Dynamics and Binding Affinity of Spin-Labeled Stearic Acids in β-Lactoglobulin: Evidences from EPR Spectroscopy and Molecular Dynamics Simulation

2012 ◽  
Vol 116 (38) ◽  
pp. 11608-11615 ◽  
Author(s):  
Rita Guzzi ◽  
Bruno Rizzuti ◽  
Rosa Bartucci
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Epr Spectroscopy ◽  
Dynamics Simulation ◽  
Β Lactoglobulin

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

Molecular dynamics simulation and EPR spectroscopy of nitroxide side chains in bacteriorhodopsin

2000 ◽  
Vol 84 (1) ◽  
pp. 17-27 ◽  
Author(s):  
Heinz-Jürgen Steinhoff ◽  
Matthias Müller ◽  
Christian Beier ◽  
Matthias Pfeiffer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Epr Spectroscopy ◽  
Dynamics Simulation ◽  
Side Chains

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

2014 ◽  
Vol 68 (11) ◽  
Author(s):  
Mehdi Sahihi ◽  
Yousef Ghayeb
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Hydrophobic Interactions ◽  
Mean Value ◽  
Transport Protein ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Accessible Surface ◽  
Β Lactoglobulin

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.

Molecular Dynamics Simulation of β-Lactoglobulin at Different Oil/Water Interfaces

2016 ◽  
Vol 17 (5) ◽  
pp. 1572-1581 ◽  
Author(s):  
Davoud Zare ◽  
Jane R. Allison ◽  
Kathryn M. McGrath
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Oil Water ◽  
Β Lactoglobulin

scholarly journals Identification of Potent Inhibitors against Aurora Kinase A Using Molecular Docking and Molecular Dynamics Simulation Studies

2019 ◽  
Author(s):  
Sathishkumar Chinnasamy ◽  
Gurudeeban Selvaraj ◽  
Aman Chandra Kaushik ◽  
Satyavani Kaliamurthi ◽  
Asma Sindhoo Nangraj ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Aurora Kinase ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Aurora Kinase A ◽  
High Binding Affinity ◽  
Kinase A

Aurora kinase A (AURKA) is a normal cell proliferation-inducing enzyme encoded by AURKA gene, with over-expression observed in different types of malignancies. Hence, the goal is to find potential inhibitors against AURKA. In this study, molecular docking, Standard Precision and Extra Precision methods were employed. After the docking study, the ligands showed an extremely low binding score which suggested very high binding affinity of the ligands. Furthermore, Quantum polarized ligand docking (QPLD) was performed to predict the binding status of the molecules. Based on the binding affinity, the top four compounds were chosen for further analysis. The docked complexes were further analyzed in explicit water conditions using 100 ns molecular dynamics simulations and binding free energy calculation. Then, density functional theory (DFT) calculation was used to calculate the molecular properties of the molecules. Finally, systems biology experiments validated the molecular docking and molecular dynamics simulation studies and indicated that quercetin, kaempferol, luteolin and rutin could inhibit the AURKA. The results show that, these four molecules have high binding affinity to the AURKA and significant interactions (LEU139, GLU211and ALA213) were also identified with the hinge region of Aurora kinase A. Thus, LEU139, GLU211, and ALA213 were identified as the crucial protein mechanisms.

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