scholarly journals Modeling, Molecular Dynamics Simulation, and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs

2014 ◽  
Vol 54 (9) ◽  
pp. 2483-2499 ◽  
Author(s):  
Zhiwei Feng ◽  
Mohammed Hamed Alqarni ◽  
Peng Yang ◽  
Qin Tong ◽  
Ananda Chowdhury ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Crystal Structures ◽  
Cannabinoid Receptor ◽  
Dynamics Simulation ◽  
Cannabinoid Receptor 2

Molecular Dynamics of the Assembly Modes of the Oligothiophene Polymers with Different Chain Lengths

2017 ◽  
Vol 727 ◽  
pp. 476-481 ◽  
Author(s):  
Li Lin Zhu ◽  
Bing Zhang ◽  
Kai Xuan Zhou ◽  
Jian Xi Yao ◽  
Song Yuan Dai
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Molecular Dynamics Simulation ◽  
Crystal Structures ◽  
Theoretical Foundation ◽  
Dynamics Simulation ◽  
High Charge ◽  
Hole Transporting ◽  
Chain Lengths ◽  
Hole Transporting Materials

The spatial packing modes of organic hole transporting materials exert a significant effect on the charge mobility. However it is difficult to reasonably design the materials with high-charge transfer performances due to the limits of the data regarding crystal structures. In this work, molecular dynamics simulation was used to find the new spatial packing ways of organic photoelectric materials containing oligothiophene based on randomly distributed initial structures. This work lays a theoretical foundation for designing favorable organic carrier transporting materials.

scholarly journals Understanding the role of the CB1 toggle switch in interaction networks using molecular dynamics simulation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sangho Ji ◽  
Wonjin Yang ◽  
Wookyung Yu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Changes ◽  
Cannabinoid Receptor ◽  
Endocannabinoid System ◽  
Interaction Network ◽  
Dynamics Simulation ◽  
Activation Mechanism ◽  
Toggle Switch

AbstractThe cannabinoid receptor 1 (CB1) is a class A G-protein coupled receptor (GPCR) that can exert various effects on the human body through the endocannabinoid system. Understanding CB1 activation has many benefits for the medical use of cannabinoids. A previous study reported that CB1 has two notable residues referred to as the toggle switch, F3.36 and W6.48, which are important for its activation mechanism. We performed a molecular dynamics simulation with a mutation in the toggle switch to examine its role in active and inactive states. We also examined structural changes, the residue–residue interaction network, and the interaction network among helices and loops of wildtype and mutant CB1 for both activation states. As a result, we found that the energetic changes in the hydrogen-bond network of the Na+ pocket, extracellular N-terminus–TM2–ECL1–TM3 interface including D2.63–K3.28 salt-bridge, and extracellular ECL2–TM5–ECL3–TM6 interface directly linked to the toggle switch contribute to the stability of CB1 by the broken aromatic interaction of the toggle switch. It makes the conformation of inactive CB1 receptor to be unstable. Our study explained the role of the toggle switch regarding the energetic interactions related to the Na+ pocket and extracellular loop interfaces, which could contribute to a better understanding of the activation mechanism of CB1.

Experimental and Molecular Dynamics Simulation Study of the Sublimation and Vaporization Energetics of Iron Metalocenes. Crystal Structures of Fe(η5-C5H4CH3)2and Fe[(η5-(C5H5)(η5-C5H4CHO)]

2008 ◽  
Vol 112 (13) ◽  
pp. 2977-2987 ◽  
Author(s):  
Cláudio M. Lousada ◽  
Susana S. Pinto ◽  
José N. Canongia Lopes ◽  
M. Fátima Minas da Piedade ◽  
Hermínio P. Diogo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Crystal Structures ◽  
Simulation Study ◽  
Dynamics Simulation
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