scholarly journals Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251910
Author(s):  
Farzin Sohraby ◽  
Hassan Aryapour
Keyword(s):  
Molecular Dynamics ◽  
Molecular Targets ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Specific Therapy ◽  
X Ray ◽  
The World ◽  
Crystallographic Structures ◽  
Potential Inhibitors ◽  
And Behavior

The COVID-19 disease has infected and killed countless people all over the world since its emergence at the end of 2019. No specific therapy for COVID-19 is not currently available, and urgent treatment solutions are needed. Recent studies have found several potential molecular targets, and one of the most critical proteins of the SARS-CoV-2 virus work machine is the Papain-like protease (Plpro). Potential inhibitors are available, and their X-ray crystallographic structures in complex with this enzyme have been determined recently. However, their activities against this enzyme are insufficient and need to be characterized and improved to be of clinical values. Therefore, in this work, by utilizing the Supervised Molecular Dynamics (SuMD) simulation method, we achieved multiple unbinding events of Plpro inhibitors, GRL0617, and its derivates, and captured and understood the details of the unbinding pathway. We found that residues of the BL2 loop, such as Tyr268 and Gln269, play major roles in the unbinding pathways, but the most important contributing factor is the natural movements and behavior of the BL2 loop, which can control the entire process. We believe that the details found in this study can be used to refine and optimize potential inhibitors like GRL0617 and design more efficacious inhibitors as a treatment for the SARS-CoV-2 virus.

Femtosecond photoelectron spectroscopy of the I2− anion: A semiclassical molecular dynamics simulation method

1999 ◽  
Vol 110 (8) ◽  
pp. 3736-3747 ◽  
Author(s):  
Victor S. Batista ◽  
Martin T. Zanni ◽  
B. Jefferys Greenblatt ◽  
Daniel M. Neumark ◽  
William H. Miller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Photoelectron Spectroscopy ◽  
Simulation Method ◽  
Dynamics Simulation

Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

2016 ◽  
Vol 30 (01) ◽  
pp. 1550253 ◽  
Author(s):  
Xinjian Liu ◽  
Yu Jin ◽  
Congliang Huang ◽  
Jingfeng He ◽  
Zhonghao Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water System ◽  
Simulation Method ◽  
The Self ◽  
Dynamics Simulation ◽  
Low Rank ◽  
Self Diffusion ◽  
Change Mechanism ◽  
Different Temperatures ◽  
Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

2004 ◽  
Vol 18 (15) ◽  
pp. 2123-2139 ◽  
Author(s):  
BIN XUE ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Conformational Changes ◽  
Canonical Ensemble ◽  
Interaction Strength ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Native Conformation ◽  
Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

scholarly journals Molecular Dynamics Study on the Mechanism of Nanoscale Jet Instability Reaching Supercritical Conditions

2018 ◽  
Vol 8 (10) ◽  
pp. 1714 ◽  
Author(s):  
Qingfei Fu ◽  
Yunxiao Zhang ◽  
Chaojie Mo ◽  
Lijun Yang
Keyword(s):  
Molecular Dynamics ◽  
Growth Rate ◽  
Theoretical Result ◽  
Molecular Model ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Jet Instability ◽  
Subcritical Region ◽  
Thermodynamic Conditions ◽  
Spatio Temporal

This paper investigates the characteristics of a nitrogen jet (the thermodynamic conditions ranging from subcritical to supercritical) ejected into a supercritical nitrogen environment using the molecular dynamics (MD) simulation method. The thermodynamic properties of nitrogen obtained by molecular dynamics show good agreement with the Soave-Redlich-Kwong (SRK) equation of state (EOS). The agreement provides validation for this nitrogen molecular model. The molecular dynamics simulation of homogeneous nitrogen spray is carried out in different thermodynamic conditions from subcritical to supercritical, and a spatio-temporal evolution of the nitrogen spray is obtained. The interface of the nitrogen spray is determined at the point where the concentration of ejected fluid component reaches 50%, since the supercritical jet has no obvious vapor-liquid interface. A stability analysis of the transcritical jets shows that the disturbance growth rate of the shear layer coincides very well with the classical theoretical result at subcritical region. In the supercritical region, however, the growth rate obtained by molecular dynamics deviates from the theoretical result.

Molecular Dynamics simulation of organic materials: Structure, potentials and the MiCMoS computer platform

CrystEngComm ◽  
2022 ◽  
Author(s):  
Angelo Gavezzotti ◽  
Leonardo Lo Presti ◽  
Silvia Rizzato
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Determination ◽  
Organic Materials ◽  
Single Point ◽  
Lattice Energy ◽  
Dynamics Simulation ◽  
Organic Crystals ◽  
X Ray ◽  
Point Lattice

The science of organic crystals and materials has seen in a few decades a spectacular improvement from months to minutes for an X-ray structure determination and from single-point lattice energy...

Sign in / Sign up

Export Citation Format

Share Document