Comparative refolding of guanidinium hydrochloride denatured bovine serum albumin assisted by cationic and anionic surfactants via artificial chaperone protocol: Biophysical insight

Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM

Since the design of metal complexes with better biological activities is important, herein a new palladium(II) complex bearing en and acac (en and acac stand for ethylenediamine and acetylacetonato, respectively) as its ligands, [Pd(en)(acac)]NO3 complex, was synthesized and fully characterized. Quantum chemical computations of the palladium(II) complex were done via DFT/B3LYP method. Cytotoxicity activity of the new compound on leukemia cell line (K562) was assessed via MTT method. The findings indicated that the metal complex has remarkable cytotoxic effect than cisplatin. OSIRIS DataWarrior software was employed to calculate in-silico physicochemical and toxicity parameters of the synthesized complex which rendered significant results. To comprehend the interaction type of new metal compound with macromolecules, the in depth investigation of interaction of mentioned complex with CT-DNA and BSA was accomplished by fluorescence, UV-Visible absorption spectroscopy, viscosity measurement, gel electrophoresis, FRET analysis and circular dichroism (CD) spectroscopy. On the other hand, computational molecular docking was carried out and the obtained data demonstrated that H-bond and van der Waals forces are the dominant forces for the binding of the compound to the mentioned biomolecules. Molecular dynamics simulation was also done and confirmed the stability of best docked pose of palladium(II) complex inside DNA or BSA over the time and in presence of water solvent. Also, Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) methodology based on the hybridization of quantum mechanics and molecular mechanics (QM/MM) methodology was accomplished to inquire about binding of Pd(II) complex with DNA or BSA.HIGHLIGHTSNew biologically active Pd(II) complex was synthesized and characterized.The in silico studies of the designed complex and its ligands were accomplished by OSIRIS DataWarrior softwareInteraction with CT-DNA and BSA was assessed by various spectroscopic methods.Molecular docking simulation supported the interaction with both macromolecules.Based on ONIOM analysis, the structures of the complex and biomolecules are altered after binding. Communicated by Ramaswamy H. Sarma.

Characterization of structural and functional properties of soybean 11S globulin during renaturation after denaturation induced by changes in pH

BACKGROUND

This study explored the denaturation of 11S globulin, a protein known for its diverse functional properties in soy protein applications, at pH 3.0 and pH 10.0, followed by a gradual return to pH 7.0 to facilitate renaturation. It investigated the structural and functional changes during renaturation induced by a change in pH, revealing the stabilization mechanism of 11S globulin.

RESULTS

The findings revealed that during pH adjustment to neutral, the denatured soybean 11S globulin - resulting from alkaline (pH 10.0) or acidic (pH 3.0) treatments - experienced a refolding of its extended tertiary structure to varying extents. The particle size and the proportions of α-helix and β-sheet in the secondary structure aligned progressively with those of the natural-state protein. However, for the alkali-denatured 11S, the β-sheet content decreased upon adjustment to neutral, whereas an increase was observed for the acid-denatured 11S. In terms of functional properties, after alkaline denaturation, the foaming capacity (FC) and emulsifying activity index (EAI) of 11S increased by 1.4 and 1.2 times, respectively, in comparison with its native state. The solubility, foamability, and emulsifiability of the alkali-denatured 11S gradually diminished during renaturation but remained superior to those of the native state. Conversely, these properties showed an initial decline, followed by an increase during renaturation triggered by pH neutralization.

CONCLUSIONS

This research contributes to the enhancement of protein functionality, offering a theoretical foundation for the development of functional soy protein products and expanding their potential applications. © 2024 Society of Chemical Industry.

Exploring the Interaction Between the Newly Designed Antitumor Zn(II) Complex and CT-DNA/BSA: Spectroscopic Methods, DFT Computational Analysis, and Docking Simulation

A new zinc(II) complex formulated as [Zn(pipr-ac)2], where pipr-ac stands for piperidineacetate, was synthesized and structurally identified with the help of experimental and DFT methods. Frontier molecular orbital (FMO) analysis demonstrated that the new complex has higher biological activity compared to the free ligand. Molecular electrostatic potential (MEP) showed the nitrogen atoms and oxygen of carbonyl groups are the active sites of Zn(II) compound. Also, natural bond orbital (NBO) analysis confirmed the charge transfer from the ligating atoms to the metal ion and formation of four coordinated Zn(II) complex. MTT assay illustrated a noticeable cytotoxic activity of the new zinc(II) complex compared to cisplatin on K562 cell line. The CT-DNA and serum albumin (SA) binding of the Zn(II) complex were explored individually. In this regard, UV-Vis spectroscopy and florescence titration revealed the occurrences of fluorescence quenching of CT-DNA/SA by metal compound via static mechanism and creation of hydrogen bonds and van der Waals interactions between them. The binding was further confirmed by viscosity measurement and gel electrophoresis assay for CT-DNA and circular dichroism spectroscopy for SA. Moreover, molecular docking simulation demonstrated that the new compound binds mainly through hydrogen bonds to the groove of DNA and hydrogen bonds and van der Waals interactions to site I of SA.

Altered Intestinal Microbiomes and Lipid Metabolism in Patients With Prolonged Disorders of Consciousness

The intestinal microbiota regulate the brain function of the host through the production of a myriad of metabolites and are associated with various neurological diseases. Understanding the intestinal microbiome of patients with prolonged disorders of consciousness (DoC) is important for the evaluation and treatment of the disease. To investigate the differences in the intestinal microbiome and short-chain fatty acids (SCFAs) among patients in a vegetative state (VS), a minimally conscious state (MCS), and emerged from MCS (EMCS), as well as the influence of antibiotics on these patients, 16S ribosomal RNA (16S rRNA) sequencing and targeted lipidomics were performed on fecal samples from patients; in addition, analysis of the electroencephalogram (EEG) signals was performed to evaluate the brain function of these patients. The results showed that the intestinal microbiome of the three groups differed greatly, and some microbial communities showed a reduced production of SCFAs in VS patients compared to the other two groups. Moreover, reduced microbial communities and five major SCFAs, along with attenuated brain functional connectivity, were observed in MCS patients who were treated with antibiotics compared to those who did not receive antibiotic treatment, but not in the other pairwise comparisons. Finally, three genus-level microbiota—Faecailbacterium, Enterococcus, and Methanobrevibacter—were considered as potential biomarkers to distinguish MCS from VS patients, with high accuracy both in the discovery and validation cohorts. Together, our findings improved the understanding of patients with prolonged DoC from the intestinal microbiome perspective and provided a new reference for the exploration of therapeutic targets.

Phytochemical thymoquinone prevents hemoglobin glycoxidation and protofibrils formation: A biophysical aspect

d-ribose, a reducing sugar, in diabetic hyperglycemia provokes non-enzymatic glycoxidation of hemoglobin (Hb), an abundant protein of red blood cells (RBCs). Different types of intermediates adduct formation occur during glycoxidation, such as advanced glycation end-products (AGEs) which lead to amyloid formation due to structural and conformational alterations in protein. Therefore, the study of these intermediate adducts plays a pivotal role to discern their relationship with diabetes mellitus and related disorders. Here, we investigated the interaction mechanism of d-ribose with Hb, and Hb prebound phytochemical thymoquinone (TQ). Our investigation reveals that the interaction of TQ with histidine residues of Hb interferes with the interaction of d-ribose with glycine residues at the glycation-site. Based on that, we had performed a time-based (21-days) in-vitro glycoxidation study at 37 °C to investigate the structural perturbation mechanism of Hb at different time-intervals in absence/presence of TQ. We found that prolonged glycoxidation induces amyloid formation in absence of TQ but in its presence, the process was prohibited. In summary, this study examined and characterized biophysically different intermediate-states of protein carrying glycoxidation-modification. Our findings suggested that TQ potentially affects interaction of d-ribose with Hb that prevents glycoxidation and protofibril formation, which establishes TQ as a potential therapeutic agent.

Effect of methotrexate and its photodegradation products on the temperature induced denaturation of human serum albumin

Effect of the photodegradation of chemotherapeutic agent methotrexate on the denaturation of human serum albumin has been studied by differential scanning calorimetry and fluorimetric measurements. Photoluminescence studies highlighted entropy driven binding of both methotrexate molecules and its degradation products to the albumin molecules. The calorimetric measurements evaluated by the Kissinger method show elevated activation energy in the presence of methotrexate. Similar but moderated enhancement of the activation energy was obtained in the presence of the photodegradation products of methotrexate. These results highlight stabilization of the human serum albumin by the methotrexate drug which finding may contribute to fine tuning of methotrexate applications in therapy.

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.

In-vitro interaction of cerium oxide nanoparticles with hemoglobin, insulin, and dsDNA at 310.15 K: Physicochemical, spectroscopic and in-silico study

Lanthanide nanoparticles and nanorods especially their biocompatible oxide forms like cerium oxide nanoparticles (CNPs) with therapeutic applications are used to cure neurological oxidative stresses. Thus it tempts to study their biocompatible aspects by interactions with several biologically significant molecules. In-Vitro interactions of 15-240 μM CNPs with water, Phosphate buffered saline (PBS), DMEM media, Insulin (Ins) hemoglobin (Hb) and ds-DNA at 37 °C were studied. Their physicochemical properties study by Borosil Mansingh Survismeter (BMS) showed the first order interaction with the protein-protein structure breaking behaviour of CNPs with Hb, Ins, and DNA. Zeta potential measurements of CNPs in different biological medium show a net increase in negative charge magnitude with good colloidal stability. K_b = 4 × 106 mM^-1 of CNPs-DNA infer noncovalent interactions. Circular dichroism and FTIR revealed a loss of secondary conformation with increasing CNPs concentration. In-silico molecular docking depicts CNP interaction via conventional hydrogen bonding, carbon hydrogen bonding and electrostatic interactions at the minor groove of DNA. The study reports in-dept unfolding functional mechanism investigated by physicochemical, spectroscopic, and In-Silico approaches of protein on interactions with CNPs for safer-by-design use in medicine and pharmaceutics. Fundamentally the CeO₂ in ~62% and Ce₂O₃ in ~38% with Ce⁴⁺ and Ce³⁺ oxidation potentials develop a unique case of electronic configurations with 4f⁰5d⁰6s⁰ and 4f¹5d⁰6s⁰ electrons respectively which these studies a novel one.