A molecular docking and molecular dynamics simulation study on the interaction between cyanidin ‐ 3 ‐O ‐glucoside and major proteins in cow's milk

Abstract

The objective of this study was to investigate the molecular interaction and complex stability of four major cow's milk (CM) proteins (α-LA, β-LG, α s1-CA, and β-CA) with cyanidin-3-O-glucoside (C3G) using computational methods. The results of molecular docking analysis revealed that hydrogen bond and hydrophobic interaction were the main binding forces to maintain the stability of the C3G-CM protein complexes. Molecular dynamics simulation results showed that all complexes except for C3Gα s1-CA were found to reach equilibrium within 50 ns of simulation. α s1-CA and β-CA switched to a more compact conformation after binding with C3G. Additionally, the radius of gyration, number of hydrogen bond, radial distribution function, and interaction energy showed that β-CA is the best C3G carrier protein among the four CM proteins. This study can provide valuable information for CM proteins to serve as C3G delivery carriers. Practical applications Anthocyanins (ACNs) are flavonoid-based pigments that play an important functional role in regulating human's health. Cow's milk (CM) proteins are the most representative protein-based carriers that can improve the short-term bioavailability and stability of ACNs. Thus, it is important to study the interactions between ACNs and CM proteins at the molecular level for the development of effective ACNs delivery carriers. Our study showed that caseins (α s1-CA and β-CA) had more hydrophobic and hydrogen-bonding sites with cyanidin-3-O-glucoside (C3G) than whey proteins using computational methods. Among the four CM proteins, β-CA was the best C3G carrier protein showing the best interaction stability with C3G. Thus, it is helpful for us to screen effective ACNs carriers from multiple protein sources by computational methods.

In silico analysis of novel dipeptidyl peptidase-IV inhibitory peptides released from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and the possible pathways involved in diabetes protection

“…All the systems were simulated by MD for 50 ns. Unless special explanation, all other parameters are consistent with the methods of our previous study ( Pan et al, 2021 ). The GROMACS package (version 19.5) was used to analyze the MD trajectories.…”

“…MD simulations were carried out according to our previous methods with slight modifications ( Pan et al, 2021 ). In brief, MD simulations were performed for 50 ns using the GROMACS 19.5 package ( https://manual.gromacs.org/ ) with Amber ff99SB-ILDN force field and TIP3P explicit water model for DPP-IV with or without peptides.…”

Interfering effects on the bioactivities of several key proteins of COVID-19/variants in diabetes by compounds from Lianqiao leaves: In silico and in vitro analyses

“…It is well known that the lumen of the protein can provide a strong hydrophobic environment and multiple hydrogen binding sites for the ligand, which contributes to the stability of the ligand [49] . In order to further understand the binding between forsythoside A and various receptors, the interactions between them were analyzed, including hydrogen bonds and hydrophobic interactions.…”

Different preparation methods affect the phenolic profiles and antioxidant properties of Qingke barley foods

“…However, due to the differences of the affinity and hydrogen, hydrophobic bonds stability between the ligand and the receptor, the stability of the complexes is different, resulting in the different breakdown degrees of the complexes under different thermal conditions. For examples, the affinity values of the glutenin–gallic acid complex and gliadin–gallic acid complex were −6.5 kcal/mol and −5.6 kcal/mol, respectively, indicating that gliadin–gallic acid complex breakdown easier than glutenin–gallic acid when they were given the same energy (Pan et al., 2020). Besides, the stability of the hydrogen bond was determined by the bond length (Å), bond energy (ΔE) (Cooper, 2000).…”