Unraveling the binding mechanisms of transglutaminase and substrate subjected to microwaves: Molecular docking and molecular dynamic simulations

Previous studies showed that transglutaminase (TGase) and microwaves acted synergistically to improve the functional properties of proteins. The mechanism behind this has yet to be elucidated. In this study, the phenomenon of microwaves enhancing TGase activity was experimentally validated. Molecular docking and molecular dynamics simulations revealed that moderate microwaves (105 and 108 V/m) increased the structural flexibility of TGase and promoted the orientation of the side chain carboxylate anion group on Asp255, driving the reaction forward. Also, TGase underwent partial transformation from α-helix to turns or coils at 105 and 108 V/m, exposing more residues in the active site and facilitating the binding of the substrate (CBZ-Gln-Gly) to TGase. However, 109 V/m microwaves completely destroyed the TGase structure, inactivating the enzyme. This study provides insights into the molecular mechanisms underlying the interactions between TGase and substrate subjected to microwaves, promoting the future applications of TGase and microwaves in food processing.

Formation and non-covalent interactions of binary and ternary complexes based on β-casein, Lentinus edodes mycelia polysaccharide, and taxifolin

Polyphenols, polysaccharides, and proteins are essential nutrients and functional substances present in food, and when present together these components often interact with each other to influence their structure and function. Proteins and polysaccharides are also excellent carrier materials for polyphenols. In this context, this study investigated the non-covalent interactions between taxifolin (TAX), Lentinus edodes mycelia polysaccharide (LMP), and β-casein (β-CN). β-CN and LMP spontaneously formed nanocomplexes by hydrogen bonds and van der Waals forces. The quenching constant and binding constant were (1.94 ± 0.02) × 1013 L mol-1 s-1 and (3.22 ± 0.17) × 105 L mol-1 at 298 K, respectively. The altered conformation of β-CN, resulting from the binding to LMP, affected the interaction with TAX. LMP significantly enhanced the binding affinity of TAX and β-CN, but did not change the static quenching binding mode. The binding constant for β-CN-TAX was (3.96 ± 0.09) × 1013 L mol-1, and that for the interaction between TAX and β-CN-LMP was (32.06 ± 0.05) × 1013 L mol-1. In summary, β-CN-LMP nanocomplexes have great potential as a nanocarrier for polyphenols, and this study provides a theoretical foundation for the rational design of non-covalent complexes involving LMP and β-CN, both in binary and ternary configurations.

Effects of Cu(II)-DOM complexation on DOM degradation: Insights from spectroscopic evidence

The fate of dissolved organic matter (DOM) is primarily governed by its sources, degradation, and transformation processes within the environment. However, the influence of metal-DOM complexation on DOM degradation remains ambiguous. In this study, controlled laboratory experiments were conducted using Cu(II) and natural water from the Duliujian River and the Beidagang Wetland to examine the effects of metal-DOM binding on the degradation pathway of DOM. Our results showed that Cu(II)-DOM complexation affected the distribution of DOM molecular weight with elevated Mw after complexed with Cu(II). Nevertheless, the concentration of DOM decreased over the incubation period due to degradation. In the absence of Cu(II) binding, both wetland and river DOM followed similar degradation pathways, transforming from high to low molecular weight with changes predominantly in the 1-10 kDa size-fraction during DOM degradation. In contrast, in the presence of Cu(II) and thus Cu(II)-DOM binding, the degradation of DOM was enhanced, resulting in higher kinetic rate constants for both wetland and river DOM. The results of differential spectra further confirmed the degradation of DOM with a decrease in bulk spectroscopic properties and an increase in the degree of DOM-Cu(II) complexation. These findings imply a mutually reinforcing relationship between metal-DOM complexation and the degradation of DOM in aquatic environments, providing new insights into the biogeochemical behavior and environmental fate of DOM.

The weakened physiological functions of human serum albumin in presence of polystyrene nanoplastics

Due to the widespread presence of nanoplastics (NPs) in daily essentials and drinking water, the potential adverse effects of NPs on human health have become a global concern. Human serum albumin (HSA), the most abundant and multi-functional protein in plasma, has been chosen to understand the biological effects of NPs after entering the blood. The esterase activity and the transport of bisphenol A in the presence of polystyrene nanoplastics (PSNPs) under physiological conditions (pH 4.0 and 7.4) have been investigated to evaluate the possible biological effects. The interactions between PSNPs and HSA have also been systematically studied by multispectral methods and dynamic light scattering techniques. The esterase activity of HSA presented a decreased trend with increasing PSNPs; conversely, higher permeabilities are accompanied by higher amounts of PSNPs. Compared with the unchanged hydrodynamic diameter and weaker interactions at pH 7.4, stronger binding between HSA and PSNPs at pH 4.0 led to a significant increase in the particle size of the PSNPs-HSA complex. The quenching mechanism belonged to the static quenching type. The electrostatic force is proposed to be the dominant factor for PSNPs binding to HSA. The work provides some information about the toxicity of NPs when exposed to humans.

Simultaneous binding characterization of different chromium speciation to serum albumin

The binding process between three species of chromium and serum albumin (SA) was investigated, as well as the interaction between K2Cr2O7 and bovine serum albumin (BSA) under coexistence of different chromium forms. CrCl3, K2Cr2O7 and Crpic bound to SA spontaneously through Van der Waals force, and their binding constants were 103-104 M-1 at 298 K, respectively. K2Cr2O7 and Crpic both had strong binding affinity for BSA, and significantly affected the secondary structure of BSA and the microenvironment surrounding amino acid residues. Chromium exhibited a greater fluorescence quenching constant towards HSA than toward BSA, and K2Cr2O7 induced greater conformational changes in human serum albumin (HSA) than in BSA. A weak binding of CrCl3 to BSA had no significant effect on the binding affinity of K2Cr2O7 to BSA. K2Cr2O7 and BSA have a greater binding affinity when coexisting with Crpic, and K2Cr2O7 induces a greater conformational change in BSA.

Synthesis of bioactive hemoglobin-based oxygen carrier nanoparticles via metal-phenolic complexation

The transfusion of donor red blood cells (RBCs) is seriously hampered by important drawbacks that include limited availability and portability, the requirement of being stored in refrigerated conditions, a short shelf life or the need for RBC group typing and crossmatching. Thus, hemoglobin (Hb)-based oxygen (O2) carriers (HBOCs) which make use of the main component of RBCs and the responsible protein for O2 transport, hold a lot of promise in modern transfusion and emergency medicine. Despite the great progress achieved, it is still difficult to create HBOCs with a high Hb content to attain the high O2 demands of our body. Herein a metal-phenolic self-assembly approach that can be conducted in water and in one step to prepare nanoparticles (NPs) fully made of Hb (Hb-NPs) is presented. In particular, by combining Hb with polyethylene glycol, tannic acid (TA) and manganese ions, spherical Hb-NPs with a uniform size around 350-525 nm are obtained. The functionality of the Hb-NPs is preserved as shown by their ability to bind and release O2 over multiple rounds. The binding mechanism of TA and Hb is thoroughly investigated by UV-vis absorption and fluorescence spectroscopy. The binding site number, apparent binding constant at two different temperatures and the corresponding thermodynamic parameters are identified. The results demonstrate that the TA-Hb interaction takes place through a static mechanism in a spontaneous process as shown by the decrease in Gibbs free energy. The associated increase in entropy suggests that the TA-Hb binding is dominated by hydrophobic interactions.

Characteristic Binding Landscape of Estrogen Receptor-α36 Protein Enhances Promising Cancer Drug Design

Breast cancer (BC) remains the most common cancer among women worldwide, and estrogen receptor-α expression is a critical diagnostic factor for BC. Estrogen receptor (ER-α36) is a dominant-negative effector of ER-α66-mediated estrogen-responsive gene pathways. ER-α36 is a novel target that mediates the non-genomic estrogen signaling pathway. However, the crystallized structure of ER-α36 remains unavailable for molecular studies. ER-positive and triple-negative BC tumors aggressively resist the FDA-approved drugs; therefore, highly potent structure-based inhibitors with preeminent benefits over toxicity will preferably replace the current BC treatment. Broussoflanol B (BFB), a B. papyrifera bark compound, exhibits potent growth inhibitory activity in ER-negative BC cells by inducing cell cycle arrest. For the first time, we unravel the comparative dynamic events of the enzymes' structures and the binding mechanisms of BFB when bound to the ER-α36 and ER-α66 ligand-binding domain using an all-atom molecular dynamics simulations approach and MM/PBSA-binding-free energy calculations. The dynamic findings have revealed that ER-α36 and ER-α66 LBD undergo timescale "coiling", opening and closing conformations favoring the high-affinity BFB-bound ER-α36 (ΔG = -52.57 kcal/mol) compared to the BFB-bound ER-α66 (ΔG = -42.41 kcal/mol). Moreover, the unbound (1.260 Å) and bound ER-α36 (1.182 Å) exhibit the highest flexibilities and atomistic motions relative to the ER-α66 systems. The RMSF (Å) of the unbound ER-α36 and ER-α66 exhibit lesser stabilities than the BFB-bound systems, resulting in higher structural flexibilities and atomistic motions than the bound variants. These findings present a model that describes the mechanisms by which the BFB compound induces downregulation-accompanied cell cycle arrest at the Gap0 and Gap1 phases.

Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations

Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.Communicated by Ramaswamy H. Sarma.

Biomimetic affinity chromatography for antibody purification: Host cell protein binding and impurity removal

Peptide affinity chromatography has received increasing attention as an alternative to protein A chromatography in antibody purification. However, its lower selectivity than protein A chromatography has impeded its success in practical applications. In particular, efficient removal of contaminants, including host cell proteins (HCPs) and DNA, is a great challenge for peptide affinity chromatography in monoclonal antibody (mAb) manufacturing. In this work, a biomimetic peptide ligand (bPL), FYWHCLDE, was coupled onto Sepharose 6 Fast Flow (SepFF) to synthesize a peptide affinity gel, SepFF-bPL, for the investigation of the binding mechanism of HCP as well as the feasibility of antibody capture. The results showed that the SepFF-bPL column exhibited effective removal of mAb aggregates as well as mAb capture from feedstocks of various origins, whereas poor removal of HCP and DNA was found. Mechanistic studies of HCP binding indicated that electrostatic interactions dominated HCP binding on the SepFF-bPL gel and that ionic conductivity had a significant influence on HCP binding at low salt concentrations. Thus, combined chromatin extraction and anion exchange adsorption were introduced prior to SepFF-bPL chromatography for initial contaminant removal to reduce mAb aggregation induced by HCP and the loading burden of contaminants in SepFF-bPL chromatography. A proof-of-concept study of the purification train demonstrated a high recovery of mAb (68.7%) and low levels of HCP (23 ppm) and DNA (below the limit of detection) in the final product, which were acceptable for the mandatory requirements in clinical applications. This research provided a deep understanding of HCP binding on the peptide affinity column and led to the development of an effective purification train.

Comparative analysis of the interaction between alpha-lactalbumin and two edible azo colorants equipped with different sulfonyl group numbers

Alpha-lactalbumin (α-La) is a crucial active component in whey protein. It would be mixed with edible azo pigments during processing. Spectroscopic analyses and computer simulations were used here to characterize the interaction between acid red 27 (C27) /acidic red B (FB) and α-La. Fluorescence, thermodynamics, and energy transfer showed the binding mechanism is a static quenching with a medium affinity. This binding process occurred spontaneously and was mainly driven by hydrophobic forces. Conformation analysis showed FB led to a greater change in the secondary structure of α-La compared with C27. C27 increased and FB decreased the surface hydrophobicity of α-La. The spatial structures of complexes were visualized with computer aid. The azo colorant binds to α-La easily and deeply with a smaller space volume and dipole moment and thereby affecting the α-La conformation and functionality. This study provides a theoretical basis for the application of edible azo pigments.

Pulsed electric field improves the EGCG binding ability of pea protein isolate unraveled by multi-spectroscopy and computer simulation

Understanding molecular mechanisms during protein modification is critical for expanding the application of plant proteins. This study investigated the conformational change and molecular mechanism of pea protein isolate (PPI) under pulsed electric field (PEF)-assisted (-)-Epigallocatechin-Gallate (EGCG) modification. The flexibility of PPI was significantly enhanced after PEF treatment (10 kV/cm) with decrease (23.25 %) in α-helix and increase (117.25 %) in random coil. The binding constant and sites of PEF-treated PPI with EGCG were increased by 2.35 times and 10.00 % (308 K), respectively. Molecular docking verified that PEF-treated PPI had more binding sites with EGCG (from 4 to 10). The number of amino acid residues involved in hydrophobic interactions in PEF-treated PPI-EGCG increased from 5 to 13. PEF-treated PPI-EGCG showed a significantly increased antioxidant activity compared to non-PEF-treated group. This work revealed the molecular level of PEF-assisted EGCG modification of PPI, which will be significant for the application of PPI in food industry.

Interaction mechanism of Cu+/Cu2+ on bovine serum albumin: Vitro simulation experiments by spectroscopic methods

Copper (Cu) is an essential trace element for organisms, while excessive concentration of Cu is toxic. In order to assess the toxicity risk of copper in different valences, FTIR, fluorescence, and UV-vis absorption techniques were conducted to study the interactions between either Cu⁺ or Cu²⁺ and bovine serum albumin (BSA) under vitro simulated physiological condition. The spectroscopic analysis demonstrated that the intrinsic fluorescence emitted by BSA could be quenched by Cu⁺/Cu²⁺ via static quenching with binding sites 0.88 and 1.12 for Cu⁺ and Cu²⁺, respectively. On the other hand, the constants of Cu⁺ and Cu²⁺ are 1.14 × 10³ L/mol and 2.08 × 10⁴ L/mol respectively. ΔH is negative whereas ΔS is positive, showing that the interaction between BSA and Cu⁺/Cu²⁺ was mainly driven by electrostatic force. In accordance with Föster's energy transfer theory, the binding distance r showed that the transition of energy from BSA to Cu⁺/Cu²⁺ is highly likely to happen. BSA conformation analyses indicated that the interactions between Cu⁺/Cu²⁺ and BSA could alter the secondary structure of proteins. Current study provides more information of the interaction between Cu⁺/Cu²⁺ and BSA, and reveals the potential toxicological effect of different speciation of copper at molecular level.

Effect of tea polyphenols on sturgeon myofibrillar protein structure in the in vitro anti-glycation model mediated by low temperature vacuum heating

The binding mechanism between tea polyphenols and sturgeon myofibrillar protein (SMP) in the early stage (0, 2, 4 min), middle stage (6, 10 min) and late stage (15 min) of low temperature vacuum heating (LTVH) in an in vitro anti-glycation model was investigated. The result indicated that the protein cross-linking during LTVH treatment were mainly induced by tea polyphenols. The loss rate of free arginine (Arg) and free lysine (Lys) of SMP at the late stage of LTVH treatment (15 min) was 73.95 % and 83.16 %, respectively. The hydrophobic force and disulfide bond were the main force between tea polyphenols and SMP in the middle and late stage of LTVH treatment. The benzene ring and phenolic hydroxyl group of tea polyphenols can interact with the amino acid residues of SMP, which was exothermic and entropy-increasing. This study provides new insights in the interaction mechanisms between tea polyphenols-protein during heat treatment process.

Suspended particulate matter-associated environmental corticosteroids in the Pearl River, China: Occurrence, distribution, and partitioning

Suspended particulate matter (SPM) plays an important role in the geochemical behavior and fate of organic micropollutants in aquatic environments. However, the presence of trace emerging endocrine disruptors such as environmental corticosteroids (ECs) in SPM is less well understood. This study focused on the occurrence, distribution, and partitioning of SPM-associated ECs in the Pearl River system, China. Ubiquitous particulate ECs were found in the surface water of the rivers at average concentrations (dry weight) between 0.46 ng/g (flumethasone) and 8.83 ng/g (clobetasone butyrate). The total EC (∑ECs) concentrations of the 24 selected target compounds varied from <1.03 ng/g to 62.3 ng/g, with an average and median of 17.6 ng/g and 13.7 ng/g, respectively. Higher SPM-bound EC levels were commonly observed in winter (dry season), and spatially, their relatively high contamination in urban tributary networks decreased while flowing to mainstreams and then gradually attenuated from upstream to the estuary. Despite the approximately 90 % mass distribution of ∑ECs in the aqueous phase, approximately 50 % of their effect burden was derived from the suspended particulate fractions. For the first time, in situ SPM-water partitioning coefficients (K_p) and their organic carbon-normalized ones (K_oc) of ECs were determined in surface waters, and a field-derived preliminary linear equation was proposed to estimate K_oc for ECs using basic physicochemical parameters n-octanol/water partitioning coefficient (K_ow), which is of importance with regard to the assessment of transport, fate, and risk of these emerging hazardous chemicals. Furthermore, the significant logK_oc-logK_ow relationship for ECs reveals that nonspecific hydrophobic partitioning is a major association mechanism between SPM and ECs. Moreover, hydrogen bonding is suggested to be a prevailing specific binding mechanism and provides more contribution to nonhydrophobic interactions between ECs and particulate organic matter than environmental estrogens.

Structural insights into the AFB1 aptamer coupled with a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB1 detection

Aflatoxin B₁ (AFB₁) is a typical food contaminant. A truncated DNA aptamer of AFB₁ was reported by our team in previous work. However, the recognition mechanism between aptamer and AFB₁ was lacking, which was crucial for the design of related aptasensor. Herein, the binding of aptamer to AFB₁ was systematically studied and found that it was an exothermic process and the conformation of aptamer changed during the recognition process. Loop bases in the secondary structure of aptamer formed a special binding pocket to recognize AFB₁. Van der Waals and electrostatic interaction were the main driving forces. By blocking the stem bases guided by the structural investigation, a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB₁ detection was constructed, and the sensitivity was improved by target recycling. Under optimal conditions, the linear detection range for AFB₁ was 0.01-20 ng/mL, and AFB₁ was accurately determined in corn and wheat samples. This work laid a theoretical foundation for the design of AFB₁ aptasensor, and the developed detection model came up with new ideas for the development of CRISPR/Cas12a-based aptasensor.

Thyroid hormone activities of neutral and anionic hydroxylated polybrominated diphenyl ethers to thyroid receptor β: A molecular dynamics study

Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been identified as the strong endocrine disrupting chemicals to humans, which show structural similarity with endogenous thyroid hormones (THs) and thus disrupt the functioning of THs through competitive binding with TH receptors (TRs). Although previous studies have reported the hormone activities of some OH-PBDEs on TH receptor β (TRβ), the interaction mechanism remains unclear. Furthermore, hydroxyl dissociation of OH-PBDEs may alter their TR disrupting activities, which has not yet been investigated in depth. In this work, we selected 18 OH-PBDEs with neutral and anionic forms and performed molecular dynamics (MD) simulations to estimate their binding interactions with the ligand binding domain (LBD) of TRβ. The results demonstrate that most of OH-PBDEs have stronger binding affinities to TRβ-LBD than their anionic counterparts, and the hydroxyl dissociation of ligands differentiate the major driving force for their binding. More Br atoms in OH-PBDEs can result in stronger binding potential with TRβ-LBD. Moreover, 5 hydrophobic residues, including Met313, Leu330, Ile276, Leu346, and Phe272, are identified to have important contributions to bind OH-PBDEs. These results clarify the binding mechanism of OH(O^-)-PBDEs to TRβ-LBD at the molecular level, which can provide a solid theoretical basis for accurate assessment of TH disrupting effects of these chemicals.

Ferric ions release from iron-binding protein: Interaction between acrylamide and human serum transferrin and the underlying mechanisms of their binding

Acrylamide (ACR) is a surprisingly common chemical due to its widespread use in industry and various other applications. However, its toxicity is a matter of grave concern for public health. Even worse, ACR is frequently detected in numerous fried or baked carbohydrate-rich foods due to the Maillard browning reaction. Herein, this study intends to delineate the underlying molecular mechanisms of Fe ions released from iron-binding protein transferrin (TF) after acrylamide binding by combining multiple methods, including multiple complementary spectroscopic techniques (UV-Vis, fluorescence, and circular dichroism spectroscopy), isothermal titration calorimetry, ICP-MS measurements, and modeling simulations. Results indicated that free Fe was released from TF only under high-dose ACR exposure (>100 μM). Acrylamide binding induced the loosening and unfolding of the backbone and polypeptide chain and destroyed the secondary structure of TF, thereby leading to protein misfolding and denaturation of TF and forming a larger size of TF agglomerates. Of which, H-binding and van der Waals force are the primary driving force during the binding interaction between ACR and TF. Further modeling simulations illustrated that ACR prefers to bind to the hinge region connecting the C-lobe and N-lobe, after that it attaches to the Fe binding sites of this protein, which is the cause of free Fe release from TF. Moreover, ACR interacted with the critical fluorophore residues (Tyr, Trp, and Phe) in the binding pocket, which might explain such a phenomenon of fluorescence sensitization. The two binding sites (Site 2 and Site 3) located around the Fe (III) ions with low-energy conformations are more suitable for ACR binding. Collectively, our study demonstrated that the loss of iron in TF caused by acrylamide-induced structural and conformational changes of transferrin.

Human hair rich in pyridinic nitrogen-base DNA biosensor for direct electrochemical monitoring of palbociclib-DNA interaction

Carbon material derived from the waste-based biomass human hair (H), which is naturally rich in pyridinic nitrogen, provides a significant benefit in biosensor applications with its dominant conductivity character. The carbon material was synthesized from human hair waste by the hydrothermal carbonization (HTC) method, which is a promising green synthesis. A morphological characterization of the carbon materials was performed. In this study, H and amine-functionalized multi-walled carbon nanotubes (NH₂-MWCNT) were combined for the first time as a modifier, which enhanced the glassy carbon electrode (GCE) surface area for deoxyribonucleic acid (DNA) biosensor studies. Palbociclib (PLB) is clinically used in the treatment of breast cancer. The novel electrochemical nanobiosensor was used to investigate the dsDNA-PLB interaction to evaluate the possibility that PLB causes conformational changes in DNA structure and/or oxidative damage. The interaction was conducted based on the voltammetric signals of deoxyguanosine (dGuo) and deoxyadenosine (dAdo) by differential pulse voltammetry (DPV) on a bare and H + NH₂-MWCNT modified GCE. The proposed analytical method was applied to a pharmaceutical dosage form with a satisfactory recovery of 98.25 %. The nanobiosensor was tested in the presence of some interfering agents. The binding mechanism of dsDNA-PLB was also evaluated by spectroscopic and theoretical calculations.

Unraveling the binding mechanism of the active form of Remdesivir to RdRp of SARS-CoV-2 and designing new potential analogues: Insights from molecular dynamics simulations

The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy. This suggest that these analogues might be able to covalently link to the primer strand as RTP, but their 3' modification would terminate the primer strand growth.

Binding mechanism and antioxidant activity of piperine to hemoglobin

Piperine (PIP) is the most active main component in pepper. The interaction of small molecules with biomolecules leads to structural and functional changes. In this study, the binding mechanism and antioxidant activity of PIP with hemoglobin (Hb) are presented using spectroscopic and computational methods. Results showed that the redox activity of PIP on Hb showed concentration dependence. Fluorescence and isothermal titration calorimetric experiments showed that the Hb-PIP system had a static quenching mechanism at a single binding site. The addition of PIP caused a slight perturbation to the secondary structure of Hb by structural analysis. The structural stability of the Hb-PIP binding system was demonstrated by molecular dynamics simulations, and molecular docking and thermodynamic constants confirmed that the electrostatic interaction force was dominant in the energy contribution of the system. Research results are conducive to the potential use of PIP in related meat products.

Exploring the interaction between Cry1Ac protein and Zn2+, Cd2+ metal ions by fluorescence quenching and molecular docking approaches

Bacillus Thuringiensis (Bt) protein has a strong ability to complex with metal ions, which may increase the transport of metal ions in the soil multi-media system. In this study, the interactions between Cry1Ac protein and metal ions (Zn²⁺ and Cd²⁺) were investigated through spectroscopies and molecular docking methods. The spectra results showed that both Zn²⁺ and Cd²⁺ quenched the fluorescence intensity of Cry1Ac protein through the static quenching. The binding constants with 4-5 orders of magnitude also indicated the interactions between the ions and the Cry1Ac protein. The thermodynamic analysis showed that hydrogen bonds and van der Waals forces were predominant during the processes. In terms of the Förster non-radiation energy transfer theory, the binding distances between metal ions and Cry1Ac protein were approximately 0.21-0.24 nm, indicating the existence of a non-radiative energy transfer between them. Furthermore, molecular docking revealed that the metal ions participated in ligand binding with the Cry1Ac at the locations Asp569, Thr560, Asn564 and Gln566. The present work provided reasonable models helping us further understand the transport effect of heavy metals in the presence of Cry1Ac. The results could provide mechanistic insights into the nature of metal ions-Cry1Ac interactions and offer important information on the toxicity risk of metal ions-Cry1Ac binding interactions.

Interaction between pH-shifted ovalbumin and insoluble neohesperidin: Experimental and binding mechanism studies

In this study, ovalbumin (OVA) formed a complex with neohesperidin (NH) via a pH-shifting method. The NH-OVA complex self-assembled into NH-OVA nano-particles, which were then characterized and whose binding mechanism was evaluated by using multi-spectroscopic, thermodynamics, and molecular docking simulation methods. Fluorescence intensity decreased after OVA was complexed with NH. The binding constant of the OVA-NH complex was in the order of 6.32 × 10⁵ M^-1 suggesting that the complex is stable. Circular dichroism (CD) analysis showed that α -helix content increased, β-folding, β -turning, and irregular crimp content decreased after OVA and NH binding. Isothermal titration calorimetry results showed that hydrophobic interactions and hydrogen bonds made an important impact in the complex formation. The molecular docking results revealed that Van der Waals forces and hydrogen bonds contributed to the free binding energy of the complex. There were multiple possible surface binding sites between OVA with NH. The obtained results provide new insights into the interaction mechanism of OVA and NH, and as a vehicle for NH, the OVA has shown promising applications in functional foods.

Discovery and computational studies of 2-phenyl-benzoxazole acetamide derivatives as promising P2Y14R antagonists with anti-gout potential

The P2Y₁₄ nucleotide receptor, a subtype of P2Y receptors, is implicated in many human inflammatory diseases. Based on the identification of favorable residues of two screening hits in the almost symmetrical P2Y₁₄ binding domain, we describe the structural optimization of previously identified virtual screening hits 6 and 7 that result in the development of P2Y₁₄R antagonists with a novel 2-phenyl-benzoxazole acetamide chemical scaffold. Notably, compound 52 showed potent P2Y₁₄R antagonistic activity (IC₅₀ = 2 nM), and a stronger inhibitory effect on MSU-induced inflammatory in vitro, better than a previously described P2Y₁₄R antagonist PPTN. In vivo evaluation demonstrated that compound 52 also had satisfactory inhibitory activity on the inflammatory response of gout flares in mice. Moreover, P2Y₁₄R antagonist 52 decreased paw swelling and inflammatory cell infiltration through cAMP/NLRP3/GSDMD signaling pathways in MSU-induced acute gouty arthritis mice. The discussions on the binding mechanism that employ MM/GBSA free energy calculations/decompositions also provide some useful clues for further structural designing of compound 52. Taken together, 2-phenyl-benzoxazole acetamide derivative 52 with potent P2Y₁₄R antagonistic activity and in vivo potency could be a promising strategy for gout therapy and deserves further optimization.

Novel ssDNA aptamer-based fluorescence sensor for perfluorooctanoic acid detection in water

Per- and polyfluoroalkyl substances (PFAS) are widely detected environmental contaminants, and there is a great need for development of sensor technologies for rapid and continuous monitoring of PFAS. In this study, we have developed fluorescence based aptasensor that can possibly monitor perfluorooctanoic acid (PFOA) in water with limit of detection (LOD) of 0.17 μM. This is first to report the successful isolation of PFAS binding ssDNA aptamers. The obtained aptamer selectively binds PFOA with dissociation constant (K_D) of 5.5 μM. Specific aptamer binding sites to PFOA were identified and the length of the fluorinated carbons was a key binding factor rather than the functional group. The aptamer binding to structurally similar PFAS compounds (i.e., perfluorocarboxylic acids and perfluorosulfonic acids with 4-8 carbon chains) was also investigated; the aptamer K_D values were 6.5 and 3.3 μM for perfluoroheptanoic acid and perfluorohexanesulfonic acid, respectively, while other analogs did not bind to the aptamer. The presence of major inorganic ions and dissolved organic matter had negligible influences on the aptamer performance (<14% at a 10 mM concentration), and the aptamer performance was also robust in real wastewater effluent conditions, with a K_D of 7.4 μM for PFOA. Fluorescence-based aptasensor developed in this study is adequate in monitoring PFOA levels in water contaminated with the accident spills and heavy usage of fire-fighting foams near the industrial sites and military bases. More importantly, the study opens up new capability of aptasensors to efficiently monitor the trace amount of various PFAS compounds and other fluorinated alternatives in natural and engineered water environments.

Interaction of mercury ion (Hg2+) with blood and cytotoxicity attenuation by serum albumin binding

Blood mercury reflects the amount available from tissues, which is an indication of the exposure level. Here we confirm that Hg²⁺ caused hemolytic effects at high concentrations; while at light concentrations, most of the ions were bound to human serum albumin (HSA). The binding mechanism of Hg²⁺ to HSA has been investigated, which indicated that the presence of Hg²⁺ significantly perturbed the structure of HSA and quenched the fluorescence of protein in a hybrid dynamic and static mode. Hg²⁺ was preferably bound to cysteine and cystine, where the R‒S‒S‒R structure is responsible for maintaining the protein's structure by stabilizing the α-helical bundles. The metal-protein interaction mitigated the cellular toxicity as concealed by A498 cell lines. The fundamental and comprehensive data in this work is beneficial to elucidating and understanding the identification and binding mechanisms of heavy metals with proteins, as well as possible risks on human beings and the environment.

Structural and molecular aspects of flavonoids as ligands for serum transferrin

Human serum transferrin (HST) acts as a carrier for Fe³⁺ and other ions. Binding of flavonoids to HST produces changes in the protein structure with direct implication on iron delivery into cells. We investigate the binding mechanism and affinity towards HST of three flavonoids: rutin, luteolin, and apigenin by different techniques: UV-Vis, fluorescence, fluorescence resonance energy transfer (FRET) combined with molecular docking. UV-Vis results indicate an interaction between flavonoids and HST. It was observed that HST fluorescence was quenched by these three flavonoids via a static process. All the interactions were moderate and the main driving forces are hydrophobic (ΔH > 0 and ΔS > 0) for rutin and luteolin binding or electrostatic (ΔH < 0 and ΔS > 0) for apigenin binding. FRET and molecular docking studies confirm the fluorescence static quenching mechanism by flavonoid binding. The binding of all three flavonoids increases HST stability. These results present the potential use of HST in target-oriented delivery of flavonoids and possibly other drugs into cells.

Extraction of Pb(II) from wheat samples via dual-frequency ultrasound-assisted enzymatic digestion and the mechanisms of its interactions with wheat proteins

A novel dual-frequency ultrasound-assisted enzymatic digestion (DUED) technique was used to extract Pb(II) from certified reference materials (CRMs) of wheat flour. Following this, the interactions of Pb(II) with wheat proteins were investigated to provide evidence for the selection of enzyme species. The results showed that the simultaneous use of α-amylase and flavourzyme resulted in the recovery of 97.9% of Pb(II) in 6 min under a 40 kHz ultrasonic bath combined with a 20 kHz ultrasonic probe. The exopeptidase activity of the flavourzyme was found to be the main contributor to the extraction of Pb(II) from the CRMs. Additionally, the proposed method exhibited a low detection limit (8.2 ng/g) and high recoveries of real samples (93.4%-112.2%) with RSD less than 7.33%. Furthermore, the oxygen-containing groups of wheat proteins, the nitrogen-containing groups of albumins and globulins, and the sulfur-containing groups of gliadins and glutenins were found to offer coordination sites for Pb(II).

Binding mechanism and functional evaluation of quercetin 3-rhamnoside on lipase

The interaction between lipase and quercetin 3-rhamnoside was studied by fluorescence spectroscopy, enzyme kinetics, and molecular dynamics simulation. The results showed that quercetin 3-rhamnoside had a strong quenching effect on the intrinsic fluorescence of lipase. The binding constant decreased with increasing temperature, and the number of binding sites approached 1. Thermodynamic parameters indicated that hydrogen bonding and van der Waals forces are the dominant forces when the interaction occurs. Circular dichroism spectroscopy and infrared spectroscopy proved that the ligand perturbed the structure of lipase. Enzyme kinetics results showed that quercetin 3-rhamnoside inhibited lipase, and the inhibitory effect was dose-dependent. Molecular dynamics simulation further explained the interaction mechanism and inhibitory effect. This study confirmed the inhibitory effect of quercetin 3-rhamnoside on lipase explained their binding mechanism, which will contribute to guiding the development of fat-reducing functional foods.

Kinetic Methods of Deducing Binding Mechanisms Involving Intrinsically Disordered Proteins

There are multiple examples of protein-protein interactions involving one intrinsically disordered protein region binding to an ordered protein domain in a coupled binding and folding reaction. Similarly to protein folding studies, much effort has been devoted to understanding the mechanisms of such coupled binding and folding reactions. In this chapter, we describe how kinetics can be used to assess binding mechanisms with focus on fluorescence-monitored stopped-flow experiments. The approach can be applied more generally to any protein interaction with or without a coupled conformational change and to other kinetic techniques. Determining binding mechanisms is a great challenge and while "proving" a mechanism may be futile, it is possible to deduce the simplest scenarios, which are consistent with experimental data.

Interactions of iron-based nanoparticles with soil dissolved organic matter: adsorption, aging, and effects on hexavalent chromium removal

The interactions and mechanisms between soil dissolved organic matter (DOM) and three types of iron-based nanoparticles (NPs), i.e., nanoscale zero-valent iron (nZVI) particles, Fe₂O₃ NPs, and Fe₃O₄ NPs, were investigated in short-term exposure experiments. The adsorption results showed that soil DOM was rapidly adsorbed on the surface of the iron-based NPs with the adsorption rate varying according to Fe₃O₄ > Fe₂O₃ > nZVI. Spectral analysis results revealed that aromatic DOM fractions with high-molecular-weights were preferentially adsorbed. The binding mechanism was determined as hydrogen bonding and ligand exchange via Fourier transform infrared spectroscopy (FT-IR) analysis. Scanning electron microscopy, FT-IR, X-ray photoelectron spectroscopy, and X-ray diffraction were used to identify the corrosion products of the three iron-based NPs at the adsorption equilibrium. The results suggest that Fe₃O₄ and/or γ-Fe₂O₃ and α-FeOOH were the main corrosion products of nZVIs and α-FeOOH was obtained as an aged product of Fe₃O₄ NPs. Results of Cr(VI) removal tests suggest that the aged nZVI achieved 79.87% of Cr(VI) removal and the Cr(VI) removal efficiency was significantly improved by coating DOM onto Fe₂O₃ NPs. The overall data indicate the fate and transformation of iron-based NPs and the enhancement for Cr(VI) removal after interactions between DOM and NPs.

Protective effects of three structurally similar polyphenolic compounds against oxidative damage and their binding properties to human serum albumin

Brazilin (Bra), hematoxylin (Hto) and hematein (Hte) are structurally similar polyphenols having rich biological activities, but their antioxidant ability has not been well studied. Here, their protective ability against human serum albumin (HSA) oxidative degradation were investigated using 2,2'-Azobis (2-methylpropionamidine) dihydrochloride (AAPH), NaClO and Fenton like reactions methods. The results indicated that polyphenols inhibited the oxidative injuries of HSA in the order: Hto > Bra > Hte. Additionally, the biological effects of polyphenols were mostly influenced by their binding to protein. Therefore, the structure-affinity relationships of polyphenols binding to HSA were also explored. Fluorescence experiments indicated that polyphenols bound to HSA through static quenching mechanism. Furthermore, some conformational changes of HSA could be observed in the presence of polyphenols. Altogether, molecular structure of polyphenols played a significant role in their protective effect against HSA oxidative damage and binding ability, which provided fundamental insights into their application as health care foods.

Binding affinity of family 4 carbohydrate binding module on cellulose films of nanocrystals and nanofibrils

The binding affinity and thermodynamics of family 4 carbohydrate-binding module (CBM4), belonging to type B CBM, on model surfaces of cellulose nanocrystals (CNC) and nanofibrils (CNF) were investigated by quartz crystal microbalance with dissipation monitoring (QCM-D) technology in real-time at different temperatures. The thermodynamic parameters associated with the interaction, such as Gibbs free energy, enthalpy change, entropy change and heat capacity were obtained using the van't Hoff analysis via a nonlinear parameter estimation. The results demonstrated CBM4 binds preferentially to both CNF and CNC, whereas the driving forces behind them were very different. The former was related to the hydrogen bonds formed in the CBM4 clefts, resulting in a favorable enthalpy but compensated by unfavorable entropy change; on the contrary, the latter was mainly driven by favorable entropy but compensated by unfavorable enthalpic change due to water rearrangement.

Exploring the biochemical properties of three polyphenol oxidases from blueberry (Vaccinium corymbosum L.)

Purification of blueberry polyphenol oxidase (PPO) has not been substantially progressed for a long time, which leads to little further study. We purified three PPOs from blueberries for the first time by modified Native-Page. The PPO-2 consists of two subunits (68 and 36 kDa), whereas PPO-3 and PPO-4 contain only one subunit (36 kDa). The optimum pH and temperature of PPO-2, PPO-3, and PPO-4 were 5.8-6.2 and 40 °C-45 °C with catechol as a substrate. The optimal substrates for them were all catechol (K_m = 14.91, 7.19, and 11.20, respectively). High-pressure processing (HPP) had a limited inhibitory effect on the three PPOs. The activities of PPO-2, PPO-3, and PPO-4 were significantly reduced with increased SDS concentration. The binding of substrate to catalytic cavity is related to the residues His76, His209, His213, Gly228, and Phe230. The carbonyl group of residue Gly228 is one of the key sites for screening substrates.

Investigation of the transformation and toxicity of trichlorfon at the molecular level during enzymic hydrolysis of apple juice

Trichlorfon is one of the most widely used organophosphorus pesticides in agriculture. In this study, the extent of transformation of trichlorfon to dichlorvos (DDVP), during the polygalacturonase (PG) treatment of apple pulp was monitored. A transformation pathway is proposed for trichlorfon molecules, based on density functional theory (DFT) calculations. The transformation of trichlorfon involves hydroxyl substitution and cleavage, which was confirmed by molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) theory. In addition, the toxicity of trichlorfon and its transformed products was analyzed using Ecological Structure Activity Relationships (ECOSAR) software. The binding sites of the two pesticides are located in the hydrophobic grooves of the acetylcholinesterase (AChE) active site region and both pesticides form hydrophobic interactions and hydrogen bonds with a large number of surrounding amino acid residues. DDVP binds more strongly with AChE, so it is a better AChE inhibitor and more toxic than trichlorfon.

Ferrihydrite nanoparticles insights: Structural characterization, lactate dehydrogenase binding and virtual screening assay

The binding between the enzyme lactate dehydrogenase (LDH) and ferrihydrite nanoparticles (Fh-NPs) was investigated by means of small-angle neutron scattering (SANS), Fourier-transform infrared (FTIR) spectroscopy, fluorescence and Förster resonance energy transfer (FRET) and molecular docking. Fh-NPs - LDH compounds of dimensions under 100 nm are formed. The conformational changes and the mechanism of interaction between LDH and Fh-NPs simple and doped with Cu and Co, and the effect of these NPs on the thermal denaturation of LDH were monitored. The quenching mechanism is static, the binding occurring with moderate affinity, being mainly driven by hydrogen bonding and van der Waals forces. FRET occurs at a minimal distance of 2.55 nm. Thermal denaturation of LDH in the presence of simple and doped Fh-NPs shows that the thermodynamic parameters of protein unfolding are significantly changed with temperature. The denaturation temperature of LDH shifts to higher values in the presence of all Fh-NPs, than in the case of simple LDH. The docking approach estimates the energy corresponding to the best fit of the ferrihydrite in the LDH binding site near Trp. These results have direct implications on the uses of the complex of LDH with Fh-NPs in various biochemical, biological, or clinical applications.

Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol

The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.

Comprehensive investigations about the binding interaction of acesulfame with human serum albumin

In this work, the binding interaction of an artificial sweetener, acesulfame (ACS) with human serum albumin (HSA) are investigated at the molecular level by using spectral methods and molecular modeling. ACS has the ability to induce static quenching of the intrinsic fluorescence of HSA by a complex formed between HSA and ACS through weak multi-noncovalent forces including hydrophobic, hydrogen bond and van der Waals forces. ACS enters subdomain IIA of HSA to induce the tertiary structure changes of HSA and decreased the hydrophobicity of protein. In addition, ACS binding does not obviously alter the secondary structure of HSA. This study is hoped to provide some crucial information for further investigations of the biosafety of sweetener.

Computational studies of potent covalent inhibitors on wild type or T790M/L858R mutant epidermal growth factor receptor

In this paper, we designed and synthesized two analog compounds M1 and T1 that have a Michael acceptor warhead. Although only slightly diversity existed in the structures of M1 and T1, their inhibitory activities against wild type epidermal growth factor receptor (EGFR^WT) and T790M/L858R mutant epidermal growth factor receptor (EGFR^T790M/L858R) were significant different. Thus, multiple computational approaches were applied to investigate the interactions between the compounds with EGFR^WT and EGFR^T790M/L858R in order to explore the effect of different compounds. The molecular docking and MD simulations were performed to study the intermolecular interactions between compounds and EGFR. The binding free energy revealed that M1-EGFR^WT and M1-EGFR^T790M/L858R complexes have stronger binding affinity compared with the corresponding T1-EGFR^WT and T1-EGFR^T790M/L858R complexes, respectively. And the binding free energy decompositions for each residue analysis indicated that the van der Waals interactions are the major contributor to enhance the compounds to bind with EGFR. In addition, covalent binding complexes of M1-EGFR^WT and M1-EGFR^T790M/L858R were constructed and studied. Moreover, quantum mechanics method was applied to investigate the reaction mechanism of covalent binding of the compound and EGFR. The results will provide the details of structural and energetic information to develop potent covalent EGFR inhibitors in the future.

XPS and two-dimensional FTIR correlation analysis on the binding characteristics of humic acid onto kaolinite surface

The stabilization and preservation of soil organic matter have been attributed to the strong reactive sites of mineral surfaces that cause physical isolation and chemical stabilization due to the organic-mineral interface. However, much of the micro-scale knowledge about interactions between organic ligands and minerals largely remains at the qualitative level, and neglects the heterogeneity of functional groups of organic matter. Here, we report the use of molecular-scale technologies of two-dimensional FTIR Correlation Spectroscopy (2D-FTIR-CoS) and X-ray Photoelectron Spectroscopy (XPS) to directly measure the binding processes of humic acid (JGHA) groups onto kaolinite surface. The spectroscopy results showed that the carboxylate groups, aliphatic OH and aromatic structure participate in the binding of JGHA on kaolinite surface. The carboxylic and phenolic hydroxyl interact with kaolinite surface through the interfacial COAl/Si bonds. Kaolinite prefers to adsorb C-groups at pH 4.0 and O-groups at pH 8.0. The interaction of COO^- group at 1566 cm^-1 of JGHA leads to the formation of inner-sphere complex first and then outer-sphere complex with increasing contact time. The interaction of COOH group at 1261 cm^-1 with the AlOH²⁺ of kaolinite was could be ascribed to ligand exchange and/or electrostatic attraction, whose contribution was evaluated to be 13.90%, 7.65% and 0% at pH 4.0, 6.0 and 8.0, respectively. These results of molecular binding provide quantitative mechanistic insights into organic-mineral interactions and expound the effect of functional groups of HA on binding mechanisms, and thus bring important clues for better understanding the mobility and transformation of land‑carbon including mineral-bound carbon.

Mechanistic modeling explains the dsRNA length-dependent activation of the RIG-I mediated immune response

In cell-intrinsic antiviral immunity, cytoplasmic receptors such as retinoic acid-inducible gene I (RIG-I) detect viral double-stranded RNA (dsRNA) and trigger a signaling cascade activating the interferon (IFN) system. This leads to the transcription of hundreds of interferon-stimulated genes (ISGs) with a wide range of antiviral effects. This recognition of dsRNA not only has to be very specific to discriminate foreign from self but also highly sensitive to detect even very low numbers of pathogenic dsRNA molecules. Previous work indicated an influence of the dsRNA length on the binding behavior of RIG-I and its potential to elicit antiviral signaling. However, the molecular mechanisms behind the binding process are still under debate. We compare two hypothesized RIG-I binding mechanisms by translating them into mathematical models and analyzing their potential to describe published experimental data. The models consider the length of the dsRNA as well as known RIG-I binding motifs and describe RIG-I pathway activation after stimulation with dsRNA. We show that internal RIG-I binding sites in addition to cooperative RIG-I oligomerization are essential to describe the experimentally observed RIG-I binding behavior and immune response activation for different dsRNA lengths and concentrations. The combination of RIG-I binding to internal sites on the dsRNA and cooperative oligomerization compensates for a lack of high-affinity binding motifs and triggers a strong antiviral response for long dsRNAs. Model analysis reveals dsRNA length-dependency as a potential mechanism to discriminate between different types of dsRNAs: It allows for sensitive detection of small numbers of long dsRNAs, a typical by-product of viral replication, while ensuring tolerance against non-harming small dsRNAs.

Effects of piceatannol on the structure and activities of bovine serum albumin: A multi-spectral and molecular modeling studies

Piceatannol (PIC) displays a wide spectrum of biological activities, such as antioxidation, antibacterial activity and anti-inflammation, but the biochemical and molecular mechanism is not fully understood. In this study, the interaction of PIC with bovine serum albumin (BSA) was studied by fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy, circular dichroism spectroscopy and molecular simulation. The effects of PIC on BSA non-enzymatic glycosylation, fibrillation, thermal stability, and structure information were also studied. The results showed that the formation of PIC-BSA complex by mainly hydrogen-bonding forces resulted in the conformational changes of protein. PIC inhibited the formation of β-sheets structures of BSA. BSA still maintained the esterase-like good activity in the presence of PIC. In addition, PIC significantly reduced the degree of BSA glycosylation. These results provided a basis for the molecular interaction between PIC and protein, and suggested the potential effect of PIC in preventing the progression of diabetes mellitus.

Insights into the binding mechanism of two-dimensional black phosphorus nanosheets-protein associations

Exploring the protein-nanomaterials interactions is the topic of high relevance for the future applications of new nanomaterials in biological system. Herein, the binding mechanism of bovine serum albumin(BSA) and bovine hemoglobin(BHB) with two-dimensional black phosphorus nanosheets (BP NSs) was reported. Muti-spectral results showed that the combination of BP NPs with protein resulted in the fluorescence quenching of BSA and BHB and induced the extension of the protein peptide chain by van der Waals forces, hydrophobic forces, and electron-transfer forces. Both BSA and BHB retain their structure in α-helix form. The induced circular dichroism (ICD) spectral results showed that the presence of BP NPs partly destroyed the binding domain of BHB with bilirubin and altered the tertiary structure of BHB by BP NPs binding.

A Water-Soluble Fluorescent Probe for the Selective Sensing of Ag+ and its Application in Imaging of Living Cells and Nematodes

In this study, an imidazole-coumarin based fluorescent probe was developed for the selective and sensitive detection of Ag⁺ in aqueous solution. Using a combination of Job plot, NMR titrations, and DFT calculations, the binding properties between Ag⁺ and the probe were deeply investigated, and the results revealed a 1:1 binding stoichiometry between the probe and Ag⁺ with a binding constant of 1.02 × 10⁶ M^-1. The detection limit was found to be 150 nM, which satisfies the requirement for the quantitative detection of Ag⁺ in real water samples. Moreover, the new probe, Ic, was successfully applied to sense Ag⁺ in HeLa and HepG2 cells as well as in C. elegans, indicating that it could be a useful tool for the environmental monitoring of Ag⁺ pollution. These results demonstrated that Ic could serve as a high-efficiency and low-cost fluorescent probe for tracking Ag⁺ in an aquatic environment and biological organisms.

Utilization of doped GQDs for ultrasensitive detection of catastrophic melamine: A new SERS platform

The detection and filtration of melamine in food products has become an emergence due to its harmful effect on humans. In present work, we have investigated the binding mechanism of melamine over carboxyl group edge-functionalized graphene quantum dots doped with oxygen and sulphur atoms (O-GQD and S-GQD). In order to monitor melamine, surface enhanced Raman scattering (SERS) is adopted which is an effective vibrational spectroscopic approach. Electronic and vibrational properties were analysed by means of well adapted density functional theory (DFT). The calculated adsorption energy of melamine over O-GQD and S-GQD is -1.18 and -0.15 eV respectively. The characteristic peak of melamine at 688 cm^-1 is in good agreement with previously reported experimental work and enhances by 348.4% in SERS spectra of Mel-O-GQD and 48% in SERS spectra of Mel-S-GQD. We have calculated the chemical enhancement factor (EF) for melamine over O-GQD and S-GQD and found the enhancement of 4.51 and 1.48 which is greater than melamine‑silver complexes. Our theoretical studies on SERS of melamine over O-GQD and S-GQD suggest that oxygen is a better candidate for SERS. Our work demonstrates that the graphene quantum dots are remarkable platforms for the detection of melamine.

Study on the stereoselective binding of cytosine nucleoside enantiomers to human serum albumin

Nucleoside drugs are known for their remarkable anticancer and antiviral properties. The development of nucleoside drugs has attracted much attention and generated a great deal of research interest. β-L-cytidine and β-D-cytidine are a pair of cytosine nucleoside enantiomers. In this work, the interactions between cytosine nucleoside enantiomers and human serum albumin were studied by ultraviolet-visible spectra, fluorescence spectrum and circular dichroism spectrum under simulated human physiological environment. The data of fluorescence spectra were corrected for the inner-filter effect to improve accuracy. Stern-Volmer quenching constants and binding constants in addition to thermodynamic parameters have been analyzed, which established that complexes formation have taken place via static quenching mechanism, and that hydrophobic force involved in these interactions. CD spectrum revealed that on addition of cytosine nucleoside enantiomers, the α-helix% of HSA increased slightly. What's more, molecular modeling method indicated that cytosine nucleoside enantiomers prefer binding at the IIIA site of HSA.

Evaluation the binding of chelerythrine, a potentially harmful toxin, with bovine serum albumin

Chelerythrine (CHE), a benzophenanthridine alkaloid, is usually used as a nutritional and functional additive in variety of health foods. However, it should be paid enough attention because of its potential toxicity to human health. In this work, the binding mechanism of CHE with bovine serum albumin (BSA) was systematically investigated with spectroscopic approaches. The results showed that the mixture of BSA with CHE could spontaneously cause the formation of BSA-CHE complex through electrostatic interaction under simulative physiological conditions (0.01 mol L^-1 Tris-HCl, 0.015 mol L^-1 NaCl, pH = 7.4). Site marker competitive displacement experiments exhibited that CHE was primarily bound to the hydrophobic pocket of the site II (subdomain IIIA) of BSA. It has been reported that the binding of small functional molecules to serum albumins remarkably impacts their absorption, distribution, metabolism, conformation, and excretion features. Therefore, this study might be helpful for human to have an in-depth understanding of the biological effect of CHE in vivo and guide human to take it safely and reasonably.

Graphene oxide-assisted non-immobilized SELEX of chiral drug ephedrine aptamers and the analytical binding mechanism

Here, we describe a study of screen characterization of aptamers targeting the chiral drug ephedrine using the non-immobilized graphene oxide (GO) SELEX. The improved method of long and short chains was here used to prepare the ssDNA library. The Resonance Rayleigh Scattering (RRS) method was first used to monitor the screening process. Through high-throughput sequencing, the genetic sequence data of 90,487 aptamers were obtained. Through the analysis of the parameters of free energy value and secondary structure prediction model of high repeatability sequence, the 10 candidate sequences were identified. Finally, a best-fit aptamer named EP08 was identified by combining the dissociation experiment. The binding affinity and binding mechanism of the aptamer and target were analyzed using an isothermal titration colorimetry (ITC) experiment and circular dichromatic (CD) experiment. The binding affinity (Kd) of the EP08 aptamer to ephedrine is approximately 2.86 ± 0.24 μM. This novel DNA aptamer will help in the future development of a new method for the identification and detection of chiral drug ephedrine.

Mechanistic understanding and binding analysis of two-dimensional MoS2 nanosheets with human serum albumin by the biochemical and biophysical approach

With the advent of molybdenum disulfide nanosheets (MoS₂ NSs) for biological applications, their complex interactions with human serum albumin (HSA) need to be understood in great detail for the molecular mechanisms of protein structure and activity. It was observed that MoS₂ NSs quench the intrinsic fluorescence of HSA as a consequence of ground-state complex formation by the electron transfer, van der Waals, and hydrophobic forces. The presence of MoS₂ NSs partly altered the conformation of HSA and destroyed the binding domain of HSA with bilirubin. In addition, MoS₂ NSs can decrease the rate of the formation of beta sheet structures of HSA, reduce the non-enzymatic glycosylation, and increase the esterase-like activity of HSA. We hope that the present study will be helpful to understand the fundamental interactions of the two-dimensional materials with various biomacromolecules in human blood.

Housing Sulfur in Polymer Composite Frameworks for Li-S Batteries

Extensive efforts have been devoted to the design of micro-, nano-, and/or molecular structures of sulfur hosts to address the challenges of lithium-sulfur (Li-S) batteries, yet comparatively little research has been carried out on the binders in Li-S batteries. Herein, we systematically review the polymer composite frameworks that confine the sulfur within the sulfur electrode, taking the roles of sulfur hosts and functions of binders into consideration. In particular, we investigate the binding mechanism between the binder and sulfur host (such as mechanical interlocking and interfacial interactions), the chemical interactions between the polymer binder and sulfur (such as covalent bonding, electrostatic bonding, etc.), as well as the beneficial functions that polymer binders can impart on Li-S cathodes, such as conductive binders, electrolyte intake, adhesion strength etc. This work could provide a more comprehensive strategy in designing sulfur electrodes for long-life, large-capacity and high-rate Li-S battery.

Binding mechanism of five typical sweeteners with bovine serum albumin

In this work, the interactions between bovine serum albumin (BSA) and five sweeteners including aspartame (APM), acesulfame (AK), sucralose (TGS), sodium cyclamate (SC), and rebaudioside-A (REB-A) have been studied by multispectroscopic techniques, and molecular simulation in order to provide much useful information for the application of new and safer artificial sweeteners. Fluorescence quenching assays indicated that the formation of complexes between sweeteners and BSA mainly induced the fluorescence quenching of protein and the binding site number were about 1 indicting that there is one mainly binding site of APM, AK, TGS, SC, or REB-A in domain of BSA with relatively weak interactions. Molecular modeling results indicated that hydrogen bonding interactions were the mainly binding forces of sweeteners with BSA. Circular dichroism spectra indicated that APM and REB-A obviously induced the secondary structure changes of BSA. The presence of APM increased the fraction of α-Helix of BSA from 65.4% to 73.8%, while the presence of REB-A resulted in decreasing the fraction of α-helix of BSA from 65.4% to 51.2%. The melting temperature studies showed that these five sweeteners except REB-A act as stabilizers to increase the thermal stability of BSA during the thermal denaturation process. In addition, AK, TGS, and SC obviously increased the esterase-like activity of BSA, and such loss of activity of BSA induced by APM and REB-A.