scholarly journals On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Guillaume Copie ◽  
Fabrizio Cleri ◽  
Ralf Blossey ◽  
Marc F. Lensink
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Complexes ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Interfacial Water ◽  
Continuum Electrostatics

scholarly journals Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 12 (6) ◽  
pp. 7239-7248
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Water Molecules ◽  
Mean Square ◽  
Main Protease ◽  
Decreasing Ph ◽  
Increasing Temperature

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

scholarly journals Molecular Dynamics Simulation of Distribution and Diffusion Behaviour of Oil–Water Interfaces

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1905 ◽  
Author(s):  
Chengbin Zhang ◽  
Hanhui Dai ◽  
Pengfei Lu ◽  
Liangyu Wu ◽  
Bo Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Interface Roughness ◽  
Dynamics Simulation ◽  
Water Phase ◽  
Water Molecules ◽  
Water Interface ◽  
Oil Water ◽  
And Diffusion ◽  
Diffusion Behaviors

The distribution and diffusion behaviors of microscopic particles at fluorobenzene–water and pentanol–water interfaces are investigated using molecular dynamics simulation. The influences of Na+/Cl− ions and the steric effects of organic molecules are examined. The concentration distributions of different species, the orientations of oil molecules at the interface, and oil–water interface morphology as well as the diffusion behaviors of water molecules are explored and analyzed. The results indicate that a few fluorobenzene molecules move into the water phase influenced by Na+/Cl− ions, while the pentanol molecules at the interface prefer orientating their hydrophilic groups toward the water phase due to their large size. The water molecules more easily burst into the pentanol phase with larger molecular spaces. As the concentration of ions in the water phase increases, more water molecules enter into the pentanol molecules, leading to larger interface roughness and interface thickness. In addition, a lower diffusion coefficient for water molecules at the fluorobenzene–water interface are observed when introducing Na+/Cl− ions in the water phase, while for the pentanol–water system, the mobility of interfacial water molecules are enhanced with less ions and inhibited with more ions.

J053022 Molecular Dynamics Simulation for Vapor/Liquid Coexistence of Water Molecules in Nanopore

2013 ◽  
Vol 2013 (0) ◽  
pp. _J053022-1-_J053022-4
Author(s):  
Toshiki Mima ◽  
Ikuya Kinefuchi ◽  
Yuta Yoshimoto ◽  
Akinori Fukushima ◽  
Takashi Tokumasu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Vapor Liquid
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