles

Molecular insights reveal how the glycolipids in cell membrane mitigates nanomaterial's invasion

Nanomaterial-cellular membrane interaction is crucial for the cytotoxicity of such materials in theoretical investigations. However, previous research often used cellular membrane models with one or few lipid types, which deviates significantly from realistic membrane compositions. Here, employing molecular dynamics (MD) simulations, we investigate the impact of a typical nanomaterial, boron nitride (BN), on a cellular membrane model based on the realistic small intestinal epithelial cell (SIEC) membrane. This membrane contains a complex composition, including abundant glycolipids. Our MD simulations reveal that BN nanosheet can partially insert into the SIEC membrane, maintaining a stable binding conformation without causing obvious structural changes. Dynamic analyses suggest that van der Waals (vdW) interactions drive the binding process between BN and the SIEC membrane. Further simulation of the interaction between BN nanosheet and deglycosylated SIEC membrane confirms that BN nanosheet cause significant structural damage to deglycosylated SIEC membranes, completely inserting into the membrane, extracting lipids, and burying some lipid hydrophilic heads within the membrane interior. Quantitative analyses of mean squared displacements (MSD) of membranes, membrane thicknesses, area per lipid, and order parameters indicate that BN nanosheet causes more substantial damage to deglycosylated SIEC membrane than to intact SIEC membrane. This comparison suggests the molecular mechanism involved in mitigating BN invasion by SIEC membrane that the polysaccharide heads of glycolipids in the SIEC membrane form a significant steric hindrance on membrane surface, not only hindering the insertion of BN, but also resisting the lipid extraction by BN. Free energy calculations further support this conclusion. Overall, our MD simulations not only shed new light into the reduced impact of BN nanosheet on the realistic SIEC membrane but also highlight the importance of glycolipids in protecting cell membranes from nanomaterial invasion, contributing to a deeper understanding of nanomaterial-realistic cell membrane interactions.

In silico analysis of potential inhibitors for breast cancer targeting 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1) catalyses.

Breast cancer (BC) is still one of the major issues in world health, especially for women, which necessitates innovative therapeutic strategies. In this study, we investigated the efficacy of retinoic acid derivatives as inhibitors of 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), which plays a crucial role in the biosynthesis and metabolism of oestrogen and thereby influences the progression of BC and, the main objective of this investigation is to identify the possible drug candidate against BC through computational drug design approach including PASS prediction, molecular docking, ADMET profiling, molecular dynamics simulations (MD) and density functional theory (DFT) calculations. The result has reported that total eight derivatives with high binding affinity and promising pharmacokinetic properties among 115 derivatives. In particular, ligands 04 and 07 exhibited a higher binding affinity with values of -9.9 kcal/mol and -9.1 kcal/mol, respectively, than the standard drug epirubicin hydrochloride, which had a binding affinity of -8.2 kcal/mol. The stability of the ligand-protein complexes was further confirmed by MD simulations over a 100-ns trajectory, which included assessments of hydrogen bonds, root mean square deviation (RMSD), root mean square Fluctuation (RMSF), dynamic cross-correlation matric (DCCM) and principal component analysis. The study emphasizes the need for experimental validation to confirm the therapeutic utility of these compounds. This study enhances the computational search for new BC drugs and establishes a solid foundation for subsequent experimental and clinical research.

Spermine and spermidine SI-PPCs: Molecular dynamics reveals enhanced biomolecular interactions

In this paper the effects on the interaction of highly positively charged substitution-inert platinum polynuclear complexes (SI-PPCs) with negatively charged DNA and heparin are examined and compared by theoretical chemistry methods. Electrostatic and hydrogen bonding interactions contribute to the overall effects on the biomolecule. Root Mean Square (RMS) deviation, Solvent Accessible Surface, RMS fluctuation, and interaction analysis all confirm similar effects on both biomolecules, dictated predominantly by the total positive charge and total number of hydrogen bonds formed. Especially, changes in structural parameters suggesting condensation and reduction of available surface area will reduce or prevent normal protein recognition and may thus potentially inhibit biological mechanisms related to apoptosis (DNA) or reduced vascularization viability (HEP). Thermodynamic analyses supported these findings with favourable interaction energies. The comparison of DNA and heparin confirms the general intersectionality between the two biomolecules and confirms the intrinsic dual-nature function of this chemotype. The distinction between the two-limiting mode of actions (HS or DNA-centred) could reflect an intriguing balance between extracellular (GAG) and intracellular (DNA) binding and affinities. The results underline the need to fully understand GAG-small molecule interactions and their contribution to drug pharmacology and related therapeutic modalities. This report contributes to that understanding.

Brownian particle diffusion in generalized polynomial shear flows.

This study presents a mathematical framework for calculating the diffusion of Brownian particles in generalized shear flows. By solving the Langevin equationsusing stochastic instead of classical calculus, we propose a mathematical formulation that resolves the particle mean-square displacement (MSD) at all timescales for any two-dimensional parallel shear flow described by a polynomial velocity profile. We show that at long timescales, the polynomial order of time of the particle MSD is n+2, where n is the polynomial order of the transverse coordinate of the velocity profile. We generalize the method to resolve particle diffusion in any polynomial shear flow at all timescales, including the order of particle relaxation timescale, which is unresolved in current theories. Particle diffusion at all timescales is then studied for the cases of Couette and plane Poiseuille flows and a polynomial approximation of a hyperbolic tangent flow while neglecting the boundary effects. We observe three main stages of particle diffusion along the timeline for Couette and plane Poiseuille flows and four main stages for hyperbolic tangent flow. The particle MSD is distinctly different across these stages due to different dominant physical mechanisms. Thus, higher temporal and spatial resolution for diffusion processes in shear flows may be realized, suggesting a more accurate analytical approach for the diffusion of Brownian particles.

The diffusion behaviour of coupled particle rings driven by self-propelled particles in a two-dimensional reflection channel

Investigated the diffusion behavior of self-propelled coupled particle rings in a two-dimensional channel considering particle collisions. The channel geometry and noise regulation play crucial roles in directing transport within the system. Observed a significant alteration in the diffusion behavior of the particle rings at specific stages of the collision process, accompanied by corresponding changes in the diffusion coefficient. As the modulation phase shift increases, the mean square displacement (MSD) of the particle rings displays periodic fluctuations. The binding force between the particle rings partially restricts the growth of the MSD. An increase in white noise intensity enhances the diffusion behavior. The impact of self-propulsion speed is influenced by the modulation parameters. The sign of the modulation parameter dictates the correlation of the self-propulsion speed. Furthermore, the number of particle rings in the channel introduces a complex effect on the diffusion behavior.

A study on the motion characteristics of particle in shear flow of active nematic fluid between two plates

Abstract The motion characteristics of particle in shear flow of active nematic fluid between two plates are investigated numerically. The influence of activity intensity of active nematic fluids on the motion characteristics of particle is focused. The results showed that, when the activity intensity is high, the particle exhibits initially smooth trajectories and ultimately approximate Brownian motion. As the activity intensity increases, both the translational mean square displacement (MSDT) and rotational mean square displacement (MSDR) of the particle increase. The particle exhibits initially super-diffusive behavior and then normal diffusion. The unique vortex lattice mode in the flow plays a role in hindering particle motion, leading to a decrease in MSDT and MSDR. An increase in particle size will lead to a weakening of particle diffusion. In addition, there are topological defects in the active nematic fluid, and the number of topological defects N def in the contractile system is greater than that in the extensible system, while the presence of particle has a smaller impact on N def in the flow.

In vitro antioxidant activity, QSAR, in silico toxicity prediction, molecular docking studies, and molecular dynamics of a series of N-ferrocenylmethylanilines as potent antioxidant agents

The superoxide anion radical scavenging activities of a series of twenty-eight ferrocenylmethylaniline derivatives were measured in an in vitro study followed by in silico studies which included quantitative structure-activity relationship (QSAR), toxicity prediction, molecular docking studies, and molecular dynamics simulations. Multilinear regression analysis was employed to establish a quantitative correlation between the scavenging activity of superoxide anion radicals and various structural properties. The QSAR model obtained underwent validation, demonstrating statistical significance with a squared fitting correlation coefficient (R2) of 0.934, an adjusted squared correlation coefficient (R2 adj) value of 0.849, and a cross-validation coefficient (Q2) value of 0.873. Additionally, the calculated Fisher ratio (F) value of 36.525 indicates the model's strong predictability. Toxicity perdition studies demonstrated that among the five most potent compounds, FMA27 and FMA12 were predicted to be non-toxic. The molecular Docking study revealed that compound FMA23 exhibited the least activity against the glutathione reductase enzyme, with the highest inhibitory concentration recorded at 4.16 × 10–6 M and the lowest docking scores observed at −7.34 kcal.mol-1. Interactions between the compound and the amino acid residues of glutathione reductase were primarily hydrophobic and π-cation in nature. Analysis of root mean square deviation (RMSD), radius of gyration (Rg), and root mean square fluctuation (RMSF), from molecular dynamics study, revealed stable fluctuations in protein backbone conformations, consistent compactness of the complex, and minimal fluctuations in most protein residues, respectively.

Functional characterization and structural prediction of hypothetical proteins in monkeypox virus and identification of potential inhibitors.

The excessive activation of the monkeypox virus (MPXV-Congo_8-156) is linked to various skin and respiratory disorders such as rashes, fluid-filled blisters, swollen lymph nodes and encephalitis (inflammation of the brain), highlighting MPXV-Congo_8-156 as a promising target for drug intervention. Despite the effectiveness of Cidofovir, in inhibiting MPXV activity, its limited ability to penetrate the skin and its strong side effects restrict its application. To address this challenge, we screened 500 compounds capable of penetrating the skin and gastrointestinal tract to identify potent MPXV inhibitors. Various characterization schemes and structural models of MPXV-Congo_8-156 were explored with bioinformatics tools like PROTPARAM, SOPMA, SWISS-MODEL and PROCHECK. Using molecular docking in PyRx, we evaluated the binding affinities of these compounds with MPXV-Congo_8-156 and identified the top five candidates ranging from - 9.2 to - 8.8kcal/mol. ADMET analysis indicated that all five compounds were safer alternatives, showing no AMES toxicity or carcinogenicity in toxicological assessments. Molecular dynamics (MD) simulations, conducted for 100ns each, confirmed the docking interactions of the top five compounds alongside the control (Cidofovir), validating their potential as MPXV inhibitors. The compounds with PubChem CID numbers 4061636, 4422538, 3583576, 4856107 and 4800629 demonstrated strong support in terms of root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA) value, hydrogen bond analysis, and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis. Thus, our investigation identified these five compounds as promising inhibitors of MPXV, offering potential therapeutic avenues. However, further in vivo studies are necessary to validate our findings.

Structural dynamics of a model of amorphous silicon

We perform extensive simulations and systematic statistical analyses on the structural dynamics of a model of amorphous silicon. The simulations follow the dynamics introduced by Wooten, Winer and Weaire: the energy is obtained with the Keating potential, and the dynamics consists of bond transpositions proposed at random locations and accepted with the Metropolis acceptance ratio. The structural quantities we track are the variations in time of the lateral lengths (Lx, Ly, Lz) of the cuboid simulation cell. We transform these quantities into the volume V and two aspect ratios B1 and B2. Our analysis reveals that at short times, the mean squared displacement (MSD) for all of them exhibits normal diffusion. At longer times, they cross over to anomalous diffusion (AD), with a temperature-dependent anomalous exponent α<1. We analyze our findings in the light of two standard models in statistical physics that feature anomalous dynamics, viz., continuous time random walker (CTRW) and fractional Brownian motion (fBm). We obtain the distribution of waiting times, and find that the data are consistent with a stretched-exponential decay. We also show that the three quantities, V, B1 and B2 exhibit negative velocity autocorrelation functions. These observations together suggest that the dynamics of the material belong to the fBm class.

Exploring Bryophyllum pinnatum compounds as potential inhibitors for Vespula vulgaris allergen proteins: A systematic computational approach

Vespula vulgaris (V. vulgaris), commonly known as the common wasp, poses a significant health threat due to its venom-induced allergic reactions. This research focused on the exploration of bioactive compounds from Bryophyllum pinnatum as potential inhibitors for V. vulgaris allergen proteins, including Phospholipase A1 (Ves V1), Hyaluronoglucosaminidase (Ves V2), and Antigen 5 (Ves V5). Through a multidisciplinary approach involving literature reviews, molecular docking analyses, ADMET assessments and Molecular Dynamics Simulations (MDS) of 100ns we identified two promising drug candidates from four bioactive compounds- Bryophyllin A, Bryophyllin B, Bryotoxin A, and Bryotoxin B of Bryophyllum pinnatum. Molecular docking results revealed strong binding interactions, with Bryophyllin B and Bryotoxin A consistently exhibiting the highest affinity (−9.6 kcal/mol and −10.0 kcal/mol) across the allergen proteins. ADMET analyses highlighted Bryophyllin B as a favorable candidate, showing high absorption (HIA: 92.1 %), minimal metabolic interactions (CYP1A2: No), and a low toxicity profile (LD50 (rat): 2.431). MDS analysis revealed Bryophyllin B and Bryotoxin A as promising drug inhibitors, exhibiting the highest binding stability with the allergen proteins of V. vulgaris, as indicated by the lowest Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (RG) values and highest protein-ligand contacts. Our study provides valuable insights into the therapeutic potential of Bryophyllum pinnatum compounds as inhibitors for V. vulgaris allergen proteins having two promising candidates- Bryophyllin B and Bryotoxin A.

Exploring the Structural Insights of Thermostable Geobacillus esterases by Computational Characterization.

This study conducted an in silico analysis of two biochemically characterized thermostable esterases, Est2 and Est3, from Geobacillus strains. To achieve this, the amino acid sequences of Est2 and Est3 were examined to assess their biophysicochemical properties, evolutionary connections, and sequence similarities. Three-dimensional models were constructed and validated through diverse bioinformatics tools. Molecular dynamics (MD) simulation was employed on a pNP-C2 ligand to explore interactions between enzymes and ligand. Biophysicochemical property analysis indicated that aliphatic indices and theoretical T m values of enzymes were between 82-83 and 55-65 °C, respectively. Molecular phylogeny placed Est2 and Est3 within Family XIII, alongside other Geobacillus esterases. DeepMSA2 revealed that Est2, Est3, and homologous sequences shared 12 conserved residues in their core domain (L39, D50, G53, G55, S57, G92, S94, G96, P108, P184, D193, and H223). BANΔIT analysis indicated that Est2 and Est3 had a significantly more rigid cap domain compared to Est30. Salt bridge analysis revealed that E150-R136, E124-K165, E137-R141, and E154-K157 salt bridges made Est2 and Est3 more stable compared to Est30. MD simulation indicated that Est3 exhibited greater fluctuations in the N-terminal region including conserved F25, cap domain, and C-terminal region, notably including H223, suggesting that these regions might influence esterase catalysis. The common residues in the ligand-binding sites of Est2-Est3 were determined as F25 and L167. The analysis of root mean square fluctuation (RMSF) revealed that region 1, encompassing F25 within the β2-α1 loop of Est3, exhibited higher fluctuations compared to those of Est2. Overall, this study might provide valuable insights for future investigations aimed at improving esterase thermostability and catalytic efficiency, critical industrial traits, through targeted amino acid modifications within the N-terminal region, cap domain, and C-terminal region using rational protein engineering techniques.

Dissipation behaviors in submerged beam-vibrated granular systems

This study investigates intruder dynamics within granular systems, focusing on energy dissipation and phase transitions influenced by beam vibrations. Using a granular-beam experimental setup and discrete element method (DEM) simulations, we explore the dynamic responses of a simply supported beam in a granular medium under various excitation conditions. Our results reveal distinct granular phase states and their evolution pathways, driven by changes in excitation amplitude and frequency, which significantly affect energy dissipation. Key findings include the identification of vortical and disordered fluidization states that correlate with extremes in energy dissipation, underscoring the importance of characteristic lengths and times in characterizing these transitions. Additionally, amplitude-frequency characteristics and mean squared displacement (MSD) analyses link microscale particle behavior with macroscale beam dynamics, providing insights into the mechanisms of energy dissipation and dynamic heterogeneity. This research enhances our understanding of granular system mechanics, offering implications for the design and optimization of engineering applications across various fields.

Mechanical and tribological properties of layered epoxy coatings synergistically enhanced by graphene and polytetrafluoroethylene: Molecular dynamics simulations and experimental verification

Epoxy resin coatings have high adhesion properties and excellent chemical resistance, and are widely used in the fields of ships, automobiles and electronic appliances. However, the shortcomings of epoxy resin, such as high brittleness, poor thermal stability and insufficient abrasion resistance, seriously affect the durability of the coating. In this paper, the mechanisms of mechanical and tribological properties of graphene (Gr) and polytetrafluoroethylene (PTFE) synergistically reinforced epoxy resin (EP) double layer coatings (with pure epoxy resin as the bottom layer) on Cu substrates were investigated by molecular dynamics simulations. The modeling includes pure epoxy double layer coating (Pure EP-EP), PTFE reinforced epoxy double layer coating (PTFE/EP-EP), and graphene and PTFE synergistically reinforced epoxy double layer coating (Gr/PTFE/EP-EP). The counter frictional part for these coatings is Cu metal. The simulation results show that by analyzing the interaction energy between the coating and the Cu substrate, the double layer coating with Pure EP as the bottom layer is found to have a better adsorption capacity, which can effectively extend the service life of the coating, compared with those with PTFE/EP or Gr/PTFE/EP as bottom layer. By calculating the shear modulus, Young's modulus and bulk modulus of the Gr/PTFE/EP-EP coating, the synergistic enhancement mechanism of the mechanical properties of the Gr/PTFE/EP-EP coating was revealed. In particular, the PTFE/EP-EP coating exhibited a reduction in mechanical properties and the mechanical property simulation results were verified experimentally. Compared with the Pure EP-EP double layer coating, the PTFE/EP-EP and Gr/PTFE/EP-EP double layer coatings showed a reduction in friction coefficient of 9.52 % and 23.81 %, wear rate of 46.69 % and 76.63 %, and mean square displacements (MSD) of 22.4 % and 81.34 %, respectively. The synergistic effect of Gr and PTFE on the tribological performance of Gr/PTFE/EP-EP coatings was better than that of PTFE/EP-EP coatings with PTFE only. The interaction of Gr and PTFE with EP was analyzed by comparing the changes in radius distribution function (RDF), relative concentration, temperature and velocity in the thickness direction of PTFE/EP-EP coatings and Gr/PTFE/EP-EP coatings, which further revealed the synergistic enhancement mechanism by Gr and PTFE.

Discovering novel targets of abscisic acid using computational approaches

Abscisic acid (ABA) is a crucial plant hormone that is naturally produced in various mammalian tissues and holds significant potential as a therapeutic molecule in humans. ABA is selected for this study due to its known roles in essential human metabolic processes, such as glucose homeostasis, immune responses, cardiovascular system, and inflammation regulation. Despite its known importance, the molecular mechanism underlying ABA's action remain largely unexplored. This study employed computational techniques to identify potential human ABA receptors. We screened 64 candidate molecules using online servers and performed molecular docking to assess binding affinity and interaction types with ABA. The stability and dynamics of the best complexes were investigated using molecular dynamics simulation over a 100 ns time period. Root mean square fluctuations (RMSF), root mean square deviation (RMSD), solvent-accessible surface area (SASA), radius of gyration (Rg), free energy landscape (FEL), and principal component analysis (PCA) were analyzed. Next, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) method was employed to calculate the binding energies of the complexes based on the simulated data. Our study successfully pinpointed four key receptors responsible for ABA signaling (androgen receptor, glucocorticoid receptor, mineralocorticoid receptor, and retinoic acid receptor beta) that have a strong affinity for binding with ABA and remained structurally stable throughout the simulations. The simulations with Hydralazine as an unrelated ligand were conducted to validate the specificity of the identified receptors for ABA. The findings of this study can contribute to further experimental validation and a better understanding of how ABA functions in humans.

Anomalous diffusion in external-force-affected deterministic systems.

This study investigates the impact of external forces on the movement of particles, specifically focusing on a type of box piecewise linear map that generates normal diffusion akin to Brownian motion. Through numerical methods, the research delves into the effects of two distinct external forces: linear forces linked to the particle's current position and periodic sinusoidal forces related to time. The results uncover anomalous dynamical behavior characterized by nonlinear growth in the ensemble-averaged mean-squared displacement (EAMSD), aging, and ergodicity breaking. Notably, the diffusion pattern of particles under linear external forces resembles an Ehrenfest double urn model, with its asymptotic EAMSD coinciding with the Langevin equationunder linear potential. Meanwhile, particle movement influenced by periodic sinusoidal forces corresponds to an inhomogeneous Markov chain, with its external force amplitude and diffusion coefficient function exhibiting a "multipeak" fractal structure. The study also provides insights into the formation of this structure through the turnstiles dynamics.

QSAR, ADMET, molecular docking, and dynamics studies of 1,2,4-triazine-3(2H)-one derivatives as tubulin inhibitors for breast cancer therapy

Breast cancer remains a leading cause of cancer-related deaths among women globally, necessitating the development of more effective therapeutic agents with minimal side effects. This study explores novel 1,2,4-triazine-3(2H)-one derivatives as potential inhibitors of Tubulin, a pivotal protein in cancer cell division, highlighting a targeted approach in cancer therapy. Using an integrated computational approach, we combined quantitative structure–activity relationship (QSAR) modeling, ADMET profiling, molecular docking, and molecular dynamics simulations to evaluate and predict the efficacy and stability of these compounds. Our QSAR models, developed through rigorous statistical analysis, revealed that descriptors such as absolute electronegativity and water solubility significantly influence inhibitory activity, achieving a predictive accuracy (R2) of 0.849. Molecular docking studies identified compounds with high binding affinities, particularly Pred28, which exhibited the best docking score of − 9.6 kcal/mol. Molecular dynamics simulations conducted over 100 ns provided further insights into the stability of these interactions. Pred28 demonstrated notable stability, with the lowest root mean square deviation (RMSD) of 0.29 nm and root mean square fluctuation (RMSF) values indicative of a tightly bound conformation to Tubulin. The novelty of this work lies in its methodological rigor and the integration of multiple advanced computational techniques to pinpoint compounds with promising therapeutic potential. Our findings advance the current understanding of Tubulin inhibitors and open avenues for the synthesis and experimental validation of these compounds, aiming to offer new solutions for breast cancer treatment.

Exploring superionic conduction in lithium oxyhalide solid electrolytes considering composition and structural factors

Lithium (Li) oxyhalides have emerged as promising solid electrolyte candidates for all-solid-state batteries (ASSBs) due to their superior ionic conductivity and excellent cathode capability. However, the mechanism of Li transport in oxyhalides has remained unclear due to the complex nature of these compounds, which often comprise multiple phases such as crystalline and amorphous structures. Herein, a first-principles study using density functional theory and ab initio molecular dynamic simulation is performed to gain a theoretical insight into the structural behavior and conduction pathway in oxyhalide electrolytes. Li2.5ZrCl5.5O0.5 electrolyte, as a case of study, is comprehensively investigated by considering various phases. It’s revealed that the P3̅m1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\rm{P}}\\bar{3}{\\rm{m}}1$$\\end{document} phase is energetically more stable and exhibits one order of magnitude higher Li conductivity compared to the C2/m phase among potential crystalline phases (1.63 mS cm−1 versus 0.24 mS cm−1 at room temperature). Interestingly, an amorphous phase with even higher ionic conductivity (~40 mS cm−1) can be generated by creating LiCl-deficient Li-Zr-O-Cl compounds. The remarkably high ionic conductivity suggests that the amorphous structure is likely the dominant conducting pathway, facilitating fast Li transport due the weak bonding between Li and other atoms. Cl anion mobility is also observed in the amorphous phase through mean square displacement (MSD) calculation, although further analyses revealed this to be localized vibration. This study sheds light on the nature of oxychloride structures and promotes a deeper understanding of the superionic conduction mechanism in oxychlorides, which will contribute to the development of advanced solid electrolytes and ASSBs.

Exploring the sedative properties of natural molecules from hop cones (Humulus lupulus) as promising natural anxiolytics through GABA receptors and the human serotonin transporter.

This research work aimed to identify the main components that are responsible for the sedative properties of hop cones and allocate their targets. This investigation was performed through molecular docking, molecular dynamic simulations, root mean square fluctuation (RMSF) analysis, and DFT calculation techniques. The tested compounds from Humulus lupulus were compared to diazepam and paroxetine. Molecular docking showed that two-thirds of the compounds had a good affinity to gamma-aminobutyric acid (GABA), outperforming diazepam, while only three surpassed paroxetine on the SERT. Compounds 3,5-dihydroxy-4,6,6-tris(3-methylbut-2-en-1-yl)-2-(3-methylbutanoyl)cyclohexa-2,4-dien-1-one (5) and (S,E)-8-(3,7-dimethylocta-2,6-dien-1-yl)-5,7-dihydroxy-2-(4-hydroxyphenyl)chromen-4-one (15) showed stable binding and favorable energy parameters, indicating their potential for targeting GABA receptors and the SERT. This study provides a basis for future clinical research on these promising compounds.

Effect of Additives on the Morphology of γ-Aminobutyric Acid Crystals.

The effect of surfactant, polymer, and tailor-made additives on the crystallization of γ-aminobutyric acid (GABA) was studied in this work. Cooling crystallization of GABA in water yielded plate-like crystals. In the presence of sodium stearate, polyhedral block-like crystals of GABA were obtained. Hydroxyethyl cellulose (HEC) led to rod-like crystals, in which the morphology was associated with additive concentrations. Six kinds of amino acids were used as tailor-made additives, and they exhibit different influences on crystal shape and size. The induction time of GABA was determined in the absence and presence of additives. The results showed that sodium stearate promoted nucleation, while HEC, l-Lysine, l-histidine, and l-tyrosine inhibited nucleation. Crystal face indexing, Hirshfeld surface analysis, and molecular dynamics (MD) simulation in aqueous solution-crystal systems were carried out to investigate the affecting factors of different crystal faces. The polymer additive was selected as an example during MD simulation to calculate intermolecular interactions between the crystal face and solvent or additive. The effect of the additive on the mobility of the solute in solution was also evaluated by mean-square displacement. The additive offers an effective approach for changing crystal morphology and particle size and adapting it to different production requirements.

A structural and biochemical approach to effect of temperature and pH on the Molten Globule phenomenon in a thermophilic protease: Molecular dynamics simulation, fluorescence spectroscopy and circular dichroism

Proteins in the molten globule (MG) stage have a reasonably stable secondary structure content, but changes in side-chain packing cause a noticeable decrease in the number of tertiary structures. Here, we investigated serine protease as a suitable model to study the folding route and characteristics of a protein in the MG state. Upon induction with IPTG, the protein exhibited a molecular weight of 42 kDa and achieved a final concentration of 1.7 mg/mL after the concentration process. Serine protease's intrinsic and extrinsic fluorescence was examined in the pH range of 1–12 using fluorescence spectroscopy with maximum intrinsic fluorescence in 335 nm and a blue shift in 510 nm for extrinsic fluorescence. It was suggested that the protein transitions probably to an MG state at pH 3. Evidences showed that serine protease's secondary structure using far-UV circular dichroism (CD) showed a little shift in the MG state intermediate, pH 3, relative to the original state, pH 8, which is typical for MG. Maximum decreases was observed in 228 to 300 nm for UV-near CD. Also revealed a notable alteration in the pH 3 of the enzyme compared to pH 8, which is the pH at which the protein takes on its natural structure. By using acrylamide to quench the fluorescence, the Stern-Volmer constant (KSV) was determined at pH values of 8 and 3, yielding values of 20 and 14 M−1, respectively. This is likely correlated with an increase in the enzyme's molecular volume in the MG state. Molecular dynamics (MD) simulation showed that although the thermal stability of this enzyme at 90° was confirmed in the Root-Mean-Square-Deviation (RMSD), Root-Mean-Square-Fluctuation (RMSF), Radius of gyration (Rg) as well as Solvent-Accessible-Surface-Area (SASA) graphs, but pH 3 may significantly disturb the tertiary structure and secondary structure. These in-silico results may also be analyzed in line with the occurrence of MG at pH 3.