Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all-atom molecular dynamics simulation

2018 ◽  
Vol 86 (11) ◽  
pp. 1127-1139 ◽  
Author(s):  
Xiao-Xuan Shi ◽  
Yi-Ben Fu ◽  
Si-Kao Guo ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Conformational Changes ◽  
Dynamics Simulation

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

The role of optical phonons in intermediate layer-mediated thermal transport across solid interfaces

2017 ◽  
Vol 19 (28) ◽  
pp. 18407-18415 ◽  
Author(s):  
Eungkyu Lee ◽  
Tengfei Luo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Optical Phonon ◽  
Thermal Transport ◽  
Intermediate Layer ◽  
Dynamics Simulation ◽  
Optical Phonons ◽  
Spectral Matching

A study with molecular dynamics simulation shows that optical phonon vibrational spectral matching by an intermediate layer can significantly impact thermal transport across diatomic solid interfaces.

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