scholarly journals Effects of Baicalein and Chrysin on the Structure and Functional Properties of β-Lactoglobulin

Foods ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 165
Author(s):  
Ang Li ◽  
Lei Chen ◽  
Weijie Zhou ◽  
Junhui Pan ◽  
Deming Gong ◽  
...  

Two flavonoids with similar structures, baicalein (Bai) and chrysin (Chr), were selected to investigate the interactions with β-lactoglobulin (BLG) and the influences on the structure and functional properties of BLG by multispectral methods combined with molecular docking and dynamic (MD) simulation techniques. The results of fluorescence quenching suggested that both Bai and Chr interacted with BLG to form complexes with the binding constant of the magnitude of 105 L·mol−1. The binding affinity between BLG and Bai was stronger than that of Chr due to more hydrogen bond formation in Bai–BLG binding. The existence of Bai or Chr induced a looser conformation of BLG, but Chr had a greater effect on the secondary structure of BLG. The surface hydrophobicity and free sulfhydryl group content of BLG lessened due to the presence of the two flavonoids. Molecular docking was performed at the binding site of Bai or Chr located in the surface of BLG, and hydrophobic interaction and hydrogen bond actuated the formation of the Bai/Chr–BLG complex. Molecular dynamics simulation verified that the combination of Chr and BLG decreased the stability of BLG, while Bai had little effect on it. Moreover, the foaming properties of BLG got better in the presence of the two flavonoids compounds and Bai improved its emulsification stability of the protein, but Chr had the opposite effect. This work provides a new idea for the development of novel dietary supplements using functional proteins as flavonoid delivery vectors.

2016 ◽  
Vol 33 (No. 5) ◽  
pp. 474-479 ◽  
Author(s):  
J. Ren ◽  
Ch. Song ◽  
P. Wang ◽  
S. Li ◽  
N. Kopparapu ◽  
...  

The structural and functional properties such as solubility, emulsifying properties, foaming properties, oil binding capacity, and surface hydrophobicity of sunflower 11S globulin hydrolysates generated by Alcalase at hydrolysis time of 30, 60, 90, and 120 min were evaluated. Circular dichroism analysis showed the hydrolysates possessed a decreased α-helix and β-structure. The hydrolysates exhibited lower surface hydrophobicity. Hydrolysates with shorter hydrolysis time showed the higher emulsifying activity index, but the same emulsion stability and oil binding capacity compared to the original 11S globulin. The longer hydrolysis resulted in lower foaming and emulsion stability. Thus it was demonstrated that by controlling the hydrolysis time of sunflower 11S globulin, hydrolysate with a desirable functional properties can be obtained.


2014 ◽  
Vol 68 (11) ◽  
Author(s):  
Mehdi Sahihi ◽  
Yousef Ghayeb

AbstractBiguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.


Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 789
Author(s):  
Mycal Dutta ◽  
Abu Montakim Tareq ◽  
Ahmed Rakib ◽  
Shafi Mahmud ◽  
Saad Ahmed Sami ◽  
...  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus’s severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography–mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics–generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (−5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (−5.39 kcal/mol), and lorazepam, 2TMS derivative (−5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand–Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.


Author(s):  
Prem Prakash Kushwaha ◽  
Atul Kumar Singh ◽  
Tanya Bansal ◽  
Akansha Yadav ◽  
Kumari Sunita Prajapati ◽  
...  

The present study explores the SARS-CoV-2 drugable target inhibition efficacy of phytochemicals from Indian medicinal plants using molecular docking, molecular dynamics (MD) simulation, and MM-PBSA analysis. A total of 130 phytochemicals were screened against SARS-CoV-2 Spike (S)-protein, RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro). Result of molecular docking showed that Isoquercetin potentially binds with the active site/protein binding site of the Spike, RdRP, and Mpro targets with a docking score of -8.22, -6.86, and -9.73 kcal/mole, respectively. Further, MS 3, 7-Hydroxyaloin B, 10-Hydroxyaloin A, showed -9.57, -7.07, -8.57 kcal/mole docking score against Spike, RdRP, and Mpro targets respectively. The MD simulation was performed to study the favorable confirmation and energetically stable complex formation ability of Isoquercetin and 10-Hydroxyaloin A phytochemicals in Mpro-unbound/ligand bound/standard inhibitor bound system. The parameters such as RMSD, RMSF, Rg, SASA, Hydrogen-bond formation, energy landscape, principal component analysis showed that the lead phytochemicals form stable and energetically stabilized complex with the target protein. Further, MM-PBSA analysis was performed to compare the Gibbs free energy of the Mpro-ligand bound and standard inhibitor bound complexes. The analysis revealed that the His-41, Cys145, Met49, and Leu27 amino acid residues were majorly responsible for the lower free energy of the complex. Drug likeness and physiochemical properties of the test compounds showed satisfactory results. Taken together, the study concludes that that the Isoquercetin and 10-Hydroxyaloin A phytochemical possess significant efficacy to bind SARS-Cov-2 Mpro active site. The study necessitates further in vitro and in vivo experimental validation of these lead phytochemicals to assess their anti-SARS-CoV-2 potential.


2012 ◽  
Vol 27 ◽  
pp. 119-128 ◽  
Author(s):  
Ai-Ping Yang ◽  
Mei-Hua Ma ◽  
Xiao-Hua Li ◽  
Mao-Yun Xue

The binding of irbesartan to bovine hemoglobin (BHb) has been investigated for the first time by using UV-Vis absorption, fluorescence, circular dichroism (CD), and molecular docking. The binding site numbernand binding constantKwere calculated to be 1 and , respectively. The alternations of protein secondary structure in the presence of irbesartan was demonstrated using CD spectroscopy. Furthermore, molecular docking indicated that irbesartan could bind to the site 2 of BHb. The analysis of the binding site of irbesartan within the BHb molecule suggested that hydrophobic interaction, hydrogen bond formation, and electrostatic interaction could account for the binding of irbesartan. The hydrogen bond of irbesartan with His87 in the C chain of BHb has been formed. The electrostatic energy, van der Waals energy, and binding free energy were calculated to be −460.3, −224.2, and−684.5 kcal, respectively.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0255866
Author(s):  
Yechuan Huang ◽  
Xicai Zhang ◽  
Huayi Suo

The binding between β-lactoglobulin and epigallocatechin gallate (EGCG) under the pressure of 600 MPa was explored using molecular docking and molecular dynamics (MD) simulation. EGCG bound mainly in two regions with site 1 in internal cavity of the β-barrel and site 2 on the surface of protein. 150 ns MD was performed starting from the structure with the optimal binding energy at the two sites in molecular docking, respectively. It was found that the protein fluctuated greatly when small molecule bound to site 2 at 0.1 MPa, and the protein fluctuation and solvent accessible surface area became smaller under high-pressure. The binding of small molecules made the protein structure more stable with increasing of α-helix and β-sheet, while high-pressure destroyed α-helix of protein. The binding energy of small molecules at site 1was stronger than that at site 2 under 0.1 MPa, with stronger van der Waals and hydrophobic interaction at site 1 while more hydrogen bonds were present at site 2. The binding energy of both sites weakened under high-pressure, especially at site 1, causing the binding force to be weaker at site 1 than that at site 2 under high-pressure.


2020 ◽  
Author(s):  
Sandeep Surendra Malviya ◽  
Ramakrishnan Edyapatti Periyasamy ◽  
Vinod Jani ◽  
Mallikarjunachari Uppuladinne V N ◽  
Ankita Sonawane ◽  
...  

Molecular dynamics (MD) is a computational technique that works on the Newton's equations of motion to study the dynamics of various biomolecules and, is commonly used by structural biologists. With the development of advanced simulation techniques and increasing computing power, large amounts of data are being generated from these simulations. Various enhanced sampling techniques are currently being used, that are able to capture rare events and generate simulation data in the form of multiple trajectories. Analyzing the simulation trajectory data and extracting meaningful information using the traditional sequential post-simulation data analysis methods are becoming increasingly untenable. Currently, molecular dynamics simulation algorithms that are scalable on high-performance computing clusters are available which generate a huge amount of MD data in short span of time. The need of the hour lies in developing a advanced and high-performance analytics platform based tool that can analyze this huge simulation data in a faster and more efficient way. The Hadoop Spark framework, provides an excellent platform that meets these requirements of handling large amounts of data parallely and perform analytics with high scalability. In this study, a tool name H-BAT has been developed using the Hadoop Spark platform to calculate hydrogen bonding within all solute-solute, solute-solvent and solvent-solvent molecules in large MD simulation trajectories. Vector geometry has been used for calculation of angle and distance between the atoms which are present in the form of triplets of filtered atoms taking part in hydrogen bond formation. The benchmarking was performed up to a data size of 48 GB which showed linear scalability. Additionally, the tool is capable of handling multiple similar trajectories simultaneously. Future enhancement of the tool would include various other analysis like normal mode analysis, RMSD, 2DRMSD and Water Density Analysis using the Hadoop Spark framework.<br>


Author(s):  
Cuiping Yu ◽  
Fan Wu ◽  
Yue Cha ◽  
Yuting Qin ◽  
Ming Du

Abstract Oyster protein isolate (OPI) suspensions (6.19 % ± 0.82 %, w/v) were treated by high-pressure homogenization (HPH) at 0 (control), 20, 40, 60, 80 or 100 MPa for three cycles. Protein profiles, secondary structure, free sulfhydryl, surface hydrophobicity, particle size distribution, zeta-potential, solubility, water and oil holding capacity (OHC), emulsifying and foaming properties of the obtained suspensions were analyzed. The results showed that HPH treatment did not cause changes in protein profiles of OPI, but caused changes in secondary structure, content of α-helix decreased but content of β-turn and random coil increased significantly (P < 0.05). Free sulfhydryl and surface hydrophobicity all increased significantly (P < 0.05) after HPH treatment, indicating that tertiary and quaternary structures changed. Functional properties of OPI significantly (P < 0.05) improved after HPH treatment, such as zeta-potential (from −12.67 to −33.57 mV), solubility (from 20.24 % to 57.99 %), OHC (from 981.77 % to 1229.40 %), foaming ability (from 17.50 % to 35.00 %), foaming stability (from 44.49 % to 66.60 %), emulsifying activity index (from 8.87 to 17.06 m2/g) and emulsion stability index (from 14.65 to 41.68 min). At 60 MPa and 80 MPa, the improvements were more remarkable. However, HPH treatment significantly (P < 0.05) decreased particle size (from 200–500 nm to 0–200 nm) and water holding capacity (from 341.15 % to 216.96 %). These improvements were closely related to structural changes and reduction of particle size. Application of different pressures affected functional properties of OPI. These results could provide information for determining HPH applying condition in OPI modification.


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