Spectroscopic and theoretical investigation of oxali-palladium interactions with β-lactoglobulin

In vitro study on the anticancer effects of oxalipalladium against PC3 human prostate carcinoma cells

Prostate cancer is a common type of cancer in men with high incidence and mortality. Our aim was to investigate the effects of oxalipalladium (ox-Pd) on metastatic human prostate cancer PC3 cells and compare them with the effects of oxaliplatin (ox-Pt) (as an approved cancer drug). We synthesized ox-Pd through a new chemical method and used FT-IR, 1H NMR, 13C NMR, and MS analyzes to characterize it. The effects of ox-Pd on PC3 cells viability, apoptosis, cell cycle, migration, and gene expression were examined. Inhibition of topoisomerase IIα activity was investigated by pHOT1 plasmid relaxation and kDNA decatenation assays. Chemical tests showed ox-Pd with the correct composition and structure. For the first time, the exact fragmentation pathway of ox-Pd and its difference with ox-Pt was obtained by MS analysis. Ox-Pd significantly decreased PC3 cell viability with less/no toxicity effect on MHFB-1 normal skin fibroblasts. Wound scratch assay confirmed the strong anti-migratory activity of ox-Pd. According to flow cytometry analysis, this drug increased the number of PC3 cells in late apoptosis and decreased DNA replication and mitosis. Furthermore, pHOT1 plasmid relaxation and kDNA decatenation assays showed that ox-Pd strongly inhibited the catalytic activity of topoisomerase IIα. The expression of topoisomerase IIα, Bcl-2, P21, and survivin was decreased while the expression of Bax and p53 was increased under ox-Pd treatment. We provide the first evidence that ox-Pd exhibits more selective anticancer effects on PC3 cells compared to ox-Pt. Taken together, these data strongly suggest a therapeutic window for ox-Pd in cancer.

Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation

This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy.

High cancer selectivity and improving drug release from mesoporous silica nanoparticles in the presence of human serum albumin in cisplatin, carboplatin, oxaliplatin, and oxalipalladium treatment

In this project, drug release was examined based on the adsorption of cisplatin, carboplatin, oxaliplatin, and oxalipalladium on aminated mesoporous silica nanoparticles (N-HMSNs) and human serum albumin (HSA). These compounds were characterized by different techniques where three clinical Pt-drugs, cisplatin, carboplatin, oxaliplatin, plus oxalipalladium were loaded and investigated for release. Based on loading analysis, the loading ability of the mentioned metallodrug on N-HMSNs was dependent on the nature of the drug structure as well as hydrophobic or hydrophilic interactions. Different adsorption and release profiles were observed for all mentioned compounds via dialysis and ICP method analysis. Although the maximum to minimum loading occurred for oxalipalladium, cisplatin, and oxaliplatin to carboplatin, respectively, release from a surface with greater control belonged to carboplatin to cisplatin systems in the absence and presence of HSA to 48 hours due to weak interaction for carboplatin drug. The quick release of all mentioned compounds from the protein level at high doses of the drug during chemotherapy occurred very fast within the first 6 hours. In addition, the cytotoxic activity of both free drugs and drug-loaded@N-HMSNs samples on cancerous MCF-7, HCT116, A549, and normal HFF cell lines was evaluated by MTT assay. It was found that free metallodrugs exhibited more active cytotoxic behavior on both cancerous and normal cell lines than drug-loaded@N-HMSNs. Data demonstrated that the Cisplatin@N-HMSNs with SI=6.0 and 6.6 for MCF7 and HCT116 cell lines, respectively, and Oxaliplatin@N-HMSNs with SI=7.4 for HCT116 cell line can be good candidates as an anticancer drug with minimal side effects by protecting cytotoxic drugs as well as controlled release and high selectivity.

Effect of mucin on β-lactoglobulin and lactose interaction

Functions of mucin, as the major macromolecular component in saliva or gastric fluids, are drawing increasing attention in the context of understanding the oral processing or digestion of dairy foods at the molecular level. This study was designed to investigate the interactions between β-lactoglobulin (BLG)-lactose, mucin-lactose and BLG-lactose-mucin at the molecular level under different temperature and pH conditions using fluorescence spectroscopy in combination with scanning electron microscopes (sem). It is the first study of its kind. There was no lactose-dependent quenching on BLG fluorophore in the range of 0–10 mM lactose concentration. On the contrary, there was a continuous increase in the fluorescence intensity of the BLG protein when the lactose concentration increased, especially at 25°C. BLG-lactose complex became thermally unstable at 37 and 45°C. Moreover, BLG exhibited a pH dependent conformational change and had higher fluorescence intensity at pH 3 than pH 6.8. The fluorescence result was in correspondence with sem images where we observed lactose crystals gathering around and on the BLG molecule, but lactose molecules could not be seen in the presence of mucin. It was anticipated that mucin molecules interacted with BLG-lactose complex via electrostatic attraction and formed an extra protective layer around the BLG molecules to avoid solvent exposure.

The interactions between Reactive Black 5 and human serum albumin: combined spectroscopic and molecular dynamics simulation approaches

Azo dyes are made in significant amounts annually and released into the environment after being employed in the industry. There are some reports about the toxic effects of these dyes on several organisms. Thus, the textile dye Reactive Black 5 (RB5) has been examined for its cytotoxic effects on the human serum albumin (HSA) structure. Molecular interaction between RB5 and HSA indicated the combination of docking methods, molecular dynamic simulation, and multi-spectroscopic approaches. HSA's intrinsic fluorescence was well quenched with enhancing RB5 level, confirming complex formation. Molecular dynamics (MD) simulation was done to study the cytotoxic effects of RB5 and HSA conformation. Molecular modeling revealed that the RB5-HSA complex was stabilized by hydrogen bonds and van der Waals interactions. The results of molecular docking revealed that the binding energy of RB5 to HSA was - 27.94 kJ/mol. The change in secondary structure causes the annihilation of hydrogen bonding networks and the reduction of biological activity. This research can indicate a suitable molecular modeling interaction of RB5 and HAS and broaden our knowledge for azo dye toxicity under natural conditions.

Designing a new alginate-fibrinogen biomaterial composite hydrogel for wound healing

Wound healing is a complex process and rapid healing necessitates a proper micro-environment. Therefore, design and fabrication of an efficacious wound dressing is an impressive innovation in the field of wound healing. The fabricated wound dressing in this scenario was designed using a combination of the appropriate coagulating and anti-bacterial materials like fibrinogen (as coagulating agent), nisin (as anti-bacterial agent), ethylenediaminetetraacetic acid (as anti-bacterial agent), and alginate (as wound healing agent). Biophysical characterization showed that the interaction of fibrinogen and alginate was associated with minor changes in the secondary structure of the protein. Conformational studies showed that the protein was structurally stable at 42 °C, is the maximum temperature of the infected wound. The properties of the hydrogel such as swelling, mechanical resistance, nisin release, antibacterial activity, cytotoxicity, gel porosity, and blood coagulation were assessed. The results showed a slow release for the nisin during 48 h. Antibacterial studies showed an inhibitory effect on the growth of Gram-negative and Gram-positive bacteria. The hydrogel was also capable to absorb a considerable amount of water and provide oxygenation as well as incorporation of the drug into its structure due to its sufficient porosity. Scanning electron microscopy showed pore sizes of about 14–198 µm in the hydrogel. Cell viability studies indicated high biocompatibility of the hydrogel. Blood coagulation test also confirmed the effectiveness of the synthesized hydrogel in accelerating the process of blood clot formation. In vivo studies showed higher rates of wound healing, re-epithelialization, and collagen deposition. According to the findings from in vitro as well as in vivo studies, the designed hydrogel can be considered as a novel attractive wound dressing after further prerequisite assessments.

Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods

Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.

New ligand-binding sites identified in the crystal structures of β-lactoglobulin complexes with desipramine

The homodimeric β-lactoglobulin belongs to the lipocalin family of proteins that transport a wide range of hydrophobic molecules and can be modified by mutagenesis to develop specificity for novel groups of ligands. In this work, new lactoglobulin variants, FAF (I56F/L39A/M107F) and FAW (I56F/L39A/M107W), were produced and their interactions with the tricyclic drug desipramine (DSM) were studied using X-ray crystallography, calorimetry (ITC) and circular dichroism (CD). The ITC and CD data showed micromolar affinity of the mutants for DSM and interactions according to the classical one-site binding model. However, the crystal structures unambiguously showed that the FAF and FAW dimers are capable of binding DSM not only inside the β-barrel as expected, but also at the dimer interface and at the entrance to the binding pocket. The presented high-resolution crystal structures therefore provide important evidence of the existence of alternative ligand-binding sites in the β-lactoglobulin molecule. Analysis of the crystal structures highlighted the importance of shape complementarity for ligand recognition and selectivity. The binding sites identified in the crystal structures of the FAF-DSM and FAW-DSM complexes together with data from the existing literature are used to establish a systematic classification of the ligand-binding sites in the β-lactoglobulin molecule.

Determinants of gold nanoparticle interactions with Proteins: Off-Target effect study

Photothermal therapy is one of the promising approaches toward cancer treatment. To date, several compounds have been developed for this application, among which nanoparticles are attracting ever-increasing attention. One of the obstacles in developing efficient photothermal nanoparticle agents is their off-target effect which is mainly mediated via non-specific interactions with proteins. Such interaction not only reduces the bioavailability of the agent but also will cause protein aggregation that can be lethal. So, gaining knowledge on the mechanisms mediating such interactions will facilitate development of more effective agents. Our last studies showed the mechanism of action of two modified gold nanoparticles, folic acid functionalized gold nanoparticles (FA-AuNPs) and gold shelled Fe₃O₄ nanoparticles (AuFeNPs), as photothermal agents. In the current work, we focus on the interaction of these two NPs with human serum albumin (HSA) and human hemoglobin (Hb) as model proteins. The complex formation between NPs and proteins was investigated by fluorescence spectroscopy, dynamic light scattering and circular dichroism. Our data distinguishes the very distinct mode of interaction of charged and neutral NPs with proteins. While the interaction of neutral AuFeNP to proteins is protein dependent, charged nanoparticles FA-AuNP interact indistinguishably with all proteins via electrostatic interactions. Moreover, complexes obtained from FA-AuNPs with proteins are more stable than that of AuFeNP. However, the secondary structure content of proteins in the presence of NPs indicates the insignificant effect of NPs on the secondary structure of these proteins. Our data propose that the charge functionalization of the NPs is an effective way for modulating the interaction of nanoparticles with proteins.

Alleviating Aspirin-Induced Gastric Injury by Binding Aspirin to β-Lactoglobulin

Purpose

Gastric injury is a major issue for long-term administration of aspirin. In this work, we tried to explore the possibility of using BLG to alleviate aspirin-induced gastric injury, because of excellent abilities of BLG in loading drug molecules.

Methods

Various spectroscopic techniques and molecular docking methods were applied to investigate the interaction mechanism between BLG and aspirin. Animal experiments were performed to figure out the effects of taking aspirin-BLG on the stomach.

Results

Our results demonstrate that aspirin could bind with BLG to form stable aspirin-BLG complex (the binding constant K_b= 2.051 × 10³ M⁻¹). The formation process is endothermic (∆H>0) and the main acting force is hydrophobic force. Our data also show that the aspirin-BLG complex is formed with a higher affinity in simulated gastric fluid and could remain stable for several hours, which might arise from its special binding mode under acidic condition and the resistance of BLG to gastric digestion. Furthermore, animal models (rats with aspirin-induced gastric damage) were built. The results of animal experiments reveal that the oral administration of aspirin-BLG could cause less damage to gastric tissue, and it also hardly triggers obvious inflammatory responses.

Conclusion

This study would contribute to an in-depth understanding of the interaction mechanism between BLG and aspirin. It is reasonable to believe that using BLG to bind with aspirin would be a potential way to alleviate the aspirin-induced gastric injury.

Molecular insights into the interaction of 5-fluorouracil and Fe3O4 nanoparticles with beta-casein: An experimental and theoretical study

We investigated the potential carrier of milk beta-casein (β-CN) and its interactions with 5-fluorouracil (5-FU) and iron oxide nanoparticles (Fe₃O₄ NPs). We used different spectroscopic methods of fluorescence, UV-Visble, circular dichroism (CD), synchronous fluorescence, zeta potential assay, and computational studies to clarify the protein interaction with 5-FU and Fe₃O₄ NPs. The fluorescence data indicated both Fe₃O₄ NPs and 5-FU could quench the intrinsic fluorescence of β-CN. Fluorescence measurements showed that the single interaction of β-CN with 5-FU or Fe₃O₄ NPs was static, while reacted β-CN with both 5-FU and Fe₃O₄ NPs simultaneously showed a dynamic quenching. Synchronous fluorescence data in both tests revealed that the tryptophan (Trp) residue of β-CN had a dominant role in quenching and the polarity of its microenvironment more than tyrosine (Tyr) increased in interaction with 5-FU. All the binding sites and thermodynamic parameters were obtained at 25, 37, and 42 °C. The analysis of thermodynamic parameters and Job's plot techniques pointed to that both of these complexes with the 1:1 M ratio were exothermic (ΔH°<0) driven with the van der Waals and H-bonding interactions (in agreement with the docking results). The CD spectra in the region of far-UV and thermal denaturation study indicated minor changes in the secondary structure of β-CN in the presence of various concentrations of Fe₃O₄ NPs and 5-FU. Also, from the molecular dynamics (MD) analysis, as a result, the protein structure was stable during 100 ns. The outcomes highlighted that β-CN protein could form a great bind with 5-FU and Fe₃O₄ NPs ligands (supporting the zeta potential assay results) by independent binding sites. These results would be helpful insight to construct a potential magnetic nanocarrier β-CN base for 5-FU drug delivery.

Polydopamine nanospheres coated with bovine serum albumin permit enhanced cell differentiation: fundamental mechanism and practical application for protein coating formation

Protein coating is a strategy for modifying and improving the surface functional properties of nanomaterials. However, the underlying mechanism behind protein coating formation, which is essential for its practical applications, remains largely unknown. Herein, we investigate the fundamental molecular mechanism of protein coating formation. Polydopamine nanospheres (PDANS) coated with bovine serum albumin (BSA) are examined in this study due to their wide biomedical potential. Our results demonstrate that BSAs can flexibly bind to PDANS and maintain their structural dynamicity. Our findings unveil that regular structure formation arises from BSAs lateral interactions via electrostatic forces. Notably, the protein coating modified PDANS surface enhances cell adhesion and proliferation as well as osteogenic differentiation. Such an enhancement is attributed to complementary surface properties provided by the dynamic PDANS-BSA complex and regular structure caused by BSA-BSA interactions in protein coating formation. This study provides a fundamental understanding of the molecular mechanism of protein coating formation, which facilitates the further development of functional protein-coated nanomaterials and guides the bioengineering decision making for biomedical applications, especially in bone tissue engineering.

Spectroscopic and Theoretical Investigation of β-Lactoglobulin Interactions with Hematoporphyrin and Protoporphyrin IX

Hematoporphyrin (HP) and protoporphyrin IX (PPIX) are useful porphyrin photosensitizers with significant application values in photodynamic therapy. Currently, many strategies have been developed to improve their clinical performance, such as incorporating them with nanoparticle (NP) carriers. In this work, we studied the possibility of using β-lactoglobulin (BLG) as a potential NP carrier due to their hydrophobic affinity, pH sensitivity, and low cost of extraction and preservation. The interaction mechanisms of BLG with HP and PPIX were investigated using spectroscopic techniques and molecular docking methods. The molecular docking results agree well with the experimental results, which demonstrate that the formations of HP-BLG and PPIX-BLG complexes are endothermic processes and the main acting force is hydrophobic force. Furthermore, the opening-closure states of EF loop have a great influence on the HP-BLG complex formation, where the central hydrophobic cavity of β-barrel is available for HP binding at pH 7.4 but not available at pH 6.2. However, the formation of the PPIX-BLG complex is less dependent on the states of the EF loop, and the binding sites of PPIX are both located on the external surface of BLG under both pH 7.4 and 6.2 conditions. All of our results would provide new insight into the mechanisms of noncovalent interactions between BLG and HP/PPIX. It is believed that this work indicated the potential application values of BLG in designing pH-sensitive carriers for the delivery of HP and PPIX, as well as other poorly soluble drugs.

Hairpin-Spacer crRNA-Enhanced CRISPR/Cas13a System Promotes the Specificity of Single Nucleotide Polymorphism (SNP) Identification

The Cas13a system has great potential in RNA interference and molecular diagnostic fields. However, lacking guidelines for crRNA design hinders practical applications of the Cas13a system in RNA editing and single nucleotide polymorphism identification. This study posits that crRNAs with hairpin spacers improve the specificity of CRISPR/Cas13a system (termed hs-CRISPR). Gibbs free energy analysis suggests that the hairpin-spacer crRNAs (hs-crRNAs) suppress Cas13a's affinity to off-target RNA. A hepatitis B virus DNA genotyping platform is established to further validate the high-specificity of hs-CRISPR/Cas13a system. Compared to ordinary crRNA, hs-crRNAs increase the specificity by threefold without sacrificing the sensitivity of the CRISPR/Cas13a system. Furthermore, the mechanism of the Cas13a/hs-crRNA/target RNA composition is elucidated with theoretical simulations. This work builds on the fundamental understanding of Cas13a activation and offers significant improvements for the rational design of crRNA for the CRISPR/Cas13a system.

Investigating the anticancer properties of the two new platinum complexes with iso- and tert-pentylglycine by the DFT, molecular docking, and ADMET assessment and experimental confirmations

In this study, two new anticancer platinum complexes formulated as [Pt(bpy)(L)]NO₃ were synthesized using the iso and tert-pentylglycine ligands, two structural isomer ligands, to investigate side branches effect on the complex-DNA interaction. According to the comparative results of the ADMET assessment, these compounds can be considered as the drug-like molecules and oral medication. Mechanism of tumor inhibition and DNA binding parameters indicated the higher ability of the tert-isomer and also, both complexes acted through the disruption of the base pairs and stacks of helicity by the endothermic process. Fluorescence spectroscopy showed that the quenching mechanism is static for both drugs with large binding constant and high binding affinity towards the DNA. Also, the amount of binding constant of the tert -isomer was about 14 times of another structural isomerous complex. CD spectra indicated the conversion of the B-DNA into A-DNA form via electrostatic interaction for positively charged complexes. The cytotoxic data showed that both compounds have antiproliferative effects against the MCF-7 cell line and the inhibitory effect of the iso-derivative was better than the tert-one. Docking studies showed that the desolvation energy and hydrogen bond are more effective between the other interactions. The torsional free energy for both complexes mainly provided the groove binding along with partially electrostatic and intercalate binding. According to the density-functional theory data and because of positive electron density on the surface of complexes and facilitating of the metal drug to DNA phosphate groups approaching, both complexes may be good candidates for the anticancer drugs. Two new anticancer Pt(II) complexes were synthesized with glycine derivatives. In vitro cytotoxicity effects were tested against the human breast cancer cell line of MCF-7. Moreover, the modes of DNA binding with synthesized compounds were investigated using ADME prediction, DFT, molecular docking and spectroscopic methods.

Interactions and effects of food additive dye Allura red on pepsin structure and protease activity; experimental and computational supports

Background and purpose:

Today, color additives such as Allura red (AR) are widely used in different kinds of food products. Pepsin is a globular protein that is secreted as a digestive protease from the main cells in the stomach. Because of the important role of pepsin in protein digestion and because of its importance in digestive diseases the study of the interactions of pepsin with chemical food additives is important.

Experimental approach:

In this study, the interactions between AR and pepsin were investigated by different computational and experimental approaches such as ultraviolet and fluorescence spectroscopy along with computational molecular modeling.

Findings/Results:

The experimental results of fluorescence indicated that AR can strongly quench the fluorescence of pepsin through a static quenching. Thermodynamic analysis of the binding phenomena suggests that van der Waals forces and hydrogen bonding played a major role in the complex formation. The results of synchronous fluorescence spectra and furrier transformed infra-red (FTIR) experiments showed that there are no significant structural changes in the protein conformation. Also, examined pepsin protease activity revealed that the activity of pepsin was increased upon ligand binding. In agreement with the experimental results, the computational results showed that hydrogen bonding and van der Waals interactions occurred between AR and binding sites.

Conclusion and implications:

From the pharmaceutical point of view, this interaction can help us to get a deeper understanding of the effect of this synthetic dye on food digestion.

Characteristics of the interaction mechanisms of xylitol with β-lactoglobulin and β-casein: Amulti-spectral method and docking study

Proteins and functional polyols are essential food ingredients coexisting in the food matrix, and therefore, interactions between them inevitably occur. In this study, the interaction mechanisms of xylitol (XY) with bovine milk β-lactoglobulin (β-LG) and β-casein (β-CN) were studied using multispectral techniques and molecular docking. It was found that XY strongly quenched the intrinsic fluorescence of β-LG and β-CN by static quenching. The values of the binding constants were K_A(β-LG-XY) = 3.369 × 10⁴ L/mol and K_{A(β-CN- XY)} = 7.821 × 10⁴ L/mol, indicating that the binding affinity of XY to β-CN was higher than that for β-LG. Hydrogen bonding and van der Waals forces played a major role in the interactions of XY with β-LG and β-CN, and both interactions were exothermic. Simultaneous fluorescence, three-dimensional fluorescence, and circular dichroism spectroscopy showed that binding of XY did not change the secondary structure of β-LG. However, XY interaction with β-CN led to the conversion of α-helices to random coils and structural loosening. In addition, molecular docking predicted the most likely binding sites of XY in both proteins and the interaction forces involved in binding, confirming the spectroscopic results. This study improves the understanding of the interactions of XY with β-LG and β-CN in functional dairy products and provides a theoretical basis for the addition of XY in a functional milk base.

Microencapsulated mulberry anthocyanins promote the in vitro-digestibility of whey proteins in glycated energy-ball models

The effects of mulberry anthocyanins (MAs) on the digestibility of whey proteins (WP) in freshly-prepared and stored energy balls were studied. Results showed that MAs increased digestibility of the energy balls by increasing their hydrolysis-degree, soluble peptides-fractions, and decreasing their particle's size and agglomeration. To understand the mechanism of the promoting and/or inhibiting digestive effects of MAs, secondary structure alterations and binding of WP-MAs-mixtures were therefore measured. Results revealed that MAs could noncovalently/covalently interact with WP and form WP-MAs-adducts. This interaction seemed to be responsible for the alterations in the secondary structure of WP which could promote the digestibility of the energy balls subsequently. MAs also partially unfolded the structure of digested-WP through fluctuating their α-helix and β-sheet. It was concluded that the unfolding in WP-structure induced by MAs-interactions might increase accessibility of the peptide bonds to the digestive enzymes and consequentially facilitate the protein's digestibility in the energy balls.

Insight into the binding of glycerol with myoglobin: Spectroscopic and MD simulation approach

Stability of proteins plays a significant role not only in their biological function but also in medical science and protein engineering. Since proteins are only stable in special conditions, maintaining their stability and function in biological and biotechnological applications may pose serious challenges. Osmolytes provide a general method of shielding proteins from the unfolding and aggregation caused by extreme stress on the environment. In such studies, the researchers used spectroscopic and simulation approaches to study the alterations of the myoglobin structure and stability in glycerol presence. Experimental results showed a stability improvement of the complex myoglobin-glycerol. After the addition of glycerol resulting in the initiation of hydrogen bonds and higher levels of hydrophobicity, the increase of the T_m was observed. The static mode quenching observed in this study. Van der Waals forces and hydrogen bindings had a decisive and significant role concerning the stability of protein which was consistent with the modeling results. Molecular dynamics simulation showed that the glycerol presence could enhance myoglobin stability. The consistency between the theoretical studies and experimental findings demonstrates that the method proposed in this study could provide a useful method for protein-ligand complex investigations.

Beta-lactoglobulin-nutrition allergen and nanotransporter of different nature ligands therapy with therapeutic action

β-lactoglobulin is one of the nutrition allergens present in the milk of many mammals, with the exception of human. This protein belongs to the family of lipocalins, consisting of nine antiparallel β-strands (β-A to β-I) and one α-helix. This structure allows it to serve as a nanotransporter of various nature ligands in a pH dependent manner, which allows us to confidently consider it as a reliable carrier of drugs directly into the intestine, bypassing the destructive acidic environment of the stomach. Based on the latest data, this review describes the currently known methods of reducing the allergenicity of beta-lactoglobulin, as well as the mechanisms and methods of forming complexes of this protein with ligands, which emphasizes its importance and versatility and explains the growing interest in studying its properties in recent decades, and also opens up prospects for its practical application in medicine and pharmaceuticals.

Preparation and Characterization of Soy Isoflavones Nanoparticles Using Polymerized Goat Milk Whey Protein as Wall Material

Soy isoflavones (SIF) are a group of polyphenolic compounds with health benefits. However, application of SIF in functional foods is limited due to its poor aqueous solubility. SIF nanoparticles with different concentrations were prepared using polymerized goat milk whey protein (PGWP) as wall material. The goat milk whey protein was prepared from raw milk by membrane processing technology. The encapsulation efficiencies of all the nanoparticles were found to be greater than 70%. The nanoparticles showed larger particle size and lower zeta potential compared with the PGWP. Fourier Transform Infrared Spectroscopy indicated that the secondary structure of goat milk whey protein was changed after interacting with SIF, with transformation of α-helix and β-sheet to disordered structures. Fluorescence data indicated that interactions between SIF and PGWP decreased the fluorescence intensity. All nanoparticles had spherical microstructure revealed by Transmission Electron Microscope. Data indicated that PGWP may be a good carrier material for the delivery of SIF to improve its applications in functional foods.

Investigating the interaction between three perfluorinated carboxylic acids and the G protein-coupled estrogen receptor: spectroscopic analyses and computational simulations

In this paper, perfluorinated compounds (PFCs), such as perfluorobutyric acid (PFBA), perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), were selected as typical representatives of perfluorinated carboxylic acids (PFCAs) to study the effects of PFCAs on the G protein-coupled estrogen receptor (GPER). The interaction mechanism of the three types of PFCAs with the GPER was investigated using steady-state fluorescence spectroscopy, ultraviolet-visible spectroscopy, three-dimensional fluorescence spectroscopy, and Fourier transform infrared spectroscopy combined with molecular docking and molecular dynamics simulations. Among these techniques, steady-state fluorescence and ultraviolet-visible spectroscopic analyses showed that PFBA, PFOA and PFDoA quenched the endogenous GPER fluorescence by combined dynamic and static quenching and non-radiative energy transfer. The binding constants (K_a) of PFCAs on the GPER were all larger than 10⁵ L mol^-1, indicating that their affinity for the GPER was strong. Fourier transform infrared spectroscopy and three-dimensional fluorescence showed that the secondary structure of the GPER changed after binding to PFCAs. Thermodynamic analysis showed ΔG < 0, which indicated that the interaction between the GPER and PFCAs was spontaneous. For the binding of PFBA and PFOA to the GPER, ΔH > 0 and ΔS > 0, indicating that the interaction was mainly driven by hydrophobic forces; for the binding of PFDoA to the GPER, ΔH < 0 and ΔS < 0, suggesting that van der Waals force and hydrogen bonding were the main interaction forces. Molecular dynamics simulations suggested that the stability of the GPER-PFCA complexes was higher than that of the free GPER, and also that the structure and hydrophobicity of the GPER changed after binding to PFCAs. Molecular docking analysis showed that all three PFCAs could form hydrogen bonds with the GPER, which improved the stability of the complex.

Experimental and theoretical investigations on the interaction of glucose molecules with myoglobin in the aqueous solution using theoretical and experimental methods

Osmolytes are generally well-known for the stabilization of proteins. The stabilizing impact of glucose on the dynamics and structure of myoglobin was probed through molecular simulation' docking and spectroscopic procedures. Using thermal stability examinations, the thermodynamic folding properties, point of melting temp. (T_m), thermodynamic enthalpy change (ΔH°) and thermodynamic entropy change (ΔS°) were determined to find out the depiction of myoglobin folding. Glucose operated as an enhancer relative to myoglobin stabilization. The quenching static model was demonstrated by fluorescence spectroscopy. There was one binding site. According to the spectroscopy analysis, glucose was capable of protecting the native structural conformation of protein as well as preventing from protein unfolding. The fluorescence spectroscopy together with simulation through molecular docking method revealed that definitely hydrogen bonding plus van der Waals forces had major contributions to the stabilization of the myoglobin-glucose complex. Hence, the direct interactions contributed slightly to the stabilization impact whereas indirect interactions resulted from the hydration arise from a molecular mechanism primarily inducing the glucose stabilizing impacts. An elevation occurred in the T_m of the myoglobin-glucose complex because of the greater H-bond creation and limited surface hydrophobic activity. Our findings indicate that glucose was capable of protecting the native conformation of myoglobin, clearly describing that glucose stabilization is preferred to be omitted from myoglobin surface. This is because water is more inclined to provide desirable interacting with myoglobin functional groups as compared to glucose. Also, MD results confirmed that the structural changes of myoglobin is the effect of complex formation with glucose.Communicated by Ramaswamy H. Sarma.

Multi-spectroscopic studies of the interaction of new synthesized platin complex with human carrier protein of serum albumin

Previous reports have shown that protein-drug interaction helps to improve the pharmacokinetics of the drugs. Human serum albumin (HSA) is one of the basic components of blood plasma and it serves as a storage and carrier protein. In the present study, the interaction of a new synthesized Pt [iso]2 complex (cis - [Pt(NH₂-Isopentylamine)₂(Isopentylglycine)]NO₃₎ with HSA was studied using the spectroscopic methods of fluorescence and circular dichroic (CD) at two different temperatures of 25 and 37 °C. Analysis of the quenching mechanism via Stern-Volmer curve, determination of HSA binding parameters (0.65 × 10⁴ and 2.27 × 10⁴) and standard Gibbs free energy (-25.8, and 21.77) at 25 and 37 °C, respectively, carried out using fluorescence quenching data. Data analysis showed that the static mechanism has the main role in fluorescence quenching. Also, the number of protein binding sites for complex indicated one binding site at two temperatures of 25 and 37 °C. The secondary structure of protein in the presence of different concentrations of Pt(II) complex did not show any significant alterations. Whereas, thermal stability of the HSA was reduced in the presence of complex. Also, thermal analysis obtained the values of ΔG°₂₅ for HSA and HSA in presence of Pt [Iso]₂ 20, 13, respectively. According to the above results, we concluded that the new synthesized Pt complex can bind to the blood carrier protein of HSA and change the stability of it which can be considered in the design of new drugs.Communicated by Ramaswamy H. Sarma.

Mulberry anthocyanins exert anti-AGEs effects by selectively trapping glyoxal and structural-dependently blocking the lysyl residues of β-lactoglobulins

Advanced glycation end-products (AGEs), which instigate many disorders, are mostly mediated by dicarbonyl rearrangements. We studied the corresponding mechanisms of the anti-glycation effects of two anthocyanins purified from mulberry fruits, namely cyanidin 3-glucoside (C3G) and cyanidin 3-rutinoside (C3R), on glycated β-lactoglobulins (β-Lg). Both mulberry anthocyanins (MAs) inhibited the AGEs-formation in a dose-dependent manner, but the effect of C3R was significantly stronger than that of C3G (p < 0.05). MAs inhibited AGEs-formation by selectively trapping dicarbonyls, especially glyoxal. The UPLC-ESI-Q-TOF-MS results characterized that C3R formed mono- and di-glyoxal adducts, where C3G only created di-glyoxal adducts. Additionally, C3R could directly interact with some of the glycation sites of β-Lg. Overall, GO-trapping and β-Lg-MAs covalent/noncovalent binding are disclosed as the key mechanisms of the anti-AGEs activity of MAs on β-Lg, which could be valorised as effectual AGEs inhibitors in proteins-rich matrices.

Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods

l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches. The results of the UV-vis absorption demonstrated that α-Chy had a maximum peak at 280 nm due to the Trp residue. Hyperchromism shift was seen in the presence of l-Met. Ground state system was formed in the presence of l-Met, as confirmed by the fluorescence studies. Fluorescence variations also revealed static quenching. The CD spectra also represented the alteration of the enzyme with an increase in the α-helix and a decrease in the β-sheet. The activity of α-Chy was incremented in the presence of l-Met. Therefore, l-Met served as an activator. Molecular docking results also indicated a negative amount for the Gibbs free energy of the binding of l-Met to the enzyme. α-Chy became more stable in the presence of l-Met, based on the molecular dynamics simulation.

Preparation, characterization and comparison of biological potency in two new Zn(II) and Pd(II) complexes of butanedione monoxime derivatives

A novel Schiff base ligand (2-iminothiophenol-2,3-butanedione monoxime, ITBM) and its complexes with Pd(II) and Zn(II) metal ions ([M(ITBM)₂]Cl₂) were synthesized and characterized in the present study. The formulated complexes were evaluated for in vitro antioxidant activity as radical scavengers against 1,1-diphenyl-2-picrylhydrazyl radicals (DPPH^•). According to the results, antioxidant activity of Pd complex (IC₅₀=36 mg L^-1) was more effective than that of Zn(II) complex (IC₅₀=72 mg L^-1). Biophysical techniques along with computational modeling were employed to examine the binding of these complexes with human serum albumin (HSA) as the model protein. The trial findings revealed an interaction between Schiff base complexes and HSA with a modest binding affinity [K_b=6.31(±0.11)×10⁴ M^-1 for Zn(II) complex and 0.71(±0.05)×10⁴ M^-1 for Pd(II) complex at 310 K]. An intense fluorescence quenching of protein through a static quenching mechanism was occurred due to the binding of both complexes to HSA. Hydrogen bonds and van der Waals forces in both examined systems were the main stabilizing forces in the development of drug-protein complex. Based on far-UV-CD observations, the content of α-helical structure in the protein was reduced through induction by both complexes. Analysis of protein-ligand docking demonstrated binding of the two Schiff base complexes to residues placed in the IIA subdomain of HSA. In addition, Zn complex with HSA showed a stronger binding ability than that of Pd complex.Communicated by Ramaswamy H. Sarma.