scholarly journals Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels

RSC Advances ◽  
2020 ◽  
Vol 10 (72) ◽  
pp. 43994-44002
Author(s):  
Yue Pan ◽  
Renrui Qi ◽  
Minghao Li ◽  
Bingda Wang ◽  
Honglan Huang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Adenosine Deaminase ◽  
Closed Conformation ◽  
Open Conformation ◽  
Nucleoside Metabolism ◽  
Critical Residues ◽  
Random Acceleration ◽  
Dynamics Simulations ◽  
Important Enzyme

Adenosine deaminase (ADA), an important enzyme related to purine nucleoside metabolism, can be divided into open conformation and closed conformation according to the inhibitors of binding.

scholarly journals Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0207234 ◽  
Author(s):  
Xiaopian Tian ◽  
Ye Liu ◽  
Jingxuan Zhu ◽  
Zhengfei Yu ◽  
Jiarui Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Adenosine Deaminase ◽  
Dynamics Simulations

scholarly journals In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Wilmar Puma-Zamora ◽  
Fabian Jimenez ◽  
Jesus Antonio Alvarado-Huayhuaz ◽  
Gerson Cordova-Serrano ◽  
Pierre-Marie Allard ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Natural Products ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Interactions ◽  
Free Energies ◽  
Main Protease ◽  
Starting Point ◽  
In Silico Studies ◽  
Dynamics Simulations ◽  
Important Enzyme

The rapid global spread of SARS-CoV-2, the causative agent of COVID-19, has set off the alarms of healthcare systems all over the world, the situation is exacerbated as no effective treatment is available to date. One therapeutic strategy consists in stopping the replication of the virus by inhibiting SARS-CoV-2 main protease, an important enzyme in the processing of polyproteins from viral RNA. Applying techniques like virtual screening, molecular docking and molecular dynamics simulations, our study evaluated the biomolecular interactions generated between more than 200 thousand natural products structures collected from the Universal Natural Product Database and the main protease active site. Through successive docking filters, we identified 3 molecules with a good affinity profile for the enzyme. These were subjected to molecular dynamics simulations and their binding free energies were calculated. Structures of the best natural products identified could be a starting point for developing novel antiviral candidates targeting SARS-CoV-2 M<sup>pro</sup>

scholarly journals Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

2021 ◽  
Vol 8 ◽  
Author(s):  
Khair Bux ◽  
Xiayu Shen ◽  
Muhammad Tariq ◽  
Junqi Yin ◽  
Syed Tarique Moin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Principal Component Analysis ◽  
Deep Learning ◽  
Horseshoe Crab ◽  
Active Form ◽  
Principal Component ◽  
Closed Conformation ◽  
Open Conformation ◽  
Explicit Solvent ◽  
Dynamics Simulations

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

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