Nanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation Study

2011 ◽  
Vol 110-116 ◽  
pp. 3888-3892
Author(s):  
N. Maftouni ◽  
M. Amininassab ◽  
F. Kowsari
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Small Proteins ◽  
Steered Molecular Dynamics Simulation ◽  
The Difference ◽  
Dynamics Simulations ◽  
Naja Atra

Experimental observations have shown that cardio toxins (cobra cytotoxins), small proteins of three-fingered cytotoxin group, damage nanobiomembranes in different cells and vesicles. However, the molecular mechanism of this damage is not yet completely cleared. Molecular dynamics simulations have been used here to study the interaction of cardiotoxins A3 and A4 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid bilayer in two separate systems. Each of studied systems included one cytotoxin molecule, 128 lipid molecules (64 molecules in each monolayer) and 11817 water molecules. It has been found that the toxin interacts with zwitterionic bilayer formed by POPC. At the beginning of simulation the cytotoxins have been oriented toward nanobiomembrane surface by their loops’ tips. This orientation has changed during first 50 ns of classical molecular dynamics simulation for both of studied cytotoxins. The A3 toxin finally meets POPC nanobiomembrane with sides of loops near tips including cytotoxin region THR148 and VAL155. The A4 cytotoxin molecule has been finally oriented toward surface of nanobiomembrane with base and one of loop's tip including THR184, ARG186 and LEU158 amino acids, after 50 ns molecular dynamics simulation. Then 25 ns steered molecular dynamics simulation has been done for both of systems. The obtained data suggest that cytotoxin A3 meets the nanobiomembrane with sides of loops near tips and A4 meets POPC nanobiomembrane with base and one of loop's tips. The difference between final orientations of these two cytotoxins comes from the difference in the structure of them.

Acceleration of molecular dynamics simulation of multiphase systems on GPU

2012 ◽  
Vol 9 (2) ◽  
pp. 76-79
Author(s):  
D.F. Marin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Intermolecular Interaction ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Lennard Jones ◽  
Multiphase Systems ◽  
And Performance ◽  
Dynamics Simulations

The paper presents results on acceleration of molecular dynamics simulations with the usage of GPUs. A system of water molecules is considered as an example of polar liquid. The intermolecular interaction is modeled with the usage of Coulomb and truncated Lennard-Jones potentials. Results of computational experiments on acceleration and performance of the developed code are presented.

scholarly journals Transport mechanisms of water molecules and ions in sub-nano channels of nanostructured water treatment liquid-crystalline membranes: a molecular dynamics simulation study

2020 ◽  
Vol 6 (3) ◽  
pp. 604-611 ◽  
Author(s):  
Hiroki Nada ◽  
Takeshi Sakamoto ◽  
Masahiro Henmi ◽  
Takafumi Ogawa ◽  
Masahiro Kimura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Treatment ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Liquid Crystalline ◽  
Dynamics Simulation ◽  
Self Organization ◽  
Water Molecules ◽  
Transport Mechanisms ◽  
Dynamics Simulations

Transport mechanisms of water molecules and ions in the liquid crystalline (LC) membranes with sub-nano channels formed by self-organization of thermotropic ionic LC compounds were elucidated by molecular dynamics simulations.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Probing the Hirudin−Thrombin Interaction by Incorporation of Noncoded Amino Acids and Molecular Dynamics Simulation†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (46) ◽  
pp. 13556-13569 ◽  
Author(s):  
Vincenzo De Filippis ◽  
Giorgio Colombo ◽  
Ilaria Russo ◽  
Barbara Spadari ◽  
Angelo Fontana
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

Molecular Dynamics Simulation of Sputtering with Mmany-Body Interactions

1988 ◽  
Vol 100 ◽  
Author(s):  
Davy Y. Lo ◽  
Tom A. Tombrello ◽  
Mark H. Shapiro ◽  
Don E. Harrison
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Single Crystal ◽  
Low Energy ◽  
Dynamics Simulation ◽  
Embedded Atom Method ◽  
Many Body ◽  
Embedded Atom ◽  
Dynamics Simulations ◽  
Small Single Crystal

ABSTRACTMany-body forces obtained by the Embedded-Atom Method (EAM) [41 are incorporated into the description of low energy collisions and surface ejection processes in molecular dynamics simulations of sputtering from metal targets. Bombardments of small, single crystal Cu targets (400–500 atoms) in three different orientations ({100}, {110}, {111}) by 5 keV Ar+ ions have been simulated. The results are compared to simulations using purely pair-wise additive interactions. Significant differences in the spectra of ejected atoms are found.

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 Icephobicity of Functionalized Graphene Surfaces

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Xiang-Xiong Zhang ◽  
Min Chen
Keyword(s):  
Molecular Dynamics ◽  
Freezing Temperature ◽  
Ice Nucleation ◽  
Chloride Ions ◽  
Water Molecules ◽  
Sodium Ions ◽  
Functionalized Graphene ◽  
Functionalized Surfaces ◽  
The Difference ◽  
Dynamics Simulations

Manipulating the ice nucleation ability of liquid water by solid surface is of fundamental importance, especially in the design of icephobic surfaces. In this paper, the icephobicity of graphene surfaces functionalized by sodium ions, chloride ions, or methane molecules is investigated using molecular dynamics simulations. The icephobicity of the surface is evaluated by the freezing temperature. The freezing temperature on surface functionalized by methane molecules decreases at first and then increases as a function of the number groups, while the freezing temperature increases monotonically as a function of the number groups upon surfaces functionalized by sodium ions or chloride ions. The difference can be partially explained by the potential morphologies near the surfaces. Additionally, the validity of indicating the ice nucleation ability of water molecules using the number of six rings in the system is examined. Current study shows that the ice nucleation upon functionalized surfaces is inhibited when compared with smooth graphene substrate, which proves the feasibility of changing the icephobicity of the surfaces by functionalizing with certain ions or molecules.

Sign in / Sign up

Export Citation Format

Share Document