Effects of undersized Fe atoms on the stability of interstitials near a dislocation core in V studied by molecular dynamics simulation

2007 ◽  
Vol 14 (S1) ◽  
pp. 121-127 ◽  
Author(s):  
Yosuke Abe ◽  
Hideki Matsui
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dislocation Core ◽  
Dynamics Simulation ◽  
The Stability

Effect of conjugated (EK)10 peptide on structural and dynamic properties of ubiquitin protein: a molecular dynamics simulation study

2020 ◽  
Vol 8 (31) ◽  
pp. 6934-6943
Author(s):  
Qing Shao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamic Properties ◽  
Protein A ◽  
Dynamics Simulation ◽  
Allosteric Effect ◽  
Peptide Conjugation ◽  
The Stability

Peptide conjugation modulates the stability and biological acitivty of proteins via the allosteric effect.

scholarly journals Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation

2019 ◽  
Vol 19 (2) ◽  
pp. 461
Author(s):  
Herlina Rasyid ◽  
Bambang Purwono ◽  
Thomas S Hofer ◽  
Harno Dwi Pranowo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Energy Calculation ◽  
Protein Receptor ◽  
The Stability

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint

2019 ◽  
Vol 22 (8) ◽  
pp. 546-554
Author(s):  
Mohadeseh Bazoobandi ◽  
Mohammad R. Bozorgmehr ◽  
Ali Mahmoudi ◽  
Ali Morsali
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Low Temperatures ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Quadruplex Structure ◽  
G Quadruplex ◽  
The Stability ◽  
Increasing Temperature

Aim and Objective: The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C. Materials and Methods: RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures. The calculation of hydrogen bonds in Guanine-tetrads in three different quadruplex sheets shows that the effect of ligands on the sheets is not the same so that the bottom sheet of G-quadruplex is most affected by the ligands at high temperatures, and the Guaninetetrads in this sheet are far away. Conformation factor was calculated as a measure of ligands binding affinity for each of the G-quadruplex residues. Results: The results show that the studied ligands interact more with the G-quadruplex than loop areas, although with increasing temperature, the binding area also includes the G-quadruplex sheets. The contribution of each of the residues involved in the G-quadruplex binding area with ligands was also calculated. Conclusion: The calculations performed are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of phenanthroline and its derivatives with quadruplex.

Homology Modeling and Evaluation of Sars-Cov-2 Spike Protein Mutant

2021 ◽  
Vol 6 (4) ◽  
pp. 38-55
Author(s):  
Hima Vyshnavi ◽  
Aswin Mohan ◽  
Shahanas Naisam ◽  
Suvanish Kumar ◽  
Nidhin Sreekumar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Antiviral Drug ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Structure Modeling ◽  
Ramachandran Plot ◽  
Global Pandemic ◽  
The Stability

Severe acute respiratory syndrome coronavirus 2 (SARS‐Cov-2), a global pandemic, affected the world, increasing every day. A mutated variant D614G, showing more virulence and transmission, was studied for forecasting the emergence of more virulent and pathogenic viral strains. This study focuses on structure modeling and validation. Characterization of proteins homologous to wild spike protein was done, and homology models of the mutated variant were modeled using these proteins. Validation of models was done using Ramachandran plot and ERRAT plot. Molecular dynamics simulation was used to validate the stability of the models, and binding affinity of these models were estimated by molecular docking with an approved antiviral drug. Docked complexes were studied and the best model was selected. Molecular dynamics simulation was used to estimate the stability of the docked complex. The model of 6VXX, a homologous of wild spike protein, was found to be stable with the interaction of the antiviral drug from this study.

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