scholarly journals Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

2018 ◽  
Vol 140 (41) ◽  
pp. 13456-13465 ◽  
Author(s):  
Samuel F. Cousin ◽  
Pavel Kadeřávek ◽  
Nicolas Bolik-Coulon ◽  
Yina Gu ◽  
Cyril Charlier ◽  
...  
2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.


RSC Advances ◽  
2018 ◽  
Vol 8 (20) ◽  
pp. 11134-11144 ◽  
Author(s):  
Lanyan He ◽  
Pingmei Wang ◽  
Lipeng He ◽  
Zhou Qu ◽  
Jianhui Luo ◽  
...  

The self-organization of five model side-chain decorated polyaromatic asphaltene molecules with or without toluene solvent was investigated by means of molecular dynamic (MD) simulations.


Sign in / Sign up

Export Citation Format

Share Document