Molecular Dynamics Simulations Research Articles

Particle topology-regulated relaxation dynamics in cluster-ordering.

The granular materials of soft particles (SPs) demonstrate unique viscoelasticity distinct from general colloidal and polymer systems. Exploiting dynamic light scattering measurements, together with molecular dynamics simulations, we study the diffusive dynamics of soft particle clusters (SPCs) with spherical and cylindrical brush topologies, respectively, in the melts of SPs. A topologically constrained relaxation theory is proposed by quantitatively correlating the relaxation time to the topologies of the SPCs, through the mean free space (Va) of tethered SPs in the cluster. The tethered SPs in SPCs are crowded by SPs of the melts to form the cage zones, and the cooperative diffusion of the tether SPs in the zones is required for the diffusive motion of SPCs. The cage zone serves as an entropic barrier for the diffusion of SP clusters, while its strength is determined by Va. Three characteristic modes can be confirmed: localized non-diffusive mode around critical Va, diffusive mode with Va deviating far from the critical value, and a sub-diffusive mode as an interlude between two limits. Our studies raise attention to the emergent physical properties of materials based on SPs via a topological design while opening new avenues for the design of soft structural materials.

Multiscale modeling of CO2 capture in dicationic ionic liquids: Evaluating the influence of hydroxyl groups using DFT-IR, COSMO-RS, and MD simulation methods.

This work employs a combination of density functional theory-infrared (IR), conductor-like screening model for real solvents (COSMO-RS), and molecular dynamic (MD) methods to investigate the impact of hydroxyl functional groups on CO2 capture within dicationic ionic liquids (DILs). The COSMO-RS reveals that hydroxyl groups in DILs reduce the macroscopic solubility of CO2 but improve the selectivity of CO2 over CO, H2, and CH4 gases. Quantum methods in the gas phase and MD simulations in the liquid phase were conducted to delve deeper into the underlying mechanisms. The IR spectrum analysis confirms red shifts in CO2's asymmetric stretching mode and blue shifts in the CR-HR bond of the dication, indicating CO2-DIL interactions and the weakening of the anion-cation interactions caused by the presence of CO2. The results show that the positioning of anions around hydroxyl groups and HR atoms in rings inhibits the proximity of CO2 molecules, causing the hydrogen atoms within methylene groups to accumulate CO2. van der Waals forces were found to dominate the interaction between ions and CO2. The addition of hydroxyl groups strengthens the electrostatic interactions and hydrogen bonds between dications and anions. The stronger interaction energy between ions in [C5(mim)2-(C2)2(OH)2][NTf2]2 limits the displacement of CO2 molecules within this DIL compared to [C5(mim)2-(C4)2][NTf2]2. Compared to [C5(mim)2-(C4)2][NTf2]2, [C5(mim)2-(C2)2(OH)2][NTf2]2 exhibits stronger ion-ion interactions, higher density, and reduced free volume, resulting in a reduction in CO2 capture. These results provide significant insights into the intermolecular interactions and vibrational properties of CO2 in DIL complexes, emphasizing their significance in developing efficient and sustainable strategies for CO2 capture.

Confined and spontaneously transformed oxidation structures due to the intrinsic heterogeneous surface morphology of C3N monolayer.

Identifying the oxidation structure of two-dimensional interfaces is crucial to improve surface chemistry and electronic properties. Beyond graphene with only phenyl rings, a novel carbon-nitrogen material, C3N, presents an intrinsic heterogeneous surface morphology where each phenyl ring is encircled by six nitrogen atoms, yet its atomistic oxidation structure remains unclear. Here, combining a series of density functional theory calculations and abinitio molecular dynamics simulations, we demonstrate that thermodynamically favorable oxidation loci are confined to the phenyl ring, and kinetic transformations of oxidation structures are feasible along the phenyl ring, whereas those toward nitrogen atoms are proven to be extremely difficult. These results are attributed to the lower barrier of oxygen atom migration along the phenyl ring, while the significantly high barriers toward nitrogen atoms are due to the heterogeneous potential energy surface for oxygen-C3N interaction. This work highlights the significance of surface morphology on the characteristics of oxidation structure, offering insights into tunable electronic properties via confined interfacial oxidation.

Three-metal ion mechanism of cross-linked and uncross-linked DNA polymerase β: A theoretical study.

In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by β-elimination. In addition, the polymerase activity of Polβ employs the "three-metal ion mechanism" instead of the long-standing "two-metal ion mechanism" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the "three-metal ion mechanism" vs the "two-metal ion mechanism" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ's catalytic mechanism provides valuable insights into DNA replication and damage repair.

Molecular dynamic investigation for Roco4 kinase inhibitor as treatment options for parkinsonism.

Parkinson's disease is a neurodegenerative condition characterized by the degeneration of dopaminergic neurons, resulting in motor disabilities such as rigidity, bradykinesia, postural instability, and resting tremors. While the exact cause of Parkinson's remains uncertain, both familial and sporadic forms are often associated with the G2019S mutation found in the kinase domain of LRRK2. Roco4 is an analogue of LRRK2 protein in Dictyostelium discoideum which is an established model organism to investigate LRRK2 inhibitors. In this study, the potential treatment of Parkinson's was explored by inhibiting the activity of the mutated LRRK2 protein using Roco4 as the base protein structure. Mongolicain-A and Bacoside-A exhibited significant selectivity towards the G2019S mutation, displaying a binding affinity of - 12.3 Kcal/mol and - 11.4 Kcal/mol respectively. Mongolicain-A demonstrated increased specificity towards Roco4, while Bacoside-A demonstrated significant binding affinity to all 34 kinases proteins alike. The Molecular Dynamics Studies (MDS) results strongly suggests that Mongolicain-A is a significant inhibitor of Roco4 kinase. ADMET and drugability analysis also suggests that among the two best ligands, Mongolicain-A demonstrates significant physicochemical properties to be suitable for best drug like molecule. Based on the in-silico molecular docking, molecular dynamic simulation, ADMET and drugability analyses, it is strongly suggested that, Mongolicain-A could be a potential candidate for treatment and management of Parkinson's disease via inhibition of LRRK2 protein. Further in-vitro and in-vivo investigations are in demand to validate these findings. To identify potential inhibitors, 3069 phytochemicals were screened using molecular docking via AutoDock Vina. Molecular Dynamics Simulation was carried out using GROMACS 2022.2 for a duration of 100ns per complex to study the stability and inhibition potential of the protein ligand complexes. ADMET analysis was carriedout using Molinspiration and preADMET web tool.

Formation of Polyimide Membranes via Non-Solvent Induced Phase Separation: Insight from Molecular Dynamics Simulations.

Molecular dynamics simulations were applied to investigate the formation of P84 polyimide membranes through the non-solvent induced phase separation (NIPS) process, considering two scenarios: one using a conventional organic solvent like n-methyl-2-pyrrolidone (NMP) and the other a greener alternative, γ-butyrolactone (GBL), with water serving as the non-solvent. Different compositions of polymer solutions were established along the binodal boundaries of the respective systems, derived from experimental cloud point data on the ternary phase diagram. The resulting polymer membranes were analyzed and compared in terms of their morphology. The wettability of their surfaces was notably affected by the polymer content in the initial casting solution and demonstrated a correlation with the Brunauer-Emmet-Teller (BET) specific surface area of the associated polymer nanostructures. The GBL solvent systems produced porous polymers qualitatively similar to those obtained with NMP, albeit with slightly narrower pore size distributions.

Computational Exploration of Naturally Occurring Flavonoids as TGF-β Inhibitors in Breast Cancer: Insights from Docking and Molecular Dynamics Simulations and In-vitro Cytotoxicity Study.

Breast cancer is a global health concern, demanding innovative treatments. Targeting the Transforming Growth Factor-beta (TGF-β) signaling pathway, pivotal in breast cancer, is a promising approach. TGF-β inhibits proliferation via G1 phase cell cycle arrest, acting as a suppressor initially, but in later stages, it promotes progression by enhancing motility, invasiveness, and metastasis formation. This study explores naturally occurring flavonoids' interactions with TGF-β. Using molecular docking against the protein's crystal structure (PDB Id: 1PY5), Gossypin showed the highest docking score and underwent molecular dynamics simulation, revealing complex flexibility and explaining how flavonoids impede TGF-β signaling in breast cancer. ADMET predictions adhered to Lipinski's rule of Five. Insights into flavonoid-TGF-β binding offer a novel angle for breast cancer treatment. Flavonoids having a good docking score like gossypin, morin, luteolin and taxifolin shown potent cytotoxic effect on breast cancer cell line, MCF-7. Understanding these interactions could inspire flavonoid-based therapies targeting TGF-β to halt breast cancer growth. These findings pave the way for personalized, targeted breast cancer therapies, offering hope against this formidable disease.

Unraveling thermodynamic anomalies of water: A molecular simulation approach to probe the two-state theory with atomistic and coarse-grained water models.

Thermodynamic and dynamic anomalies of water play a crucial role in supporting life on our planet. The two-state theory attributes these anomalies to a dynamic equilibrium between locally favored tetrahedral structures (LFTSs) and disordered normal liquid structures. This theory provides a straightforward, phenomenological explanation for water's unique thermodynamic and dynamic characteristics. To validate this two-state feature, it is critical to unequivocally identify these structural motifs in a dynamically fluctuating disordered liquid. In this study, we employ a recently introduced structural parameter (θavg) that characterizes the local angular order within the first coordination shell to identify these LFTSs through molecular dynamics simulations. We employ both realistic water models with a liquid-liquid critical point (LLCP) and a coarse-grained water model without an LLCP to study water's anomalies in low-pressure regions below 2 kbar. The two-state theory consistently describes water's thermodynamic anomalies in these models, both with and without an LLCP. This suggests that the anomalies predominantly result from the two-state features rather than criticality, particularly within experimentally accessible temperature-pressure regions.

The potential molecular markers of inflammatory response in KOA with AD based on single-cell transcriptome sequencing analysis and identification of ligands by virtual screening.

Alzheimer's disease (AD) and osteoarthritis (OA) are both senile degenerative diseases.Clinical studies have found that OA patients have a significantly increased risk of AD in their later life. This study hypothesized that chronic aseptic inflammation might lead to AD in KOA patients. However, current research has not yet clarified the potential mechanism between AD and KOA. Therefore, this study intends to use KOA transcriptional profiling and single-cell sequencing analysis technology to explore the molecular mechanism of KOA affecting AD development, and screen potential molecular biomarkers and drugs for the prediction, diagnosis, and prognosis of AD in KOA patients. It was found that the higher the expression of TXNIP, MMP3, and MMP13, the higher the risk coefficient of AD was. In addition, the AUC of TXNIP, MMP3, and MMP13 were all greater than 0.70, which had good diagnostic significance for AD. Finally, through the virtual screening of core proteins in FDA drugs and molecular dynamics simulation, it was found that compound Cobicistat could be targeted to TXNIP, Itc could be targeted to MMP3, and Isavuconazonium could be targeted to MMP13.To sum up, TXNIP, MMP3, and MMP13 are prospective molecular markers in KOA with AD, which could be used to predict, diagnose, and prognosis.

Engineering of Halide Methyltransferase BxHMT through Dynamic Cross-correlation Network Analysis.

Halide methyltransferases (HMTs) provide an effective way to regenerate S-adenosyl methionine (SAM) from S-adenosyl homocysteine and reactive electrophiles such as methyl iodide (MeI) or methyl toluene sulfonate (MeOTs). Compared with MeI, the cost-effective unnatural substrate MeOTs can be accessible directly from cheap and abundant alcohols, but shows only limited reactivity in SAM production. Herein, we developed a dynamic cross-correlation network analysis (DCCNA) strategy for quickly identifying hot spots influencing the enzyme's catalytic efficiency, and applied it to the evolution of HMT from Paraburkholderia xenovorans. Finally, the optimal mutant, M4 (V55T/C125S/L127T/L129P), exhibited remarkable improvements, with a specific activity of 4.08 U/mg towards MeOTs, representing an 82-fold increase compared to the wild-type (WT). Notably, M4 also demonstrated a positive impact on the catalytic ability with other methyl donors. The structural mechanism behind the enhanced enzyme activity was uncovered by molecular dynamics simulations. Our work not only contributes promising biocatalyst for the regeneration of SAM, but also offers a strategy for efficient enzyme engineering.

Solvation dynamics on the diffusion timescale elucidated using energy-represented dynamics theory.

Photoexcitation of a solute alters the solute-solvent interaction, resulting in the nonequilibrium relaxation of the solvation structure, often called a dynamic Stokes shift or solvation dynamics. Thanks to the local nature of the solute-solvent interaction, the characteristics of the local solvent environment dissolving the solute can be captured by the observation of this process. Recently, we derived the energy-represented Smoluchowski-Vlasov (ERSV) equation, a diffusion equation for molecular liquids, which can be used to analyze the solvation dynamics on the diffusion timescale. This equation expresses the time development for the solvent distribution on the solute-solvent pair interaction energy (energy coordinate). Since the energy coordinate can effectively treat the solvent flexibility in addition to the position and orientation, the ERSV equation can be utilized in various solvent systems. Here, we apply the ERSV equation to the solvation dynamics of 6-propionyl-2-dimethylamino naphthalene (Prodan) in water and different alcohol solvents (methanol, ethanol, and 1-propanol) for clarifying the differences of the relaxation processes among these solvents. Prodan is a solvent-sensitive fluorescent probe and is thus widely utilized for investigating heterogeneous environments. On the long timescale, the ERSV equation satisfactorily reproduces the relaxation time correlation functions obtained from the molecular dynamics (MD) simulations for these solvents. We reveal that the relaxation time coefficient on the diffusion timescale linearly correlates with the inverse of the translational diffusion coefficients for the alcohol solvents because of the Prodan-solvent energy distributions among the alcohols. In the case of water, the time coefficient deviates from the linear relationship for the alcohols due to the difference in the extent of importance of the collective motion between the water and alcohol solvents.

The synergy between the PscC subunits for electron transfer to the P840 special pair in Chlorobaculum tepidum.

The primary photochemical reaction of photosynthesis in green sulfur bacteria occurs in the homodimer PscA core proteins by a special chlorophyll pair. The light induced excited state of the special pair producing P840+ is rapidly reduced by electron transfer from one of the two PscC subunits. Molecular dynamics (MD) simulations are combined with bioinformatic tools herein to provide structural and dynamic insight into the complex between the two PscA core proteins and the two PscC subunits. The microscopic dynamic model involves extensive sampling at atomic resolution and at a cumulative time-scale of 22µs and reveals well defined protein-protein interactions. The membrane complex is composed of the two PscA and the two PscC subunits and macroscopic connections are revealed within a putative electron transfer pathway from the PscC subunit to the special pair P840 located within the PscA subunits. Our results provide a structural basis for understanding the electron transport to the homodimer RC of the green sulfur bacteria. The MD based approach can provide the basis to further probe the PscA-PscC complex dynamics and observe electron transfer therein at the quantum level. Furthermore, the transmembrane helices of the different PscC subunits exert distinct dynamics in the complex.

The Effect of Lipopolysaccharides on the Electrostatic Properties of Gram-Negative General Porins from Enterobacteriaceae.

We investigated, by using all-atom molecular dynamics simulations, the effect of the asymmetric outer membrane layer of Gram-negative bacteria, composed in the outer leaflet by polar/charged lipopolysaccharides (LPS), on the electrostatic properties of general porins from the Enterobacteriaceae family. These porins constitute the main path for the facilitated diffusion of polar antibiotics to cross the outer membrane. As model system we selected OmpK36 from Klebsiella pneumoniae, the ortholog of OmpC from Escherichia coli. This species presents high variability of amino acid composition of porins, with the effect to increase its resistance to the penetration of antibiotics. The various properties we analyzed seem to indicate that LPS acts as an independent layer without affecting the internal electrostatic properties of OmpK36. The only apparent effect at this time scale is the appearance of calcium ions, when present at moderate concentration in solution, inside the pore, though we noticed only increased fluctuations of the polarization density and slight changes on its average value.

Understanding the Modulatory Role of E2012 on the γ-Secretase-Substrate Interaction.

Allosteric modulation plays a critical role in enzyme functionality and requires a deep understanding of the interactions between the active and allosteric sites. γ-Secretase (GS) is a key therapeutic target in the treatment of Alzheimer's disease (AD), through its role in the synthesis of amyloid β peptides that accumulate in AD patients. This study explores the structure and dynamic effects of GS modulation by E2012 binding, employing well-tempered metadynamics and conventional molecular dynamics simulations across three binding scenarios: (1) GS enzyme with and without L458 inhibitor, (2) the GS-substrate complex together with the modulator E2012 in two different binding modes, and (3) E2012 interacting with a C99 substrate fragment. Our findings reveal that the presence of L458 induces conformational changes that contribute to stabilization of the GS enzyme dynamics, previously reported as a key factor that allowed the resolution of the cryo-EM structure and the enhanced binding of E2012. Furthermore, we identified the most favorable binding site for E2012 within the GS-substrate complex, uncovering significant modulatory effects and a complex network of interactions that influence the position of the substrate for catalysis. In addition, we explore a potential substrate-modulator binding before the formation of the enzyme-substrate complex. The insights gained from our study emphasize the importance of these interactions in the development of potential therapeutic interventions that target the functionality of the GS enzyme in AD.

Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein.

Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8nm, a setting that allowed > 0.8nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100kJ/mol·nm with a 0.01nm step size. Minimization was followed by 30ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10ns without any restraint using an integral time step of 1fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2nm.

Lanmodulin's EF 2-3 Domain: Insights from Infrared Spectroscopy and Simulations.

Lanmodulins are small, ∼110-residue proteins with four EF-hand motifs that demonstrate a picomolar affinity for lanthanide ions, making them efficient in the recovery and separation of these technologically important metals. In this study, we examine the thermodynamic and structural complexities of lanthanide ion binding to a 41-residue domain, EF 2-3, that constitutes the two highest-affinity metal-binding sites in the lanmodulin protein from Methylorubrum extorquens. Using a combination of circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC), two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics (MD) simulations, we characterize the metal binding capabilities of EF 2-3. ITC demonstrates that binding occurs between peptide and lanthanides with conditional dissociation constants (Kd) in the range 20-30 μM, with no significant differences in the Kd values for La3+, Eu3+, and Tb3+ at pH 7.4. In addition, CD spectroscopy suggests that only one binding site of EF 2-3 undergoes a significant conformational change in the presence of lanthanides. 2D IR spectroscopy demonstrates the presence of both mono- and bidentate binding configurations in EF 2-3 with all three lanthanides. MD simulations, supported by Eu3+ luminescence measurements, explore these results, suggesting a competition between water-lanthanide and carboxylate-lanthanide interactions in the EF 2-3 domain. These results underscore the role of the core helical bundle of the protein architecture in influencing binding affinities and communication between the metal-binding sites in the full-length protein.

Identification of 1,3,8-triazaspiro[4.5]decane-2,4-dione Derivatives as a Novel Delta Opioid Receptor-Selective Agonist Chemotype.

Delta opioid receptors hold potential as a target for neurological and psychiatric disorders, yet no delta opioid receptor agonist has proven efficacious in critical phase II clinical trials. The exact reasons for the failure to produce quality drug candidates for the delta opioid receptor is nuclear. However, it is known that certain delta opioid receptor agonists can induce seizures and exhibit tachyphylaxis. Several studies have suggested that those adverse effects are more prevalent in delta agonists that share the SNC80/BW373U86 chemotype. There is a need to find novel lead candidates for drug development that have improved pharmacological properties to differentiate them from the current failed delta agonists. Our objective in this study was to identify novel delta opioid receptor agonists. We used a beta-arrestin assay to screen a small GPCR-focused chemical library. We identified a novel chemotype of delta opioid receptor agonists, that appears to bind to the orthosteric site based of docking and molecular dynamic simulation. The most potent agonist hit compound is selective for the delta opioid receptor over a panel of 167 other GPCRs, is slightly biased towards G-protein signaling and has anti-allodynic efficacy in a complete Freund's adjuvant model of inflammatory pain in C57BL/6 male and female mice. The newly discovered chemotype contrasts with molecules like SNC80 that are highly efficacious beta-arrestin recruiters and may suggest this novel class of delta opioid receptor agonists could be expanded on to develop a clinical candidate drug. Significance Statement Delta opioid receptors are a clinical target for various neurological disorders, including migraine and chronic pain. Many of the clinically tested delta opioid agonists share a single chemotype, which carries risks during drug development. Through a small-scale high throughput screening assay, we identified a novel delta opioid receptor agonist chemotype, with anti-allodynic efficacy which may serve as alternative for the current clinical candidates.

Exploring the evolution mechanisms of indentation and scratching on diamond structural transformation based on molecular dynamics

Abstract Diamond, possessing high hardness and chemical stability, finds wide-ranging applications across various industries. However, during the friction process, a graphitization phenomenon may occur, which changes the mechanical properties of the diamond. In this study, molecular dynamics simulation was performed using SiC ball to investigate the influence of indentation depth and temperature on the graphitization transition of the diamond surface. The results showed that the dominant factor affecting the sp2 hybridization ratio during the indentation process was stress, while the temperature was the dominant factor during sliding. The results of this study can be used to understand the friction and wear behavior of diamonds and SiC ball and provide theoretical references for the industrial application of diamonds.

Design and expression of recombinant Xuanwei ham antioxidant peptide in Escherichia coli BL21

Xuanwei Ham Peptide (XHP) is a bioactive compound isolated and extracted from Xuanwei ham. It enhances the oxidative defense system by down-regulating CYP2E1 expression, reducing ROS production, and by activating the Nrf2/HO-1 pathway. In order to solve the problems of low yield, high cost and time-consuming separation process of active peptides from ham. In this study, we designed three peptide sequences derived from Xuanwei ham and expressed them recombinantly. The results showed that the peptides using flexible linker peptide ((GGGGS)2), rigid linker peptide ((EAAAK)2) linkage as well as the head-to-tail tandem linkage were successfully expressed in the E. coli expression system. Peptide monomers were released from the fusion proteins by formic acid cleavage and purified sequentially by Ni-IDA affinity chromatography, membrane filtration and RP-HPLC. The molecular weight of XHP was confirmed to be 717.35 by ESI-MS analysis. The results of the antioxidant activity of XHP showed that the hydroxyl radical scavenging rates of the three recombinant peptides were as high as 79.46%, 87.42%, and 53.60%, respectively. The hydroxyl radical activity of formic acid-cleaved XHP was reduced to 35.31%, but it showed good stability in heat, pH, metal ions and gastrointestinal digestion (GID). The molecular docking results showed that the docking of XHP to Keap1 protein was evaluated by five Molecular dynamics simulation with a maximum binding energy of -8.5 kcal/mol. This study provides references and ideas for the expression of active peptides, which can be widely used in the future can be used in the field of nutraceuticals, functional foods and pharmaceuticals.

Importance of the Electrostatic Correlations in Surface Tension of Hydrated Reline Deep Eutectic Solvent from Combined Experiments and Molecular Dynamics Simulations.

In this study, the surface tension and the structure of hydrated reline are investigated by using diverse methods. Initially, the surface tension displays a nonlinear pattern as water content increases, decreasing until reaching 45 wt %, then gradually matching that of pure water. This fluctuation is associated with strong electrostatic correlations present in pure reline, which decrease as more water is added. Changes in surface tension reflect a shift from charge layering in pure reline to an increased interfacial hydrogen bonding as the water content rises. This shift causes the segregation of urea molecules into the bulk phase and a gradual anchoring of water molecules to the air-reline interface. An interesting observation is the antisurfactant effect, where heightened interfacial anchoring results in an unexpected increase in real contribution of surface tension. This, along with weakened electrostatic correlations beyond 45 wt % due to reinforced interfacial hydrogen bonding, contributes to the complex behavior of surface tension observed in this study.