scholarly journals Identification of Deleterious Mutations inMyostatinGene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Kiran Dashrath Rasal ◽  
Vemulawada Chakrapani ◽  
Swagat Kumar Patra ◽  
Shibani D. Mohapatra ◽  
Swapnarani Nayak ◽  
...  
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Negative Impact ◽  
Labeo Rohita ◽  
Functional Relationships ◽  
Simulation Techniques ◽  
Significant Negative Impact ◽  
The Impact

The myostatin (MSTN) is a known negative growth regulator of skeletal muscle. The mutated myostatin showed a double-muscular phenotype having a positive significance for the farmed animals. Consequently, adequate information is not available in the teleosts, including farmed rohu carp,Labeo rohita. In the absence of experimental evidence, computational algorithms were utilized in predicting the impact of point mutation of rohu myostatin, especially its structural and functional relationships. The four mutations were generated at different positions (p.D76A, p.Q204P, p.C312Y, and p.D313A) of MSTN protein of rohu. The impacts of each mutant were analyzed using SIFT, I-Mutant 2.0, PANTHER, and PROVEAN, wherein two substitutions (p.D76A and p.Q204P) were predicted as deleterious. The comparative structural analysis of each mutant protein with the native was explored using 3D modeling as well as molecular-dynamic simulation techniques. The simulation showed altered dynamic behaviors concerning RMSD and RMSF, for either p.D76A or p.Q204P substitution, when compared with the native counterpart. Interestingly, incorporated two mutations imposed a significant negative impact on protein structure and stability. The present study provided the first-hand information in identifying possible amino acids, where mutations could be incorporated into MSTN gene of rohu carp including other carps for undertaking furtherin vivostudies.

scholarly journals Discovery of Potential Anti-Ischemic Stroke Agents Through Inhibiting Sulfonylurea Receptor 1 (SUR1): A Pharmacophore-based Screening, Docking, and Molecular Dynamic Simulation

2021 ◽  
Vol 12 (5) ◽  
pp. 6915-6932
Keyword(s):  
Ischemic Stroke ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Sulfonylurea Receptor ◽  
Brain Membrane ◽  
Simulation Based ◽  
Intact Brain ◽  
Docking Energy

Stroke is the leading cause of disability and death worldwide. Inhibition of sulfonylurea 1 receptor (SUR1) using glibenclamide previously has been studied in CNS ischemic tissues and faster recovery from stroke injury in different animal models of stroke. Unfortunately, glibenclamide cannot enter the brain through an intact brain membrane (BBB) due to its ionization at physiological pH. Therefore, it was hypothesized that compounds with structural properties similar to glibenclamide but with the ability to penetrate through BBB would be superior to glibenclamide in ischemic stroke. Docking energy and interactions of glibenclamide with SUR1 active site were assessed using AutoDock Vina. NCI databases search engines with limitations for penetration to CNS were used to find the best compounds with desired properties. Then two selected compounds were assessed with dynamic molecular studies. Two compounds called CID-415537 and CID-419074 with docking energies of -10.3 kcal/mol and -11 kcal/mol were identified. CID-415537 was selected as the best compound due to its proper interactions with SUR1 amino acids and stability in molecular dynamic simulation. Based on this study, compound CID-415537 would be a good candidate for a SUR1 inhibitor in ischemic stroke. However, further in vivo investigations are required to confirm these findings.

scholarly journals Multicomponent Shale Oil Flow in Real Kerogen Structures via Molecular Dynamic Simulation

Energies ◽  
2020 ◽  
Vol 13 (15) ◽  
pp. 3815
Author(s):  
Jie Liu ◽  
Yi Zhao ◽  
Yongfei Yang ◽  
Qingyan Mei ◽  
Shan Yang ◽  
...  
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Boundary Layers ◽  
Dynamic Simulation ◽  
Driving Force ◽  
High Speed ◽  
Driving Forces ◽  
Negative Impact ◽  
Shale Oil ◽  
Positive Role

As an unconventional energy source, the development of shale oil plays a positive role in global energy, while shale oil is widespread in organic nanopores. Kerogen is the main organic matter component in shale and affects the flow behaviour in nanoscale-confined spaces. In this work, a molecular dynamic simulation was conducted to study the transport behaviour of shale oil within kerogen nanoslits. The segment fitting method was used to characterise the velocity and flow rate. The heterogeneous density distributions of shale oil and its different components were assessed, and the effects of different driving forces and temperatures on its flow behaviours were examined. Due to the scattering effect of the kerogen wall on high-speed fluid, the heavy components (asphaltene) increased in bulk phase regions, and the light components, such as methane, were concentrated in boundary layers. As the driving force increased, the velocity profile demonstrated plug flow in the bulk regions and a half-parabolic distribution in the boundary layers. Increasing the driving force facilitated the desorption of asphaltene on kerogen walls, but increasing the temperature had a negative impact on the flow velocity.

Discovery of Trypanocidal Bioactive Leads by Docking Study, Molecular Dynamic Simulation and In Vivo Screening

2018 ◽  
Vol 3 (8) ◽  
pp. 2386-2389
Author(s):  
Akachukwu Ibezim ◽  
Chukwunonso B. Obi ◽  
Nneoma M. Oforkansi ◽  
Chika J. Mbah ◽  
Ngozi J. Nwodo
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Docking Study ◽  
In Vivo Screening

scholarly journals The Influence of Urban Sprawl on Air Pollution and the Mediating Effect of Vehicle Ownership

Processes ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 1261
Author(s):  
Aiping Tao ◽  
Qun Liang ◽  
Peng Kuai ◽  
Tao Ding
Keyword(s):  
Air Pollution ◽  
Urban Sprawl ◽  
Negative Impact ◽  
Empirical Support ◽  
Mediating Effect ◽  
Vehicle Ownership ◽  
Mediating Role ◽  
Effect Model ◽  
Significant Negative Impact ◽  
The Impact

Based on the panel data of 224 prefecture-level and above cities in China from 2003 to 2016, this paper empirically studies the impact of urban sprawl on air pollution and introduces a mediating effect model to test the mediating role of vehicle ownership concerning the impact of urban sprawl on air pollution. The research in this paper arrives at three conclusions. First, urban sprawl has a significant positive effect on air pollution, and this conclusion is still valid after solving the endogeneity problem and conducting a robustness test. Second, the results of mediating effect test show that urban sprawl indirectly affects air pollution through the partial mediating effect of vehicle ownership. By removing the mediating effect, urban sprawl has a significant negative impact on air pollution, indicating that the mediating effect of vehicle ownership is higher concerning the impact of urban sprawl on air pollution. Third, further panel quantile regression results show that the higher the level of air pollution, the weaker the mediating effect of vehicle ownership and the stronger the direct effect of urban sprawl on air pollution. These conclusions can provide some empirical support for solving the air pollution problems caused by urban sprawl in China.

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