Kinetic and thermodynamic-based studies on the interaction mechanism of novel R. roxburghii seed peptides against pancreatic lipase and cholesterol esterase

Pancreatic lipase (PL) and cholesterol esterase (CE) are vital digestive enzymes that regulate lipid digestion. Three bioactive peptides (LFCMH, RIPAGSPF, YFRPR), possessing enzyme inhibitory activities, were identified in the seed proteins of R. roxburghii. It is hypothesized that these peptides could inhibit the activities of these enzymes by binding to their active sites or altering their conformation. The results showed that LFCMH exhibited superior inhibitory activity against these enzymes compared to the other peptides. The inhibition mechanisms of the three peptides were identified as either competitive or mixed, according to inhibition models. Further studies have shown that peptides could bind to the active sites of enzymes, thus affecting their spatial conformation and restricting substrate entry into the active site. Molecular simulation further proved that hydrogen bonds and hydrophobic interactions played a vital role in the binding of peptides to enzymes. This study enriches our understanding of interaction mechanisms of peptides on PL and CE.

Luminescent carbon dots-rooted polysaccharide crosslinked hydrogel adsorbent for sensitive determination and efficient removal of Cu2

In this study, a novel luminescent carbon dot-rooted polysaccharide hydrogel (CDs@CCP hydrogel) was prepared by crosslinking cellulose, chitosan (CS), and polyvinyl alcohol (PVA) for simultaneous fluorescent sensing and adsorption of Cu2+. The crosslinking of these low-cost, polysaccharide polymers greatly enhance the mechanical strength of the composite hydrogel while making the polysaccharide-based adsorbent easy to reuse. This composite hydrogel exhibited an excellent adsorption capacity (124.7 mg∙g-1) for residual Cu2+ in water, as well as a sensitive and selective fluorescence response towards Cu2+ with a good linear relationship (R2 > 0.97) and a low detection limit (LOD) of 0.02 μM. The adsorption isotherms, adsorption kinetics, and thermodynamics studies were also conducted to investigate the adsorption mechanism. This composite hydrogel offers an efficient tool for simultaneous monitoring and treatment of Cu2+ from wastewater.

Insight into the promoted recrystallization and water distribution of bread by removing starch granule - surface and - associated proteins during storage

The influence of starch granule surface proteins (SGSPs) and starch granule-associated proteins (SGAPs) on bread retrogradation was investigated in a reconstituted dough system. The removal of both SGSPs and SGAPs resulted in poor bread qualities, decreasing specific volume and crumb porosity, leading to more baking loss and compact crumb structure. Particularly, removing SGSPs was effective in promoting the bread retrogradation. After 7 days of storage, the hardness of bread without SGSPs showed an increase of 353.34 g than the bread without SGAPs. Proton population and relaxation times exhibited that the absence of SGSPs significantly decreased the content of bound water from 11.51 % to 7.03 %, indicating lower water-holding capacity due to the loosen gelling structure. Compared to the control group, bread without SGSPs accelerated the starch recrystallinity by a reduction in soluble starch content, thereby increasing the retrogradation enthalpy and relative crystallinity through promoting the molecular reassociation in starch.

Thermal characterization and separation of whey proteins by differential scanning calorimetry

Most commercially available whey products contain a mixture of 6-7 whey proteins; however, there is an increased focus on using the individual whey proteins for their unique biological activities. Before extracting individual whey proteins for use, it is important to quantify how much of a particular protein is present in whey mixtures as well as if the protein is still structurally folded. We first characterized the denaturation temperature and enthalpy values for the six purified whey proteins at six pHs (3-9) and under ion chelation using a nano-differential scanning calorimeter (DSC). From the individual protein scans, we determined the optimal condition for detecting all 6 proteins on a single DSC scan was whey in an EDTA MOPs pH 6.7 buffer.

Design and analysis of self-priming extension DNA hairpin probe for miRNA detection based on a unified dynamic programming framework

MicroRNAs (miRNAs) are potential biomarkers for cancer diagnosis and prognosis, methods for detecting miRNAs with high sensitivity, selectivity, and stability are urgently needed. Various nucleic acid probes that have traditionally been for this purpose suffer several drawbacks, including inefficient signal-to-noise ratios and intensities, high cost, and time-consuming method establishment. Computing tools used for investigating the thermodynamics of DNA hybridization reactions can accurately predict the secondary structure of DNA and the interactions between DNA molecules. Herein, NUPACK was used to design a series of nucleic acid probes and develop a phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) signal amplification strategy, which enabled the ultrasensitive detection of miR-200a in serum samples. The free and binding energies of the DNA detection probes calculated using NUPACK, as well as the biological experimental results, were considered synthetically to select the best sequence and experimental conditions. A unified dynamic programming framework, NUPACK analysis and the experimental data, were complementary and improved the designed model in all respects. Our study demonstrates the feasibility of using computer technology such as NUPACK to simplify the experimental process and provide intuitive results.

Investigating the binding interaction of quinoline yellow with bovine serum albumin and anti-amyloidogenic behavior of ferulic acid on QY-induced BSA fibrils

Protein aggregation induces profound changes in the structure along with the conformation of the protein, and is responsible for the pathogenesis of a number of neurodegenerative conditions such as Huntington's, Creutzfeldt-Jacob, Type II diabetes mellitus, Alzheimer's, etc. Numerous multi-spectroscopic approaches and in-silico experiments were utilized to investigate BSA's biomolecular interaction and aggregation in the presence of quinoline yellow. The present research investigation evaluated the interaction of BSA with the food colorant (QY) at two different pH (7.4 and 2.0). The development of the BSA-QY complex was established with UV visible and fluorescence spectroscopy. The quenching of fluorescence upon the interaction of BSA with QY revealed the static nature of quenching mechanism. The Kb value obtained from our result is 4. 54 × 10-4 M-1. The results from the competitive site marker study infer that quinoline yellow is binding with the sub-domain IB of bovine serum albumin, specifically on site III. Three-dimensional fluorescence and synchronous fluorescence spectroscopy were applied for monitoring the alterations in the microenvironment of BSA upon the addition of quinoline yellow. The results from turbidity and RLS studies showed that higher concentrations of QY (80-400 µM) triggered bovine serum albumin (BSA) aggregation at pH 2.0. At pH 7.4, QY couldn't manage to trigger bovine serum albumin aggregation, perhaps because of the repulsion between negatively charged dye (QY) and anionic bovine serum albumin. The results from far-UV CD, Congo Red, and scanning electron microscopy implicate that the QY-induced aggregates exhibit amyloid fibril-like structures. Molecular docking results revealed that hydrophobic interactions, hydrogen bonding, and Pi-Sulfur interactions contribute to QY-induced aggregation of BSA. Further, the amyloid inhibitory potential of ferulic acid (FA), a phenolic acid on QY-induced aggregation of BSA, has also been assessed. The QY-induced amyloid fibrils are FA-soluble, as confirmed by turbidity, RLS, and far-UV CD studies. Far-UV CD results showed that FA retains α helix and inhibits cross β sheet formation when the BSA samples were pre-incubated with increasing concentrations of FA (0-500 µM). Our findings conclude that QY dye successfully stimulates BSA aggregation, but ferulic acid inhibits QY-induced aggregation of BSA. Thus, FA can serve as a therapeutic agent and can help in the treatment of various amyloid-related conditions.

Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid

In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M-1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.

Modulation of protein-ligand interactions in the presence of ZIF-8: Spectroscopy and molecular dynamics simulation

In this paper, we investigated the protein-ligand interactions in the presence of ZIF-8 using multi-spectroscopic approaches and molecular dynamics simulation. Fluorescence experiments and molecular docking results showed that ZIF-8 did not change the type of quenching and interaction force between ciprofloxacin (CIP) and human serum albumin (HSA), but made the binding constant of HSA-CIP to be smaller, suggesting that ZIF-8 maybe accelerate the dissociation of CIP from HSA-CIP complex. Moreover, the effect of ZIF-8 on the physiological function of HSA was explored. Multi-spectroscopic methods revealed that ZIF-8 did not significantly alter the microenvironment of amino acid groups, but cause a slight decrease in the content of α-helical conformation, and a sparse and flexible structure of the protein backbone. These peculiarities might lead to the diminution of HSA's ability to control drugs. In short, ZIF-8 might enhance drug effect due to affecting the binding of drugs to proteins. However, the present study is only a preliminary investigation of the suitability of ZIF-8 as a drug carrier in vitro, and subsequent in vivo experimental studies will be required to further confirm the idea.

Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications

Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics-Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.

Single-and double transition metal atoms anchored C2N as a high-activity catalyst for CO oxidation: A first-principles study

The oxidation of CO has attracted great interest in recent years due to its important role in enhancing the catalyst durability in fuel cells and solving the growing environmental problems caused by CO emissions. Consequently, the catalytic oxidation of CO at double non-noble metal atoms anchored C2N is investigated using density functional theory (DFT) computations. All the screened Ti@C2N and Ti2@C2N are thermodynamically stable based on their binding energy calculations. The electronic characteristics, the natural bond orbital analyses (NBO), Frontier orbital, statistical thermodynamics, projected densities of states (PDOS) characteristics, non-covalent interactions (NCI), and quantum theory of atoms in molecules (QTAIM) descriptors of these systems have been examined to analyze the interaction process. Our comparative study suggested that the newly predicted double-atom catalyst (Ti2@C2N) is highly active for CO oxidation, which is a useful guideline for further development. The calculated static first-order hyperpolarizability (βo) illustrated that the double-atom catalyst under investigation can be considered a potential candidate for non-linear optical behavior and could be used for NLO applications. CO oxidation on Ti2@C2N along the Eley-Rideal (ER) mechanism with a low energy barrier of 0.16 eV, which is smaller than the maximum energy barrier (0.73 eV) of CO oxidation along the Langmuir-Hinshelwood (LH) mechanism. Consequently, the ER mechanism is more favorable both thermodynamically and dynamically. This work can provide useful insights and guidelines for future theoretical and experimental investigations to promote the design and development of highly effective and low-cost non-precious-metal Ti2@C2N nanocatalysts towards CO oxidation at ambient temperature.

Responses to commentaries on "The gene: An appraisal"

The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.

Integrating biosorption and machine learning for efficient remazol red removal by algae-bacteria co-culture and comparative analysis of predicted models

This research investigates into the efficacy of algae and algae-bacteria symbiosis (ABS) in efficiently decolorizing Remazol Red 5B, a prevalent dye pollutant. The investigation encompasses an exploration of the biosorption isotherm and kinetics governing the dye removal process. Additionally, various machine learning models are employed to predict the efficiency of dye removal within a co-culture system. The results demonstrate that both Desmodesmus abundans and a composite of Desmodesmus abundans and Rhodococcus pyridinivorans exhibit significant dye removal percentages of 75 ± 1% and 78 ± 1%, respectively, after 40 min. The biosorption isotherm analysis reveals a significant interaction between the adsorbate and the biosorbent, and it indicates that the Temkin model best matches the experimental data. Moreover, the Langmuir model indicates a relatively high biosorption capacity, further highlighting the potential of the algae-bacteria composite as an efficient adsorbent. Decision Trees, Random Forest, Support Vector Regression, and Artificial Neural Networks are evaluated for predicting dye removal efficiency. The Random Forest model emerges as the most accurate, exhibiting an R2 value of 0.98, while Support Vector Regression and Artificial Neural Networks also demonstrate robust predictive capabilities. This study contributes to the advancement of sustainable dye removal strategies and encourages future exploration of hybrid approaches to further enhance predictive accuracy and efficiency in wastewater treatment processes.

Sequence-dependent and -independent information in a combined random energy model for protein folding and coding

Random energy models (REMs) provide a simple description of the energy landscapes that guide protein folding and evolution. The requirement of a large energy gap between the native structure and unfolded conformations, considered necessary for cooperative, protein-like, folding behavior, indicates that proteins differ markedly from random heteropolymers. It has been suggested, therefore, that natural selection might have acted to choose nonrandom amino acid sequences satisfying this particular condition, implying that a large fraction of possible, unselected random sequences, would not fold to any structure. From an informational perspective, however, this scenario could indicate that protein structures, regarded as messages to be transmitted through a communication channel, would not be efficiently encoded in amino acid sequences, regarded as the communication channel for this transmission, since a large fraction of possible channel states would not be used. Here, we use a combined REM for conformations and sequences, with previously estimated parameters for natural proteins, to explore an alternative possibility in which the appropriate shape of the landscape results mainly from the deviation from randomness of possible native structures instead of sequences. We observe that this situation emerges naturally if the distribution of conformational energies happens to arise from two independent contributions corresponding to sequence-dependent and -independent terms. This construction is consistent with the hypothesis of a protein burial folding code, with native structures being determined by a modest amount of sequence-dependent atomic burial information with sequence-independent constraints imposed by unspecific hydrogen bond formation. More generally, an appropriate combination of sequence-dependent and -independent information accommodates the possibility of an efficient structural encoding with the main physical requirement for folding, providing possible insight not only on the folding process but also on several aspects sequence evolution such as neutral networks, conformational coverage, and de novo gene emergence.

Microalgae derived honeycomb structured mesoporous diatom biosilica for adsorption of malachite green: Process optimization and modeling

The present study investigated the removal of malachite green dye from aquifers by means of microalgae-derived mesoporous diatom biosilica. The various process variables (dye concentration, pH, and adsorbent dose) influencing the removal of the dye were optimized and their interactive effects on the removal efficiency were explored by response surface methodology. The pH of the solution (pH = 5.26) was found to be the most dominating among other tested variables. The Langmuir isotherm (R2 = 0.995) best fitted the equilibrium adsorption data with an adsorption capacity of 40.7 mg/g at 323 K and pseudo-second-order model (R2 = 0.983) best elucidated the rate of dye removal (10.6 mg/g). The underlying mechanism of adsorption was investigated by Weber-Morris and Boyd models and results revealed that the film diffusion governed the overall adsorption process. The theoretical investigations on the dye structure using DFT-based chemical reactivity descriptors indicated that malachite green cations are electrophilic, reactive and possess the ability to accept electrons, and are strongly adsorbed on the surface of diatom biosilica. Also, the Fukui function analysis proposed the favorable adsorption sites available on the adsorbent surface.

Probing the toxic effect of chlorpyrifos as an environmental pollutant on the structure and biological activity of lysozyme under physiological conditions

The pervasive use of pesticides like chlorpyrifos (CPY) has been associated with deleterious effects on biomolecules, posing significant risks to environmental integrity, public health, and overall ecosystem equilibrium. Accordingly, in this study, we investigated the potential binding interaction between the well-conserved enzyme, lysozyme (LSZ), and CPY through various spectroscopic techniques and molecular modeling. The UV-vis absorption and fluorescence experiments confirmed the complex formation and static quenching of the intrinsic fluorescence intensity. LSZ revealed a singular binding site for CPY, with binding constants around 105 M-1 across different temperature ranges. Analysis of thermodynamic parameters showed the spontaneous nature of the complexation process, while also revealing the pivotal role of hydrophobic interactions in stabilizing the LSZ-CPY system. According to circular dichroism and Fourier transform infrared studies, CPY binding changed the secondary structure of LSZ by boosting α-helix presence and reducing the levels of β-sheet and β-turn content. Further, CPY decreased the stability and activity of LSZ. Computational docking delineated the specific and highly preferred binding site of CPY within the structure of LSZ. Molecular dynamic simulation indicated the enduring stability of the LSZ/CPY complex and revealed structural modifications in the LSZ after binding with CPY. This research provides a detailed understanding of the intermolecular dynamics between CPY and LSZ, concurrently elucidating the molecular-level implications for the potential hazards of pesticides in the natural environment.

In silico design of misfolding resistant proteins: the role of structural similarity of a competing conformational ensemble in the optimization of frustration

Most state-of-the-art in silico design methods fail due to misfolding of designed sequences to a conformation other than the target. Thus, a method to design misfolding resistant proteins will provide a better understanding of the misfolding phenomenon and will also increase the success rate of in silico design methods. In this work, we optimize the conformational ensemble to be selected for negative design purposes based on the similarity of the conformational ensemble to the target. Five ensembles with different degrees of similarity to the target are created and destabilized and the target is stabilized while designing sequences using mean field theory and Monte Carlo simulation methods. The results suggest that the degree of similarity of the non-native conformations to the target plays a prominent role in designing misfolding resistant protein sequences. The design procedures that destabilize the conformational ensemble with moderate similarity to the target have proven to be more promising. Incorporation of either highly similar or highly dissimilar conformations to the target conformation into the non-native ensemble to be destabilized may lead to sequences with a higher misfolding propensity. This will significantly reduce the conformational space to be considered in any protein design procedure. Interestingly, the results suggest that a sequence with higher frustration in the target structure does not necessarily lead to a misfold prone sequence. A successful design method may purposefully choose a frustrated sequence in the target conformation if that sequence is even more frustrated in the competing non-native conformations.

Structure, Self-Assembly, and Phase Behavior of Neuroactive N-Acyl GABAs: Doxorubicin Encapsulation in NPGABA/DPPC Liposomes and Release Studies

N-Acylated amino acids and neurotransmitters in mammals exert significant biological effects on the nervous system, immune responses, and vasculature. N-Acyl derivatives of γ-aminobutyric acid (N-acyl GABA), which belong to both classes mentioned above, are prominent among them. In this work, a homologous series of N-acyl GABAs bearing saturated N-acyl chains (C8-C18) have been synthesized and characterized with respect to self-assembly, thermotropic phase behavior, and supramolecular organization. Differential scanning calorimetric studies revealed that the transition enthalpies and entropies of N-acyl GABAs are linearly dependent on the acyl chain length. The crystal structure of N-tridecanoyl GABA showed that the molecules are packed in bilayers with the acyl chains aligned parallel to the bilayer normal and that the carboxyl groups from opposite layers associate to form dimeric structures involving strong O-H···O hydrogen bonds. In addition, N-H···O and C-H···O hydrogen bonds between amide moieties of adjacent molecules within each layer stabilize the molecular packing. Powder X-ray diffraction studies showed odd-even alternation in the d spacings, suggesting that the odd chain and even chain compounds pack differently. Equimolar mixtures of N-palmitoyl GABA and dipalmitoylphosphatidylcholine (DPPC) were found to form stable unilamellar vesicles with diameters of ∼300-340 nm, which could encapsulate doxorubicin, an anticancer drug, with higher efficiency and better release characteristics than DPPC liposomes at physiologically relevant pH. These liposomes exhibit faster release of doxorubicin at acidic pH (<7.0), indicating their potential utility as drug carriers in cancer chemotherapy.

Insight into the molecular interaction between the anticancer drug, enzalutamide and human alpha-2-macroglobulin: Biochemical and biophysical approach

The drug pharmacokinetics is affected upon binding with proteins, thus making drug-protein interactions crucial. This study investigated the interaction between enzalutamide and human major antiproteinase alpha-2-macroglobulin (α2M) by using multi spectroscopic and calorimetric techniques. The spectroscopic techniques such as circular dichroism (CD), intrinsic fluorescence, and UV-visible absorption were used to determine the mechanism of enzalutamide-α2M interaction. Studies on the quenching of fluorescence at three different temperatures showed that the enzalutamide-α2M complex is formed through static quenching mechanism. The change in microenvironment around tyrosine residues in protein was detected through synchronised fluorescence. The secondary structure of α2M was slightly altered by enzalutamide according to far UV-CD spectral analysis. Changes in position of amide I band in FTIR spectra further confirm the secondary structural alteration in α2M. According to thermodynamic characteristics such as fluorescence quenching and isothermal titration calorimetry (ITC), hydrogen bonds and hydrophobic interactions were involved in the interaction machanism. The ITC reiterated the exothermic and spontaneous nature of the interaction. The lower proteinase inhibitory activity of the α2M-enzalutamide conjugate as reflects the disruption of the native α2M structure upon interaction with enzalutamide.

Solubility determination and thermodynamic model analysis of L-α-glyceryl phosphorylcholine in different organic solvents of 278.15 K to 323.15 K

L-α-glyceryl phosphorylcholine, also referred to as choline ethanol phosphate and phosphocholine glycerophosphate, is a naturally occurring metabolite of water-soluble phospholipids in animals. This molecular property is important for informing the crystallization and purification of drugs. The solubility of L-α-glyceryl phosphorylcholine was determined in ten pure solvents and three mixed solvents under atmospheric pressure. The experimental results indicate that L-α-glyceryl phosphorylcholine is most soluble in methanol and least soluble in acetone. Additionally, the solubility of L-α-glyceryl phosphorylcholine was found to increase with temperature within the experimental range. Furthermore, the solubility of L-α-glyceryl phosphorylcholine in binary solvents is dependent on the proportion of positive solvent and temperature. The solubility of L-α-glyceryl phosphorylcholine increases with the proportion of positive solvent. XRD and DSC results indicate that the crystal form of L-α-glyceryl phosphorylcholine remains unchanged before and after dissolution in the reagent, and its melting point temperature is 413.15 K. Various models, including the modified Apelblat model, λh model, Jouyban-Acree model, SUN model, and CNIBS/R-K model, were used to fit the solubility data of L-α-glyceryl phosphorylcholine in different solvents. The study found that the modified Apelblat model and CNIBS/R-K model were the most appropriate for fitting the data. The KAT-LSER model was used to analyze the molecular interactions between solvents and solutes, revealing that the solvent step method with non-specific polarity/polarization interaction had the greatest impact on solubility.

Eco-friendly synthesis of clay-chitosan composite for efficient removal of alizarin red S dye from wastewater: A comprehensive experimental and theoretical investigation

Alizarin Red S (ARS) is commonly utilized for dyeing in textile industry. The dye represents a refractory pollutant in the aquatic environment unless properly treated. To tackle this pollutant, the applicability of chitosan-clay composite (3C) for the ARS removal from textile wastewater was studied. Characterization studies were conducted on the synthesized adsorbent using Fourier transformation infrared (FT-IR), X-ray diffraction (XRD), and energy dispersive X-ray (EDX) techniques. Optimized parameters such as adsorbent's dosage, pH, reaction time, and initial concentrations were tested in a batch system. Additionally, density functional theory (DFT) was calculated to understand the adsorption mechanism and the role of benzene rings and oxygen atoms in the ARS as electron donors. At the same initial concentration of 30 mg/L and optimized conditions of 50 mg of dose, pH 2, and 10 min of reaction time, about 86% of ARS removal was achieved using the composite. The pseudo-second-order kinetic was applicable to model a reasonable fitness of the adsorption reaction, while the Temkin model was representative to simulate the reaction with a maximum adsorption capacity of 44.39 mg/g. This result was higher than magnetic chitosan (40.12 mg/g), or pure chitosan (42.48 mg/g). With ΔH = 27.22 kJ/mol and ΔG<0, the data implied the endothermic and spontaneous nature of the adsorption process. Overall, this implies that the clay-chitosan composite is promising to remove target dye from contaminated wastewater.

Thermodynamic and molecular dynamic insights into how fusion influences peptide-tag recognition of an antibody

To understand the effect of protein fusion on the recognition of a peptide-tag by an antibody, we fused a CCR5-derived peptide-tag (pep1) to GFP and investigated its recognition by an anti-pep1 antibody, 4B08. First, to characterize the thermodynamic properties associated with the pep1-4B08 binding, isothermal titration calorimetry experiments were conducted. It was found that pep1 fused to the C-terminus of GFP (GFP-CT) enhanced the enthalpic gain by 2.1 kcal mol-1 and the entropic loss only by 0.9 kcal mol-1, resulting in an 8-fold increase in the binding affinity compared to the unfused pep1. On the other hand, pep1 fused to the N-terminus of GFP (GFP-NT) enhanced the enthalpic gain by 3.0 kcal mol-1 and the entropic loss by 3.2 kcal mol-1, leading to no significant enhancement of the binding affinity. To gain deeper insights, molecular dynamics simulations of GFP-NT, GFP-CT, and pep1 were performed. The results showed that the location of the fusion point sensitively affects the interaction energy, the solvent accessible surface area, and the fluctuation of pep1 in the unbound state, which explains the difference in the experimental thermodynamic properties.

Break oily water emulsion during petroleum enhancing production processes using green approach for the synthesis of SnCuO@FeO nanocomposite from microorganisms

The aim of this work was to synthesize a green nanoparticle SnCuO@FeO nanocomposite core-shell to break oily water emulsions during petroleum-enhancing production processes as an alternative to chemical and physical processes. In this study, eight bacterial isolates (MHB1-MHB8) have been isolated from tree leaves, giant reeds, and soil samples. The investigation involved testing bacterial isolates for their ability to make FeO nanoparticles and choosing the best producers. The selected isolate (MHB5) was identified by amplification and sequencing of the 16S rRNA gene as Bacillus paramycoides strain OQ878685. MHB5 produced the FeO nanoparticles with the smallest particle size (78.7 nm) using DLS. XRD, FTIR, and TEM were used to characterize the biosynthesized nanoparticles. The jar experiment used SnCuO@FeO with different ratios of Sn to CuO (1:1, 2:1, and 3:1) to study the effect of oil concentration, retention time, and temperature. The most effective performance was observed with a 1:1 ratio of Sn to CuO, achieving an 85% separation efficiency at a concentration of 5 mg/L, for a duration of 5 min, and at a temperature of 373 K. Analysis using kinetic models indicates that the adsorption process can be accurately described by both the pseudo-first-order and pseudo-second-order models. This suggests that the adsorption mechanism likely involves a combination of film diffusion and intraparticle diffusion. Regarding the adsorption isotherm, the Langmuir model provides a strong fit for the data, while the D-R model indicates that physical interactions primarily govern the adsorption mechanism. Thermodynamic analysis reveals a ∆H value of 18.62 kJ/mol, indicating an exothermic adsorption process. This suggests that the adsorption is a favorable process, as energy is released during the process. Finally, the synthesized green SnCuO@FeO nanocomposite has potential for use in advanced applications in the oil and gas industry to help the industry meet regulatory compliance, lower operation costs, reduce environmental impact, and enhance production efficiency.

Calculations of Absolute Free Energies, Enthalpies, and Entropies for Drug Binding

Computer simulation methods can aid in the rational design of drugs aimed at a specific target, typically a protein. The affinity of a drug for its target is given by the free energy of binding. Binding can be further characterized by the enthalpy and entropy changes in the process. Methods exist to determine exact free energies, enthalpies, and entropies that are dependent only on the quality of the potential model and adequate sampling of conformational degrees of freedom. Entropy and enthalpy are roughly an order of magnitude more difficult to calculate than the free energy. This project combines a replica exchange method for enhanced sampling, designed to be efficient for protein-sized systems, with free energy calculations. This approach, replica exchange with dynamical scaling (REDS), uses two conventional simulations at different temperatures so that the entropy can be found from the temperature dependence of the free energy. A third replica is placed between them, with a modified Hamiltonian that allows it to span the temperature range of the conventional replicas. REDS provides temperature-dependent data and aids in sampling. It is applied to the bromodomain-containing protein 4 (BRD4) system. We find that for the force fields used, the free energies are accurate but the entropies and enthalpies are not, with the entropic contribution being too positive. Reproducing the entropy and enthalpy of binding appears to be a more stringent test of the force fields than reproducing the free energy.

Toward Post-Hartree-Fock Accuracy for Protein-Ligand Affinities Using the Molecules-in-Molecules Fragmentation-Based Method

The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation. Employing DLPNO-based post-Hartree-Fock methods in conjunction with the three-layer MIM method (MIM3), this study demonstrates the achievement of protein-ligand binding energies with remarkable accuracy (errors <1 kcal mol-1), while significantly reducing computational costs. Furthermore, noteworthy correlations between theoretically computed interaction energies and their experimental equivalents were observed, with R2 values of approximately 0.90 and 0.78 for CDK2 and BZT-ITK sets, respectively, thus validating the efficacy of the MIM method in calculating binding energies. By highlighting the crucial role of diffuse or small Pople-style basis sets in the middle layer for reducing energy errors, this work provides valuable insights and practical methodologies for interaction energy computations in large molecular complexes and opens avenues for their application across a diverse range of molecular systems.

Explainable Supervised Machine Learning Model To Predict Solvation Gibbs Energy

Many challenges persist in developing accurate computational models for predicting solvation free energy (ΔGsol). Despite recent developments in Machine Learning (ML) methodologies that outperformed traditional quantum mechanical models, several issues remain concerning explanatory insights for broad chemical predictions with an acceptable speed-accuracy trade-off. To overcome this, we present a novel supervised ML model to predict the ΔGsol for an array of solvent-solute pairs. Using two different ensemble regressor algorithms, we made fast and accurate property predictions using open-source chemical features, encoding complex electronic, structural, and surface area descriptors for every solvent and solute. By integrating molecular properties and chemical interaction features, we have analyzed individual descriptor importance and optimized our model though explanatory information form feature groups. On aqueous and organic solvent databases, ML models revealed the predictive relevance of solutes with increasing polar surface area and decreasing polarizability, yielding better results than state-of-the-art benchmark Neural Network methods (without complex quantum mechanical or molecular dynamic simulations). Both algorithms successfully outperformed previous ΔGsol predictions methods, with a maximum absolute error of 0.22 ± 0.02 kcal mol-1, further validated in an external benchmark database and with solvent hold-out tests. With these explanatory and statistical insights, they allow a thoughtful application of this method for predicting other thermodynamic properties, stressing the relevance of ML modeling for further complex computational chemistry problems.

Seed-Induced Living Two-Dimensional (2D) Supramolecular Polymerization in Water: Implications on Protein Adsorption and Enzyme Inhibition

In biological systems, programmable supramolecular frameworks characterized by coordinated directional non-covalent interactions are widespread. However, only a small number of reports involve pure water-based dynamic supramolecular assembly of artificial π-amphiphiles, primarily due to the formidable challenge of counteracting the strong hydrophobic dominance of the π-surface in water, leading to undesired kinetic traps. This study reveals the pathway complexity in hydrogen-bonding-mediated supramolecular polymerization of an amide-functionalized naphthalene monoimide (NMI) building block with a hydrophilic oligo-oxyethylene (OE) wedge. O-NMI-2 initially produced entropically driven, collapsed spherical particles in water (Agg-1); however, over a span of 72 h, these metastable Agg-1 gradually transformed into two-dimensional (2D) nanosheets (Agg-2), favoured by both entropy and enthalpy contributions. The intricate self-assembly pathways in O-NMI-2 enable us to explore seed-induced living supramolecular polymerization (LSP) in water for controlled synthesis of monolayered 2D assemblies. Furthermore, we demonstrated the nonspecific surface adsorption of a model enzyme, serine protease α-Chymotrypsin (α-ChT), and consequently the enzyme activity, which could be regulated by controlling the morphological transformation of O-NMI-2 from Agg-1 to Agg-2. We delve into the thermodynamic aspects of such shape-dependent protein-surface interactions and unravel the impact of seed-induced LSP on temporally controlling the catalytic activity of α-ChT.

Multiple spectroscopic and computational studies on binding interaction of 2-phenylamino-4-phenoxyquinoline derivatives with bovine serum albumin

Binding characteristics of potent non-nucleoside HIV-1 reverse transcriptase inhibitors, 4-(2',6'-dimethyl-4'-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (1) and 4-(2',6'-dimethyl-4'-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino) quinoline (2), to bovine serum albumin (BSA) under simulative physiological conditions were investigated by multiple spectroscopic and computational methods. The experimental results demonstrated that (1) and (2) bound to BSA at site III (subdomain IB), and quenched BSA fluorescence through a static quenching process. The binding interaction of (1) or (2) to BSA forms stable complexes with the binding constants (Kb) at the level of 104 L/mol and the number of binding site was determined to be 1 for both systems, indicating that new synthesized compounds occupied one site in BSA with moderate binding affinities. Based on the analysis of the thermodynamic parameters, it can be indicated that the main binding forces for interaction between BSA and both compounds were hydrogen bonding and van der Waals force. Synchronous fluorescence results revealed that the interaction of two compounds with BSA led to modifications in the microenvironment surrounding tryptophan residue of BSA. Circular dichroism spectra demonstrated alterations in the secondary structure of BSA induced by (1) and (2). Moreover, the experimental data of molecular docking and molecular dynamics (MD) simulations supported the results obtained from multiple spectroscopic techniques, confirming the binding interactions between both compounds and BSA.

Uranium capture from aqueous solution using palm-waste based activated carbon: sorption kinetics and equilibrium

Carbonaceous materials produced from agricultural waste (palm kernel shell) by pyrolysis can be a proper type of low-cost adsorbent for wide uses in radioactive effluent treatment. In this context, the as-produced bio-char (labeled as PBC) and its sub-driven sulfuric acid and zinc oxide activated carbons (labeled as PBC-SA, and PBC-Zn respectively) were employed as adsorbents for uranium sorption from aqueous solution. Various analytical techniques, including SEM (Scanning Electron Microscopy), EXD (X-ray Diffraction), BET (Brunauer-Emmett-Teller), FTIR (Fourier Transform Infrared Spectroscopy), and Zeta potential, provide insights into the material characteristics. Kinetic and isotherm investigations illuminated that the sorption process using the three sorbents is nicely fitted with Pseudo-second-order-kinetic and Langmuir isotherm models. The picked data display that the equilibrium time was 60 min, and the maximum sorption capacity was 9.89, 16.8, and 21.9 mg/g for PBC, PBC-SA, and PBC-Zn respectively, which reflects the highest affinity for zinc oxide, activated bio-char, among the three adsorbents, for uranium taking out from radioactive wastewater. Sorption thermodynamics declare that the sorption of U(VI) is an exothermic, spontaneous, and feasible process. About 92% of the uranium-loaded PBC-Zn sorbent was eluted using 1.0 M CH3COONa sodium ethanoate solution, and the sorbent demonstrated proper stability for 5 consecutive sorption/desorption cycles.

Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop

The N6-methyladenosine modification is one of the most abundant post-transcriptional modifications in ribonucleic acid (RNA) molecules. Using molecular dynamics simulations and alchemical free-energy calculations, we studied the structural and energetic implications of incorporating this modification in an adenine mononucleotide and an RNA hairpin structure. At the mononucleotide level, we found that the syn configuration is more favorable than the anti configuration by 2.05 ± 0.15 kcal/mol. The unfavorable effect of methylation was due to the steric overlap between the methyl group and a nitrogen atom in the purine ring. We then probed the effect of methylation in an RNA hairpin structure containing an AUCG tetraloop, which is recognized by a "reader" protein (YTHDC1) to promote transcriptional silencing of long noncoding RNAs. While methylation had no significant conformational effect on the hairpin stem, the methylated tetraloop showed enhanced conformational flexibility compared to the unmethylated tetraloop. The increased flexibility was associated with the outward flipping of two bases (A6 and U7) which formed stacking interactions with each other and with the C8 and G9 bases in the tetraloop, leading to a conformation similar to that in the RNA/reader protein complex. Therefore, methylation-induced conformational flexibility likely facilitates RNA recognition by the reader protein.

Comparing the Chemistry of Malvidin-3-O-glucoside and Malvidin-3,5-O-diglucoside Networks: A Holistic Approach to the Acidic and Basic Paradigms with Implications in Biological Studies

The kinetics, thermodynamics, and degradation of malvidin mono- and diglucosides were studied following a holistic approach by extending to the basic medium. In acidic conditions, the reversible kinetics of the flavylium cation toward the equilibrium is controlled by the hydration and cis-trans isomerization steps, while in the basic medium, the OH- nucleophilic addition to the anionic quinoidal bases is the slowest step. There is a pH range (transition pHs), between the acidic and basic paradigms, that includes physiological pH (7.4), where degradation reactions occur faster, preventing the system from reaching the equilibrium. The transition pH of the diglucoside is narrower, and in contrast with the monoglucoside, there is no evidence for the formation of colored oligomers among the degradation products. Noteworthy, OH- addition in position 4 to form B42-, a kinetic product that decreases the overall equilibration rate, was observed only for the diglucoside.

The Impact of Activating Agents on Non-Enzymatic Nucleic Acid Extension Reactions

Non-enzymatic template-directed primer extension is increasingly being studied for the production of RNA and DNA. These reactions benefit from producing RNA or DNA in an aqueous, protecting group free system, without the need for expensive enzymes. However, these primer extension reactions suffer from a lack of fidelity, low reaction rates, low overall yields, and short primer extension lengths. This review outlines a detailed mechanistic pathway for non-enzymatic template-directed primer extension and presents a review of the thermodynamic driving forces involved in entropic templating. Through the lens of entropic templating, the rate and fidelity of a reaction are shown to be intrinsically linked to the reactivity of the activating agent used. Thus, a strategy is discussed for the optimization of non-enzymatic template-directed primer extension, providing a path towards cost-effective in vitro synthesis of RNA and DNA.

Polymyxin B-Enriched Exogenous Lung Surfactant: Thermodynamics and Structure

The use of an exogenous pulmonary surfactant (EPS) to deliver other relevant drugs to the lungs is a promising strategy for combined therapy. We evaluated the interaction of polymyxin B (PxB) with a clinically used EPS, the poractant alfa Curosurf (PSUR). The effect of PxB on the protein-free model system (MS) composed of four phospholipids (diC16:0PC/16:0-18:1PC/16:0-18:2PC/16:0-18:1PG) was examined in parallel to distinguish the specificity of the composition of PSUR. We used several experimental techniques (differential scanning calorimetry, small- and wide-angle X-ray scattering, small-angle neutron scattering, fluorescence spectroscopy, and electrophoretic light scattering) to characterize the binding of PxB to both EPS. Electrostatic interactions PxB-EPS are dominant. The results obtained support the concept of cationic PxB molecules lying on the surface of the PSUR bilayer, strengthening the multilamellar structure of PSUR as derived from SAXS and SANS. A protein-free MS mimics a natural EPS well but was found to be less resistant to penetration of PxB into the lipid bilayer. PxB does not affect the gel-to-fluid phase transition temperature, Tm, of PSUR, while Tm increased by ∼+ 2 °C in MS. The decrease of the thickness of the lipid bilayer (dL) of PSUR upon PxB binding is negligible. The hydrophobic tail of the PxB molecule does not penetrate the bilayer as derived from SANS data analysis and changes in lateral pressure monitored by excimer fluorescence at two depths of the hydrophobic region of the bilayer. Changes in dL of protein-free MS show a biphasic dependence on the adsorbed amount of PxB with a minimum close to the point of electroneutrality of the mixture. Our results do not discourage the concept of a combined treatment with PxB-enriched Curosurf. However, the amount of PxB must be carefully assessed (less than 5 wt % relative to the mass of the surfactant) to avoid inversion of the surface charge of the membrane.

Atomistic simulations of RNA duplex thermal denaturation: Sequence- and forcefield-dependence

Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that greatly improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.

Bisphenol A adsorption using modified aloe vera leaf-wastes derived bio-sorbents from aqueous solution: kinetic, isotherm, and thermodynamic studies

Reactive-oxygen-species are produced more often in the body when bisphenol A (BPA), an endocrine-disrupting-substance, is present. In this investigation, bio-sorbents from an aqueous solution adapted from Aloe-vera were used to survey BPA removal. Aloe-vera leaf wastes were used to create activated carbon, which was then analyzed using Fourier transform infrared (FTIR), Field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), Thermogravimetric analysis (TGA), Zeta potential, and Brunauer-Emmett-Teller (BET) techniques. It was revealed that the adsorption process adheres to the Freundlich isotherm model with R2>0.96 and the pseudo-second-order kinetic model with R2>0.99 under ideal conditions (pH = 3, contact time = 45 min, concentration of BPA = 20 mg.L-1, and concentration of the adsorbent = 2 g.L-1). After five-cycle, the efficacy of removal was greater than 70%. The removal of phenolic-chemicals from industrial-effluent can be accomplished with the assistance of this adsorbent in a cost-effective and effective-approach.

Unexpected high yield of acrolein underlies the importance of the hydrogen-abstraction mechanism in photooxidation of allyl methyl sulfide (AMS)

This work explores theoretically the gas phase oxidation of allyl methyl sulfide (AMS, H2CCHCH2SCH3) initiated by •OH radicals, focusing on the H-abstraction pathway at the M06-2X-D3/aug-cc-pVTZ and MN15/aug-cc-pVTZ levels of theory (m06Tz and mn15Tz). The formation of a prereactive complex (PRC) is involved in H-abstraction processes with two potential directions of approach for the OH radical, denoted as "α" and "β". The PRCs, demonstrate increased reactivity, primarily due to the interaction between the sulfur atoms and the hydroxyl hydrogen. A scheme for the H-abstraction mechanism that supports the experimentally identified products and predicts the formation of some S-containing low volatility products is proposed. The comparison of the potential energy surface (PES) between the double bond addition and H-abstraction paths in the AMS molecule shows that at the m06Tz level of theory, the H-abstraction on C3 and the addition to C1 have nearly the same profile of energy, while at the mn15Tz level, the minimum energy channel is the addition to C1. The theoretical rate coefficient for each reaction channel was calculated, considering the formation of a PRC prior to reaching the transition state of each channel and assuming thermal equilibrium between reactants and the PRC. The rate constants were calculated in a multi-TS/multi-conformer way at the SVECV-f12/m06Tz and SVECV-f12/mn15Tz levels of theory. The SVECV-f12 method is consistent in its predictions in both systems and exhibits only minor deviations from the experimental rate constants. Despite some specific differences due to the DFT method supporting the SVECV-f12 calculations, both methodologies predict a significant H-abstraction contribution in the AMS + OH gas phase reaction, which explains the high formation yield for acrolein determined experimentally.

Life and fate of Ervin Bauer (1890-1938), the eminent scholar and foundational theoretical biologist

Ervin Bauer (1890-1938) was the first to build a general molecular-based biological theory. He defined the basic principles of theoretical biology from a thermodynamic perspective, focusing on the capacity of biological systems to produce and support the state of sustainable non-equilibrium. His central work "Theoretical Biology" (1935) was written long before modern advances in molecular biology, genetics, and information theory. Ervin Bauer and his wife Stefánia were executed in Stalin's Great Terror. This paper presents a brief introduction to Ervin Bauer's life and includes his short biography.

Solubility of digitoxin in supercritical CO2: Experimental study and modeling

In this communication, the solubility of digitoxin drug in supercritical CO2 was studied at different operating conditions (311 < T (K) < 343, 120 < P (bar) < 300). The results revealed digitoxin drug solubility (in mole fraction) was between 0.095 × 10-5 to 1.12 × 10-5. In the case of thermodynamic solubility modeling, cubic and non-cubic equation of states i.e. SAFT (statistical associating fluid theory), SRK (Soave-Redlich-Kwong) and sPC-SAFT (simplified perturbed chain SAFT) EoSs and six density-based correlations (Chrastil, Kumar-Johnston (KJ), Mendez-Santiago-Teja (MST), Garlapati and Madras (GM), Bartle et al. and Sung-Shim models) were considered. All used equations indicated reasonable behavior with appropriate accuracy for the solubility of the digitoxin drug. Meanwhile, sPC-SAFT EoS and Kumar-Johnston correlation with AARD% set to 8.96 % and 6.25 %, respectively exhibited greater accuracy in fitting the solubility data. Moreover, total, solvation and vaporization enthalpies of the digitoxin/supercritical carbon dioxide binary mixture were calculated based on KJ, Chrastil and Bartle et al. models.

Studies on the binding of wedelolactone to human serum albumin with multi-spectroscopic analysis, molecular docking and molecular dynamic simulation

Wedelolactone (WEL) is a small molecule compound isolated from Eclipta prostrate L., which has been reported to possess various biological activities such as anti-hepatotoxicity, anti-hypertension, anti-tumour, anti-phospholipase A2 and detoxification activity against snake venom. In the present study, we investigated the interaction of WEL with human serum albumin (HSA) using simultaneous fluorescence, UV-visible spectroscopy, 3D fluorescence spectroscopy, Fourier transform infrared spectroscopy (FTIR), molecular docking technique and molecular dynamics simulation. We found that the interaction between HSA and WEL can exhibit a static fluorescence burst mechanism, and the binding process is essentially spontaneous, with the main forces manifested as hydrogen bonding, van der Waals force and electrostatic interactions. Competitive binding and molecular docking studies showed that WEL preferentially bound to HSA in substructural region IIA (site I); molecular dynamics simulations showed that HSA interacted with WEL to form a stable complex, which also induced conformational changes in HSA. The study of the interaction between WEL and HSA can provide a reference for a more in-depth study of the pharmacodynamic mechanism of WEL and its further development and utilisation.

Deciphering the binding behavior and interaction mechanism of apigenin and α-glucosidase based on multi-spectroscopic and molecular simulation studies

This study investigated the molecular mechanism underlying the binding interaction between apigenin (API) and α-glucosidase (α-glu) by a combination of experimental techniques and computational simulation strategies. The spontaneously formation of stable API-α-glu complex was mainly driven by hydrogen bonds and hydrophobic forces, leading to a static fluorescence quenching of α-glu. The binding of API induced secondary structure and conformation changes of α-glu, decreasing the surface hydrophobicity of protein. Computational simulation results demonstrated that API could bind into the active cavity of α-glu via its interaction with active residues at the binding site. The important roles of key residues responsible for the binding stability and affinity between API and α-glu were further revealed by MM/PBSA results. In addition, it can be found that the entrance of active site tended to close after API binding as a result of its interaction with gate keeping residues. Furthermore, the structural basis for the binding interaction behavior of API was revealed and visualized by weak interaction analysis. The findings of our study revealed atomic-level mechanism of the interaction between API, which might shed light on the development of better inhibitors.

Pyrolysis of Euphorbia Rigida: A study on thermal characterizations, kinetics, thermodynamics via TG-FTIR analysis

Euphorbia Rigida (E. Rigida), a lignocellulosic biomass with low ash content, is a suitable feedstock for pyrolysis. This work investigated the physicochemical characteristics and thermokinetic analysis of E. Rigida pyrolysis by using isoconversional and master plots methods. Ultimate and proximate analyses and oxygen bomb calorimeter were used to determine the physicochemical parameters. The activation energies were calculated using model-free methods (KAS, Friedman and Starink) and were found as 184, 178 and 185 kJ/mol, respectively. Using Fraser-Suzuki deconvolution, pseudo-components were also calculated and the active pyrolysis region was divided into three zones. The master plots showed that reaction order mechanisms (Fn) were effective in Zone I, and diffusion mechanisms (Dn) were well matched in Zone II and Zone III. The thermodynamic parameters (ΔH, ΔG and ΔS) were calculated and according to these results, E. Rigida pyrolysis was an endothermic and non-spontaneous process.

Microwave promoted graft copolymerization of poly(ethylacrylate) onto k-carrageenan for removal of Cd and Ni from aqueous solution

Microwave promoted graft copolymerization of poly (ethyl acrylate) onto kappa-carrageenan in presence of a redox pair (ascorbic acid and potassium persulfate) led to the formation of a novel copolymer hydrogel, kappa-carrageenan-graft-poly (ethylacrylate). By varying the reaction conditions such as the microwave power, reaction time, concentration of kappa-carrageenan, ascorbic acid and persulfate, copolymers of highest percentage grafting was obtained and characterized by FT-IR, SEM, TGA and XRD. The copolymer was evaluated as an adsorbent for the adsorption of Ni(II) and Cd(II). Various adsorption parameters such as contact time, pH, initial metal ion concentration, temperature, electrolyte strength and adsorbent dosage were varied to obtain the optimum conditions for the adsorption. The adsorption data for Cd(II), fitted better for Langmuir and Ni(II), fitted much better for Freundlich adsorption isotherm model. Maximum adsorption obtained for cadmium ions and nickel ions was 308.6 mg/g-1 and 305.8 mg/g-1 respectively. The adsorption of both metal ions followed pseudo second order kinetic model. The positive ΔH values endorsed the adsorption process to be endothermic in nature. The negative values of ΔG indicate the spontaneity of the adsorption process while the positive ΔS values showed that the adsorption of metal ions proceeded with increased randomness at the surface of the copolymer. High recovery percentage of the metal ions from the adsorbent indicates that the copolymer can be used for more adsorption cycles.

A label-free high-throughput protein solubility assay and its application to Aβ40

A major hallmark of Alzheimer's disease is the accumulation of aggregated amyloid β peptide (Aβ) in the brain. Here we develop a solubility assay for proteins and measure the solubility of Aβ40. In brief, the method utilizes 96-well filter plates to separate monomeric Aβ from aggregated Aβ, and the small species are quantified with the amine reactive dye o-phthalaldehyde (OPA). This procedure ensures that solubility is measured for unlabeled species, and makes the assay high-throughput and inexpensive. We demonstrate that the filter plates successfully separate fibrils from monomer, with negligible monomer adsorption, and that OPA can quantify Aβ peptides in a concentration range from 40 nM to 20 μM. We also show that adding a methionine residue to the N-terminus of Aβ1-40 decreases the solubility by <3-fold. The method will facilitate further solubility studies, and contribute to the understanding of the thermodynamics of amyloid fibril formation.

Effect of different iron ratios on interaction and thermodynamic stability of bound whey protein isolate

Whey protein isolates (WPI) are known to have mineral-binding capacity to promote iron absorption. The aim of this study was to investigate the effect of iron ratio on the conformational structure of iron-bound whey protein isolate (WPI-Fe) and its thermodynamic stability. It was shown that the iron to protein ratio affects both the iron binding capacity of WPI and the iron valence state on the surface of WPI-Fe complexes. As the iron content increases, aggregation between protein molecules occurs. In addition, WPI-Fe nanoparticles have thermodynamic stability and Fe2+ has a high affinity with WPI for spontaneous exothermic reactions. This study demonstrates that WPI-Fe complexes can be used to efficiently deliver high-quality iron source (Fe2+) for future iron supplements.

DNA polyhedrons cube, prism, and square pyramid protect the catalytic activity of catalase: A thermodynamics and kinetics study

DNA is widely used as building block material for the construction of polyhedral nanostructures. DNA polyhedrons (DNA prism, cube, and square pyramid) are small 3D wireframed nanostructures with tunable shapes and sizes. Despite substantial progress in synthesis, the study regarding cellular responses to DNA polyhedrons is limited. Herein, the molecular interaction between DNA polyhedrons and the antioxidant enzyme, catalase has been explored. The enzymatic activity of bovine liver catalase (BLC) remains unaltered in the presence of DNA polyhedrons after 1 h of incubation. However, the activity of BLC was protected after 24 h of incubation in the presence of DNA polyhedrons as compared to the natural unfolding. The kinetics study confirmed the protective role of DNA polyhedrons on BLC with lower KM and higher catalytic efficiency. Furthermore, no profound conformational changes of BLC occur in the presence of DNA polyhedrons as observed in spectroscopic studies. From fluorescence quenching data we confirmed the binding between DNA polyhedrons and BLC. The thermodynamic parameters indicate that non-covalent bonds played a major role during the interaction of BLC with DNA polyhedrons. Moreover, the hepatic catalase activity remains unaltered in the presence of DNA polyhedrons. The cytotoxicity assay revealed that DNA polyhedrons were biocompatible in the cellular environment. The protective role of DNA polyhedrons on enzyme activity and the unaltered conformational change of protein ensures the biocompatibility of DNA polyhedrons in the cellular environment.

Potential relation between starch granule-associated proteins and retrogradation properties of buckwheat starch

To elucidate the effect of starch granule-associated proteins (SGAPs) on retrogradation properties of buckwheat starch, the retrogradation properties of Tartary buckwheat starch (TBS) and common buckwheat starch (CBS) before and after removal of SGAPs were systematically investigated, with wheat starch (WS) as reference. A significant decrease in gel strength of starches and density of starch aggregates were observed after removing SGAPs. The results were in line with the changes in retrogradation enthalpy of starches and short-range ordered structure of starch aggregates. After removing SGAPs, the retrogradation enthalpy of TBS decreased from 4.16 J/g to 3.74 J/g, CBS decreased from 4.05 J/g to 3.35 J/g and WS decreased from 3.27 J/g to 2.81 J/g, respectively. Taken together the results of LF-NMR, FTIR and rheological analysis, it can be concluded that SGAPs could promote the hydrogen bond interactions between starch molecules by competitively binding with water molecules, enhancing the rearrangement of starch molecules and forming a more ordered structure. Overall, the study suggested that the presence of SGAPs could enhanced the interaction between starch molecules chains, thus accelerated the retrogradation process. The research results provide more information about SGAPs in buckwheat starch and support further study for manipulation of starch properties.

Reuse of polymeric waste for the treatment of marine water polluted by diesel

Accidental diesel spills can occur in marine environments such as harbors, leading to adverse effects on the environmental compartment and humans. This study proposes the surgical mask as an affordable and sustainable adsorbent for the remediation of diesel-contaminated seawater to cope with the polymeric waste generated monthly in hospital facilities. This approach can also be helpful considering a possible future pandemic, alleviating the pressure on the waste management system by avoiding improper mask incineration and landfilling, as instead occurred during the previous COVID-19. Batch adsorption-desorption experiments revealed a complete diesel removal from seawater after 120 min with the intact laceless mask, which showed an adsorption capacity of up to 3.43 g/g. The adsorption curve was better predicted via Weber and Morris's kinetic (R2 = 0.876) and, in general, with Temkin isotherm (R2 = 0.965-0.996) probably due to the occurrence of chemisorption with intraparticle diffusion as one of the rates-determining steps. A hysteresis index of 0.23-0.36 was obtained from the desorption isotherms, suggesting that diesel adsorption onto surgical masks was faster than the desorption mechanism. Also, the effect of pH, ionic strength and temperature on diesel adsorption was examined. The results from the reusability tests indicated that the surgical mask can be regenerated for 5 consecutive cycles while decreasing the adsorption capacity by only approximately 11%.

Medium chain Fatty acids production from Food Waste via homolactic fermentation and lactate/ethanol elongation: Electron balance and thermodynamic assessment

This study explored the potential of Food Waste (FW) extract as a suitable substrate for Medium Chain Fatty Acids (MCFAs) production, in a single-phase reactor, where both fermentation and Chain Elongation (CE) processes occurred simultaneously. A continuous experiment was conducted with an Organic Loading Rate (OLR) = 20 gCOD L-1 d-1 and was fed in batch mode twice a week with pH = 6. In addition, four batch tests were performed, to assess the effects on the MCFAs production of caproate inhibition, hydrogen partial pressure (PH2) and different lactate/acetate ratios. Thermodynamics and electron flux were calculated to gain insights into the process pathways. Due to the presence of aminoacids, fermentation was mostly homolactic and both lactate and ethanol were produced as Electron Donors (EDs); the average MCFAs production efficiency was ∼ 12 %, although after 4 weeks the elongation process was halted, resulting in EDs accumulation. This occurred regardless of inoculum selection and the presence of caproate as a possible inhibitor, suggesting that EDs accumulation was due to the elongation process kinetics being slower than those of the fermentation step, thus calling for a longer Hydraulic Retention Time (HRT). It's worth noting that lactate was prevalently self-elongated to butyrate, whereas ethanol elongation only took place after lactate depletion, but was more efficient since it required other Electron Acceptors (EAs) such as butyrate, propionate or valerate. Moreover, the selected pH limited the acrylate pathway to a reasonable extent, whereas the high PH2 prevented both ethanol and lactate oxydation to acetate.

Spectroscopic and in silico evaluation of hesperetin, aglycone flavanone, as a prospective regulatory ligand for human salivary α-amylase

The insight into the binding mechanism of hesperetin, an aglycone flavanone, with human salivary α-amylase (HSAA), simulated under physiological salivary condition, was explored using various spectroscopic approaches and in silico method. Hesperetin effectively quenched the intrinsic fluorescence of HSAA and the quenching was mixed quenching mechanism. The interaction perturbed the HSAA intrinsic fluorophore microenvironment and the enzyme global surface hydrophobicity. The negative values of ΔG for thermodynamic parameters and in silico study revealed the spontaneity of HSAA-hesperetin complex while the positive values of enthalpy change (ΔH) and entropy change (ΔS) showed noticeable involvement of hydrophobic bonding in the stabilization of the complex. Hesperetin was a mixed inhibitor for HSAA with a KI of 44.60 ± 1.63 μM and having apparent inhibition coefficient (α) of 0.26. Macromolecular crowding, given rise to microviscosity and anomalous diffusion, regulated the interaction. Sodium ion (Na+) created high ionic strength, also, modulated the interaction. The in silico study proposed the preferential binding of hesperetin at the active cleft domain of HSAA with the least energy of -8.0 kcal/mol. This work gives a novel insight on the potentials of hesperetin as a future prospective medicinal candidate in the management of postprandial hyperglycemic condition.Communicated by Ramaswamy H. Sarma.