Molecular dynamics simulation of energy migration between tryptophan residues in apoflavodoxin

RSC Advances ◽  
2014 ◽  
Vol 4 (59) ◽  
pp. 31443-31451 ◽  
Author(s):  
Nadtanet Nunthaboot ◽  
Fumio Tanaka ◽  
Sirirat Kokpol ◽  
Nina V. Visser ◽  
Herbert van Amerongen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Fluorescence Anisotropy ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Fluorescence Anisotropy Decay ◽  
Anisotropy Decay ◽  
Tryptophan Residues ◽  
Anisotropy Model ◽  
Atomic Coordinates

By performing molecular dynamics (MD) simulations of apoflavodoxin over the same timescale as fluorescence anisotropy decay measurements, the anisotropy model of two unidirectional FRET steps from two tryptophan residues to a third one can be reproduced from the tryptophan atomic coordinates in the MD trajectory.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

Molecular Dynamics Simulation of Neutron Damage in β-SIC

1998 ◽  
Vol 540 ◽  
Author(s):  
J.M. Perlado ◽  
L. Malerba ◽  
T. Diaz De La Rubia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Point Defects ◽  
Damage Accumulation ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Temperature Sensitive ◽  
Neutron Damage ◽  
Preliminary Study ◽  
Threshold Displacement

AbstractMolecular Dynamics (MD) simulations of neutron damage in β-SiC have been performed using a modified version of the Tersoff potential. The Threshold Displacement Energy (TDE) for Si and C atoms at 300 K has been determined along directions [001], [110], [111] and [ 1 1 1 ]. The existence of recombination barriers, which allow the formation of metastable, temperature-sensitive defects even below the threshold, has been observed. Displacement cascades produced by both C- and Si-recoils of energies spanning from 0.5 keV up to, respectively, 5 keV and 8 keV have also been simulated at 300 K and 1300 K. Their analysis, together with the analysis of damage accumulation (∼3.4×10-3 DPA) at 1300 K, reveals that the two sub-lattices exhibit opposite responses to irradiation: whereas only a little damage is produced on the “ductile” Si sub-lattice, many point-defects accumulate on the much more “fragile” C sub-lattice. A preliminary study of the nature and clustering tendency of these defects is performed. The possibility of disorder-induced amorphization is considered and the preliminary result is that no amorphization takes place at the dose and temperature simulated.

scholarly journals Molecular dynamics simulation of α-unsubstituted oligo-thiophenes: dependence of their high-temperature liquid-crystalline phase behaviour on molecular length

2019 ◽  
Vol 7 (32) ◽  
pp. 9984-9995 ◽  
Author(s):  
Flora D. Tsourtou ◽  
Stavros D. Peroukidis ◽  
Vlasis G. Mavrantzas
Keyword(s):  
Molecular Dynamics ◽  
Phase Diagram ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Liquid Crystalline ◽  
Md Simulations ◽  
Phase Behaviour ◽  
Dynamics Simulation ◽  
Molecular Length ◽  
Temperature Liquid

Phase diagram of α-nT oligomers with n = 5–8 from the MD simulations.

scholarly journals Influence on ferric chloride aqueous solution caused by external electrostatic field: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (68) ◽  
pp. 38706-38714 ◽  
Author(s):  
Shi Zhibo ◽  
Li Liyi ◽  
Han Yong ◽  
Bai Jie
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Ferric Chloride ◽  
Electrostatic Field ◽  
Simulation Study ◽  
Dynamic Properties ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Electrostatic Fields

A detailed analysis of structural properties and dynamic properties of ferric chloride aqueous solution under external electrostatic fields with different intensities was performed by molecular dynamics (MD) simulations.

Molecular dynamics simulation of the local concentration and structure in multicomponent aerosol nanoparticles under atmospheric conditions

2017 ◽  
Vol 19 (25) ◽  
pp. 16681-16692 ◽  
Author(s):  
Katerina S. Karadima ◽  
Vlasis G. Mavrantzas ◽  
Spyros N. Pandis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Organic Compound ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Core Shell ◽  
Local Concentration ◽  
Atmospheric Conditions ◽  
Aerosol Nanoparticles

MD simulations predicted core–shell or partially engulfed morphologies (depending on the type of the organic compound present) in multicomponent aerosol nanoparticles.

scholarly journals Methanol diffusion in zeolite HY: a combined quasielastic neutron scattering and molecular dynamics simulation study

2016 ◽  
Vol 18 (26) ◽  
pp. 17294-17302 ◽  
Author(s):  
Alexander J. O'Malley ◽  
Victoria García Sakai ◽  
Ian P. Silverwood ◽  
Nikolaos Dimitratos ◽  
Stewart F. Parker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Simulation Study ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Quasielastic Neutron ◽  
Quasielastic Neutron Scattering

The diffusion of methanol in zeolite HY is studied using tandem quasielastic neutron scattering (QENS) experiments and molecular dynamics (MD) simulations at 300–400 K.

A Combined Experimental and Molecular Dynamics Simulation Study on the Miscibility of Eucommia Ulmoides Gum with Several Rubbers

2017 ◽  
Vol 25 (1) ◽  
pp. 87-92 ◽  
Author(s):  
Fei-Zhou Li ◽  
Zhen-Lin Lu ◽  
Dong-Ping Tian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Phase Diagrams ◽  
Interaction Parameter ◽  
Simulation Study ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Eucommia Ulmoides ◽  
Mixing Energy ◽  
Eucommia Ulmoides Gum

This paper analyzes the miscibility state of EUG blended with CR, BR, SBR, NR and NBR via Molecular Dynamics (MD) simulations performed using Blends and the Flory-Huggins interaction parameter, phase diagrams, and mixing energy. The results showed that EUG can be miscible with CR, BR, SBR, NR, and NBR above 350K, and the simulation predictions and experimental results were mainly the same.

Molecular dynamics simulation of Al–SiO2 sandwich nanostructure melting and low-temperature energetic reaction behavior

RSC Advances ◽  
2016 ◽  
Vol 6 (64) ◽  
pp. 59313-59318 ◽  
Author(s):  
Jinping Zhang ◽  
Yubing Si ◽  
Can Leng ◽  
Baocheng Yang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Low Temperature ◽  
Force Field ◽  
Melting Temperature ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Reaction Behavior

The heating and low temperature thermite reactions of the Al/SiO2 sandwich nanostructure are investigated by MD simulations in combination with the reactive force field. The results show that the melting temperature of this structure is ∼1400 K.

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