Changes In Molecular Interactions Research Articles

Small modifications of endo-functionalized cavities lead to large changes in molecular interaction in water

Small modifications of endo-functionalized cavities lead to large changes in molecular interaction in water

Impact of Pretreatment With Acid and Ultrasound on the Production and Characteristics of Goat Skin Gelatin

Goat skin is a potential raw material source for gelatin production using acid-ultrasound pretreatment. The objective of this study was to investigate the use of ultrasound in combination with acid pretreatment for the preparation of goat skin gelatin. Gelatin was extracted from goat skin using different pretreatments: acetic acid (T1), acetic acid followed by ultrasound (20 kHz and 750 W) (T2), and without pretreatment (T0). The results showed that the combination of acetic acid and ultrasound pretreatment significantly impacted the quality of the resulting gelatin. The study results showed an increase in yield (9.24 to 25.48%), hydroxyproline content (102.07 to 231.31 mg/g), gel strength (4.76 to 197.62 g), viscosity (6.80 to 48.00 cP), melting point (32.47 to 35.85 oC), EAI (18.24 to 23.58 m2/g), and ESI (24.90 to 62.63 min). However, there was a decrease in pH, the value of color L*, and turbidity. The SDS-PAGE patterns showed differences in molecular weight distribution due to variations in pretreatment. All gelatin samples exhibited α1 and α2 chains as the predominant components. Interestingly, the ultrasound effect highlighted the β-chain more boldly compared to other pretreatments. FTIR spectroscopy analysis shows changes in molecular interactions due to acetic acid pretreatment followed by ultrasound, which results in shifts in the Amide A, Amide B, Amide I, Amide II, and Amide III groups. Ultrasonic treatment caused more dense and disturbed structures in the sample. Therefore, the combination of acetic acid and ultrasound pretreatment yielded the superior properties of goat skin gelatin.

Advancing molecular understanding in high moisture extrusion for plant-based meat analogs: Challenges and perspectives

In recent years, meat analogs based on plant proteins have received increasing attention. However, the process of high moisture extrusion (HME), the method for their preparation, has not been thoroughly explored, particularly in terms of elucidating the complex interactions that occur during extrusion, which remain challenging. These interactions arise from the various ingredients added during HME, including proteins, starches, edible gums, dietary fibers, lipids, and enzymes. These ingredients undergo intricate conformational changes and interactions under extreme conditions of high temperature, pressure, and shear, ultimately forming the fibrous structure of meat analogs. This review offers a overview of these ingredients and the molecular interaction changes they undergo during the extrusion process. Additionally, it delves into the major molecular interactions such as disulfide bonding, hydrogen bonding, and hydrophobic interactions, providing detailed insights into each.

Exploring the rheological and thermal behavior of cowpea protein concentrate: Impact of pH and concentration

This study confronts challenges from global population growth, focusing on protein supply strains and the environmental impact of traditional animal sources. Delving into unexplored territory, this study investigates the combined effects of pH, concentration, and temperature on the rheological and thermal properties of cowpea protein concentrate (CPC). Steady-state and oscillatory rheological tests, along with differential scanning calorimetric analysis, were conducted to unveil the behavior of CPC solutions. The results revealed sensitivity to protein concentration and shear rate, especially at higher concentrations (>10%), and pH emerged as a critical factor, significantly influencing shear stress and viscosity. The elastic and viscous components of alkaline CPC solutions exhibit weak gel behavior, influenced by both pH and frequency. Temperature-induced changes in viscosity and gelation highlight the interaction between thermal conditions and protein structures. The thermal cycle helps explain changes in molecular interactions induced by temperature, with pH playing a role in influencing gelatinization and denaturation. The denaturation temperature (Td) in the thermograms corresponds to vicilin fractions and emphasizes the prominence of denaturation and gelation at neutral pH, where Td was pH 7 > pH 9 > pH 11. Alkaline pH induced significant structural changes, resulting in a gelation onset temperature below the denaturation onset temperature. This study provides a deeper understanding into the rheological and thermal properties of CPC solutions, emphasizing the roles of concentration, pH, and temperature, useful for various steps of industrial processing, before and after thermal gelation. These findings are important for promoting the use of cowpea proteins in the food industry in response to the evolving needs of a growing global population.

Local temperature changes in molecular interactions

The local temperature in quantum mechanics is a non-univocal quantity; however, one can select a proper kinetic energy to compute it and obtain a physically consistent behavior. Herein, we study the local temperature and local temperature differences in atoms, molecules, and chemical interactions in a topographic fashion. Our results indicate that atomic temperatures can be defined at a given cut-off distance while maintaining qualitative periodicity. When two atoms in a molecule experience a bonding interaction, there exists a temperature decrease between the interacting species. This endows stability to the system by lowering the kinetic energy. Our findings also suggest that when two chemical species are weakly bonded, an isosurface reflects a temperature decrease and might serve as a criterion to identify and characterize weak interactions from a thermodynamic viewpoint.

Hypothalamic FTO promotes high-fat diet-induced leptin resistance in mice through increasing CX3CL1 expression

Long-term consumption of a high-fat diet (HFD) disrupts energy homeostasis and leads to weight gain. The fat mass and obesity-associated (FTO) gene has been consistently identified to be associated with HFD-induced obesity. The hypothalamus is crucial for regulating energy balance, and HFD-induced hypothalamic leptin resistance contributes to obesity. FTO, an N6-methyladenosine (m6A) RNA methylation regulator, may be a key mediator of leptin resistance. However, the exact mechanisms remain unclear. Therefore, the present study aims to investigate the association between FTO and leptin resistance. After HFD or standard diet (SD) feeding in male mice for 22 weeks, m6A-sequencing and western blotting assays were used to identify target genes and assess protein level, and molecular interaction changes. CRISPR/Cas9 gene knockout system was employed to investigate the potential function of FTO in leptin resistance and obesity. Our data showed that chemokine (C-X3-C motif) ligand 1 (CX3CL1) was a direct downstream target of FTO-mediated m6A modification. Furthermore, upregulation of FTO/CX3CL1 and suppressor of cytokine signaling 3 (SOCS3) in the hypothalamus impaired leptin-signal transducer and activator of transcription 3 signaling, resulting in leptin resistance and obesity. Compared to wild-type (WT) mice, FTO deficiency in leptin receptor-expressing neurons of the hypothalamus significantly inhibited the upregulation of CX3CL1 and SOCS3, and partially ameliorating leptin resistance under HFD conditions. Our findings reveal that FTO involved in the hypothalamic leptin resistance and provides novel insight into the function of FTO in the contribution to hypothalamic leptin resistance and obesity.

The changes in molecular interaction and conformation of lysozyme mediated by ionic liquids

Using Ionic liquids（ILs）to regulate protein crystallization has attracted great attention, but the mechanism of ILs mediating crystallization is still unclear. Herein, we chose 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) and 1,3-dimethylimidazolium iodide ([C1mim]I) as additives to mediate lysozyme crystallization, and use situ Raman to track the conformational changes of lysozyme in solution. Meanwhile, molecular simulation was used to explore the binding between ILs and lysozyme molecules. The results demonstrated that the addition of ILs produced new characteristic peaks in Raman spectra, suggesting some changes to occur in solution structure. The changes of peaks at 1340 cm−1 and 1359 cm−1, and the enhancement of peak at 1450 cm−1 indicated the unfolding of lysozyme molecules. The quantitative analysis of amide Ⅰ band showed that the addition of ILs increased the β-sheet content in secondary structures. Molecular docking showed that [C4mim]Cl and [C1mim]I could both bind to the active site of lysozyme molecules, and the binding energy were −3.1 kcal/mol and −4.5 kcal/mol, respectively. Molecular dynamics results showed that [C4mim]Cl could stably bind to lysozyme molecules, while [C1mim]I left the active site after several ns, which means that [C4mim]Cl brought about stronger impact on interaction of lysozyme molecules than [C1mim]I in solution.

Molecular profile of metastasis, cell plasticity and EMT in pancreatic cancer: a pre-clinical connection to aggressiveness and drug resistance.

The metastasis is a multistep process in which a small proportion of cancer cells are detached from the colony to enter into blood cells for obtaining a new place for metastasis and proliferation. The metastasis and cell plasticity are considered major causes of cancer-related deaths since they improve the malignancy of cancer cells and provide poor prognosis for patients. Furthermore, enhancement in the aggressiveness of cancer cells has been related to the development of drug resistance. Metastasis of pancreatic cancer (PC) cells has been considered one of the major causes of death in patients and their undesirable prognosis. PC is among the most malignant tumors of the gastrointestinal tract and in addition to lifestyle, smoking, and other factors, genomic changes play a key role in its progression. The stimulation of EMT in PC cells occurs as a result of changes in molecular interaction, and in addition to increasing metastasis, EMT participates in the development of chemoresistance. The epithelial, mesenchymal, and acinar cell plasticity can occur and determines the progression of PC. The major molecular pathways including STAT3, PTEN, PI3K/Akt, and Wnt participate in regulating the metastasis of PC cells. The communication in tumor microenvironment can provide by exosomes in determining PC metastasis. The components of tumor microenvironment including macrophages, neutrophils, and cancer-associated fibroblasts can modulate PC progression and the response of cancer cells to chemotherapy.

Formation and characterization of konjac glucomannan/ethyl cellulose films by using ethanol and water as the solvents

Hydrophilic konjac glucomannan (KGM)/hydrophobic ethyl cellulose (EC) film was prepared in the ethanol/water environment. The film-forming solution and film properties were both characterized to analyze the molecular interaction changes. Although higher ethanol usage enhanced the stability of the film-forming solution, it did not benefit the film property improvement. The SEM images showed some fibrous structure on the air surface of the films, consistent with the XRD results. The changing trend of mechanical properties and the FTIR results suggested that both ethanol content and ethanol evaporation impacted the molecular interaction during the film formation. The surface hydrophobicity results indicated that the ethanol content could cause significant EC aggregation changes on the film surface only with high EC contents. The water vapor permeability results suggested that higher ethanol usage decreased the compactness of the films. Considering all results, the 20 % ethanol content and the weight ratio of KGM: EC = 7:3 were suggested for the film preparation due to the superior properties in most properties. This study contributed to the understanding of polysaccharide interaction in the ethanol/water environment and offered an alternative biodegradable packaging film.

Studies on the Prediction and Extraction of Methanol and Dimethyl Carbonate by Hydroxyl Ammonium Ionic Liquids.

The separation of dimethyl carbonate (DMC) and methanol is of great significance in industry. In this study, ionic liquids (ILs) were employed as extractants for the efficient separation of methanol from DMC. Using the COSMO-RS model, the extraction performance of ILs consisting of 22 anions and 15 cations was calculated, and the results showed that the extraction performance of ILs with hydroxylamine as the cation was much better. The extraction mechanism of these functionalized ILs was analyzed by molecular interaction and the σ-profile method. The results showed that the hydrogen bonding energy dominated the interaction force between the IL and methanol, and the molecular interaction between the IL and DMC was mainly Van der Waals force. The molecular interaction changes with the type of anion and cation, which in turn affects the extraction performance of ILs. Five hydroxyl ammonium ILs were screened and synthesized for extraction experiments to verify the reliability of the COSMO-RS model. The results showed that the order of selectivity of ILs predicted by the COSMO-RS model was consistent with the experimental results, and ethanolamine acetate ([MEA][Ac]) had the best extraction performance. After four regeneration and reuse cycles, the extraction performance of [MEA][Ac] was not notably reduced, and it is expected to have industrial applications in the separation of methanol and DMC.

Characterization of mutations modulating enhanced transmissibility of SARS-CoV-2 B.1.617+ (Delta) variant using In Silico tools

Since the beginning of the of SARS-CoV-2 (Covid-19) pandemic, variants of concern (VOC) have emerged taxing health systems worldwide. In October 2020, a new variant of SARS-CoV-2 (B.1.617+/Delta variant) emerged in India, triggering a deadly wave of Covid-19. Epidemiological data strongly suggests that B.1.617+ is more transmissible and previous reports have revealed that B.1.617+ has numerous mutations compared to wild type (WT), including several changes in the spike protein (SP). The main goal of this study was to use In Silico (computer simulation) techniques to examine mutations in the SP, specifically L452R and E484Q (part of the receptor binding domain (RBD) for human angiotensin-converting enzyme 2 (hACE2)) and P681R (upstream of the Furin cleavage motif), for effects in modulating the transmissibility of the B.1.617+ variant. Using computational models, the binding free energy (BFE) and H-bond lengths were calculated for SP-hACE2 and SP-Furin complexes. Comparison of the SP-hACE2 complex in the WT and B.1.617+ revealed both complexes have identical receptor-binding modes but the total BFE of B.1.617+ binding was more favorable for complex formation than WT, suggesting L452R and E484Q have a moderate impact on binding affinity. In contrast, the SP-Furin complex of B.1.617+ substantially lowered the BFE and revealed changes in molecular interactions compared to the WT complex, implying stronger complex formation between the variant and Furin. This study provides an insight into mutations that modulate transmissibility of the B.1.617+ variant, specifically the P681R mutation which appears to enhance transmissibility of the B.1.617+ variant by rendering it more receptive to Furin.

Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover.

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔCP‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme–substrate interactions and the global dynamics of the protein. We find that changes in ΔCP‡ and protein dynamics can be mapped to specific substrate–enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.

Evaluation of molecular interactions in binary mixtures comprising ethylene and di-ethylene glycol with ethyl lactate through thermophysical and spectroscopic studies

In this article, the study of molecular interactions in liquid systems containing industrially and biologically important solvents with minimal environmental damage has been done. Density (ρ) and refractive index (nD) of binary systems comprising ethyl lactate (EL) + ethylene glycol (EG) and di-ethylene glycol (DEG) at various mole fractions and T = (298.15 to 313.15) K along with pure components have been measured. The observed parameters were further used for determination of excess molar volumes (VmE), partial molar volumes (V¯m), excess partial molar volumes (V¯mE), deviations in refractive index (ΔϕnD) and deviations in molar refraction (ΔϕRM). Redlich-Kister coefficients along with standard deviations have been obtained by approximation of data to polynomial equation. The obtained VmE results have been investigated theoretically by means of Prigogine-Flory-Patterson (PFP) and Graph theories to estimate type and nature of interactions among constituent molecules which can be used to explain the changes in physicochemical properties of the mixtures. By analysing experimental data in light of PFP Theory, Interactional and characteristic pressure contributions have been found negative values for both the binary systems whereas free volume contribution possess positive sign. The structural variation of the components in the mixtures due to change in molecular interactions has been discussed by Graph theory. Fourier Transform InfraRed (FT-IR) studies have also been performed for pure and equimolar mixtures to enlighten the experimental outcomes. It confirmed the rupture of pre-existing bonding in lactate and the formation of new hydrogen bonds with glycols.

Protein nanofibril design via manipulation of hydrogen bonds

The process of amyloid nanofibril formation has broad implications including the generation of the strongest natural materials, namely silk fibers, and their major contribution to the progression of many degenerative diseases. The key question that remains unanswered is whether the amyloidogenic nature, which includes the characteristic H-bonded β-sheet structure and physical characteristics of protein assemblies, can be modified via controlled intervention of the molecular interactions. Here we show that tailored changes in molecular interactions, specifically in the H-bonded network, do not affect the nature of amyloidogenic fibrillation, and even have minimal effect on the initial nucleation events of self-assembly. However, they do trigger changes in networks at a higher hierarchical level, namely enhanced 2D packaging which is rationalized by the 3D hierarchy of β-sheet assembly, leading to variations in fibril morphology, structural composition and, remarkably, nanomechanical properties. These results pave the way to a better understanding of the role of molecular interactions in sculpting the structural and physical properties of protein supramolecular constructs.

Long – term storage effect on molecular interactions of biodiesels and blends

ABSTRACT In this era of fuel crisis, biodiesel is the better alternative to Petroleum Diesel (PD). In general, biodiesel is composed of Fatty acid Methyl Esters (FAME). In the present investigation, change in molecular interactions of two year long-term stored biodiesels and blends were studied by measuring ultrasonic parameters. The results were analyzed with respect to fatty acid profile of biodiesels. The biodiesels collected were Cotton Seed Oil Methyl Esters (CSOME) and Palm Stearin Methyl Esters (PSME). The CSOME biodiesel was rich in unsaturated FAME and PSME in saturated FAME. Five different blends of both the biodiesels with Petroleum Diesel (PD) in the volume percent of 10, 20, 30, 40, and 50 were prepared. The blends were stored for two years in their as it was condition at room temperature without interaction of light. The measurements have been done using an ultrasonic interferometer of fixed frequency of 2 MHz. The measured parameters were density, ultrasonic velocity, adiabatic compressibility, acoustic impedance and intermolecular free length. Sediments were formed in CSOME biodiesel blends only which was rich in unsaturated FAME. No sediment was formed in PSME blends. The highest decrease was found in adiabatic compressibility for 10% volume blends by 5.96% and 5.65% for CSOME and PSME biodiesels, respectively. The lowest increase was found in density for 10% volume blend by 0.13% for both biodiesels. The difference between large and small values was found highest for 10% volume blend of PSME biodiesel by 5.17% for adiabatic compressibility. Poor stability was noticed in low-level blends than high-level blends. Pure biodiesels were found more stable than blends. Strong molecular interactions were observed in low-level blends. Systematic trend in the variation of percent change in parameters with respect to blend level was found in both biodiesel blends.

Experimental Protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement

Protein dynamics covers multiple spatiotemporal scale processes, among which slow motions, not much understood even though they are underlying protein folding and protein functions. Protein slow motions are associated with structural heterogeneity, short-lived and poorly populated conformations, hard to detect individually. In addition, they involve collective motions of many atoms, not easily tracked by simulation and experimental devices. Here we propose a biophysical approach, coupling geometrical nanoconfinement and broadband dielectric spectroscopy (BDS), which distinguishes protein conformations by their respective molecular dynamics. In particular, protein-unfolding intermediates, usually poorly populated in macroscopic solutions are detected. The protein dynamics is observed under unusual conditions (sample nanoconfinement and dehydration) highlighting the robustness of protein structure and protein dynamics to a variety of conditions consistent with protein sustainability. The protein dielectric signals evolve with the temperature of thermal treatments indicating sensitivity to atomic and molecular interaction changes triggered by the protein thermal unfolding. As dipole fluctuations depend on both collective large-scale motions and local motions, the approach offers a prospect to track in-depth unfolding events.

Sub-second infrared broadband-laser single-shot phase-amplitude polarimetry of thin films.

We report on the first, to the best of our knowledge, sub-second, sub-mm2 infrared (IR) spectroscopic measurements of thin organic films employing a laser-based phase-amplitude polarimeter in reflection geometry. The polarimeter uses a broadband mid-IR quantum cascade laser tunable between 1318 cm-1 and 1765 cm-1, as well as a single-shot beam division scheme for simultaneous single-pulse phase and amplitude measurements. The instrument achieves 120 μm spatial and <0.5 cm-1 spectral resolution, while providing unrivaled performance in terms of acquisition times. Spectral measurements within 100 ms and single-wavelength tracking at 16 μs are now possible. Investigating the vibrational properties accessible in the mid-IR, the polarimeter was applied for monitoring changes in molecular interactions of a 150 nm thin myristic acid film during its thermal phase transition around 55°C.

Lipids alter microbial transport through intestinal mucus.

Mucus constitutes a protective layer which coats the gastrointestinal tract, controlling interactions of both commensal and pathogenic microbes with underlying tissues. Changes to the mucus barrier, for example due to altered mucin expression or external stimuli, may impact interactions with microbes and thus potentially contribute to altered gut homeostasis, onset of inflammation, or pathogen invasion. Food-associated stimuli, including lipids, have been shown to change mucus barrier properties and reduce transport of model drug carriers through mucus. Here, we explore the impact of lipids, specifically triglycerides in a model intestinal medium mimicking a fed state, on Escherichia coli (E. coli) transport through mucus by directly imaging swimming patterns and analyzing associated changes in mucus structure. Lipids in model fed state intestinal contents reduced E. coli speed and track linearity within mucus. These changes may be due in part to changes in molecular interactions within the mucus network as well as crowding of the mucus network by lipid emulsion droplets, which visibly stay intact in the mucus gel. In addition, observed physical interactions between bacteria and lipid structures may impact microbial speed and trajectories. As lipids are normal food components and thus represent safe, mild stimuli, these results support exploration of lipid-based strategies to alter the mucus barrier to control interactions with microbes and potentially prevent microbial invasion of underlying epithelium.

Functional Nano-Coating Materials by Michael Addition and Ring-opening Polymerization: Reactivity, Molecular Architecture and Refractive index

Understanding the molecular interaction and morphology of organic-inorganic hybrid materials is an important and fundamental assignment to develop novel high-performance materials. In this work, we developed two types of hybrid coating materials by using different silane coupling agents via Michael addition reaction and ring-opening polymerization. The changes in molecular interaction and morphology of the hybrid coatings due to chemical composition and curing temperature were studied by electron microscopy, spectroscopy and solid state 29Si nuclear magnetic resonance analysis. Fundamental differences were observed in HYBRID I and HYBRID II coatings during the nucleation stage that was dependent on the curing temperature. Higher curing temperature of the hybrid coatings resulted in improved uniformity and greater crystallinity of dispersed phases, and better control of the morphology compared with coatings cured at lower temperatures. The higher curing temperature provided more consistent nucleation sites for the growth of larger nanostructures of desired characteristics (e.g., size and surface features). There is great flexibility in synthesizingg these hybrid materials where different structure and morphology can be achieved to produce materials whose applications can range from adhesives to protective coatings. Refractive index results revealed that HYBRID I (90 °C) coating showed higher refractive index than HYBRID II (90 °C) coating.

Effects of ultrasonic/microwave-assisted treatment on the properties of corn distarch phosphate/corn straw cellulose films and structure characterization.

Edible films were casted using aqueous solutions of corn distarch phosphate (CDP, 3wt%) and corn straw cellulose (CSC, 0.5wt%). The effects of ultrasonic, microwave and ultrasonic/microwave-assisted treatment on mechanical properties and light transmittance, as well as the water vapour permeability (WVP) of edible films, were evaluated. It was found that corn distarch phosphate/corn straw cellulose (CDP/CSC) films treated using ultrasonic waves/microwaves for a certain condition has a distinct increase in tensile strength, elongation at break and light transmittance and a drastic decrease in WVP. Moreover, scanning electron microscopy demonstrated that the surface and cross-section morphology of CDP/CSC films after ultrasonic/microwave-assisted treatment were smoother, denser and without a notable phase separation compared with control films. The results of mechanical properties and barrier properties were in agreement with the changes in molecular interactions detected by Fourier transform infrared spectroscopy and X-ray diffraction analysis. These findings indicate that ultrasonic/microwave-assisted treatment can improve the application of biodegradable films.