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

Evaluation of the structure and stability of myoglobin after interaction with ribose: spectroscopic and molecular simulation approach

Osmolytes, as small organic molecules, possess a remarkable ability to exert protective effects on biomacromolecules, including proteins, while preserving their inherent functionality. Myoglobin, a globular protein comprising a sequence of 153 amino acids, fulfills a crucial biological role by exhibiting reversible oxygen binding capabilities and facilitating its efficient transfer to the muscular tissues. In this study, the effects of ribose on myoglobin protein in sodium phosphate buffer were studied by UV-Vis's spectrophotometry and spectrofluorimetric investigations at pH 7.4. Also, the interaction was theoretically studied through molecular dynamics simulation and molecular docking techniques. The results showed that the ribose stabilizes the protein structure by increasing the melting temperature (Tm) of myoglobin. The fluorescence intensity of myoglobin decreased with a static quenching mechanism at different temperatures. The thermodynamic data obtained from the experimental results also predicted that the intermolecular forces affecting the formation of a myoglobin-ribose complex are mainly the van der Waals interactions and hydrogen bindings. Theoretical molecular docking analyses unveiled the favored binding site of ribose within the structure of myoglobin. Subsequent molecular dynamics simulations validated the stability of the complex formed between ribose and myoglobin. Our findings are fundamental for understanding the molecular-level details of myoglobin-ligand interactions, opening avenues for innovative approaches to prevent or alleviate myoglobin dysfunction in various disease conditions.

Molecular and technical aspects on the interaction of bovine serum albumin with pyrazine derivatives: From molecular docking to spectroscopy study

In order to better understand the transport and action mechanism of flavor substance and proteins in human body, the interaction mechanism between pyrazine derivatives and bovine serum albumin (BSA) was studied by molecular dynamics simulation and a series of spectroscopic methods. In molecular docking, it was observed that the small molecules were surrounded by hydrophobic amino acid residues of the protein, and the main amino acid residues formed π-π interaction and hydrogen bond interaction with BSA. The results of fluorescence emission spectroscopy combined with thermodynamic analysis showed that static quenching was the main mechanism of the interaction between three pyrazine derivatives and BSA, which was dominated by hydrophobic interaction. Synchronous fluorescence spectroscopy and three-dimensional fluorescence spectroscopy combined with molecular dynamics simulation proved that the pyrazine derivatives changed the conformation of BSA. In summary, pyrazine derivatives can interact with BSA, and the complexation of the complex changes its spatial conformation. The research in this paper has positive significance for understanding the binding, transport, and metabolism of pyrazine compounds in the process of blood circulation and provides key data for the metabolism of pyrazine compounds in vivo. PRACTICAL APPLICATION: The interaction of pyrazine derivatives-BSA is studied by multi-spectra and MD. The fluorescence quenching of pyrazine derivatives-BSA is static quenching. The main force between pyrazine derivatives and BSA is hydrophobic force. There is only one site of association between pyrazine derivatives and BSA. Pyrazine derivatives have effects on conformation of BSA.

Probing the binding mode and interactions of proteinase K and glutathione: molecular simulation and experiments

Proteinase K, a serine protease from Tritirachium album Limber, is crucial in research due to its potent proteolytic activity, which relies on conformational stability and substrate affinity. Glutathione (GSH), an essential intracellular antioxidant, regulates various physiological processes by interacting with proteins, influencing their stability and function. Despite the importance of both proteinase K and GSH, their potential interaction remains unexplored. Understanding this interaction could uncover new regulatory mechanisms affecting proteinase K, with significant implications for research and therapeutic applications. In this study, we systematically investigated the binding of GSH to proteinase K using a comprehensive approach in which theoretical and experimental methods mutually validate each other. Molecular docking determined the binding mode and the interaction mechanism of proteinase K and GSH. Molecular dynamics (MD) simulations revealed that GSH binding significantly improved the stability of proteinase K, affirming the binding process was spontaneous, with hydrogen bonds and van der Waals forces emerging as the predominant contributors throughout the interaction. At the same time, the fluorescence spectrum and circular dichroism spectrum confirmed the interaction mechanism between GSH and proteinase K, as well as the conformational changes of proteinase K induced by GSH binding. We believe this study could offer valuable insights for future research into the structure and binding dynamics of other protein-ligand complexes under physiological conditions.

Interaction between the antioxidant compound safranal and α-chymotrypsin in spectroscopic fields and molecular modeling approaches

Among various herbal plants, saffron has been the subject of study in various medical and food fields. Among the compounds of saffron, safranal is one of them. Safranal is a monoterpene aldehyde. The precursor of safranal is called picrocrocin, whose hydrolysis leads to the production of safranal. picrocrocin has two sugar components and aglycone. sugar component was separated during the drying process of saffron and safranal is produced. Saffron is the cause of the saffron aroma. Previous studies have shown that safranal offers many benefits such as antioxidants, blood pressure regulation and anti-tumor qualities. On the other hand, α-Chy is an enzyme secreted by the pancreas into the intestine and then acts as an efficient protease. In this study, various methods, such as molecular dynamics (MD) simulation and molecular binding, and different spectroscopic techniques, as well as protein stability techniques, were used to investigate the possible interactions between safranal and α-Chy. UV spectroscopic studies were showing that the existence of safranal decreased α-Chy absorption intensity. safranal caused the intrinsic fluorescence of α-Chy to be quenched too. According to the Stern-Volmer equation, the interaction between safranal and α-Chy was of the static type. In thermodynamic calculations, the interaction between safranal and α-Chy was stabilized by hydrophobic forces. And it was found that this interaction continued spontaneously. These results were, thus, consistent with the Docking data simulation (with the negative ΔG° number and positive changes in enthalpy and entropy). The thermal stability of α-Chy was also measured, showing that its melting point was shifted to a higher threshold as a result of the interaction. also, MD simulation indicated that α-Chy became more stable in the presence of safranal. In this paper, all the results of the laboratory techniques were confirmed by molecular dynamic simulations, so the correctness of the results was confirmed. From this research, we hope to carefully observe the possible changes in the behavior and structure of the enzyme in the presence of safranal.Communicated by Ramaswamy H. Sarma.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.