Unbinding of nicotine from the acetylcholine binding protein: steered molecular dynamics simulations.
The ligand binding/unbinding process is critical to our understanding of the pharmacology of both the nicotinic acetylcholine receptor (nAChR) and the acetylcholine binding protein (AChBP). Steered molecular dynamics simulations were performed to learn about the unbinding process of the full agonist nicotine. Three different pulling models were designed to investigate the possible binding/unbinding pathways: radial and tangent models, and also a mixed model. Of the three, the tangent pulling model finally failed to dissociate nicotine from the ligand binding pocket. The efficiency of the pulling force profiles was superior, and the opening of the C-loop was smaller in the mixed pulling model than that in the radial model. The most favorable pathway for the cholinergic agonist nicotine to enter or leave the binding pocket is through the principal binding side, following a curvilinear track. Noticeably, it has been seen that the unbinding of the nicotine is concomitant with a global rotation of the protein-ligand complex which could be caused by the interactions of the ligand with protein at the tangent direction.
Liu
Xinli
X
Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, Liaoning, 116024, China.
Xu
Yechun
Y
Wang
Xicheng
X
Barrantes
Francisco J
FJ
Jiang
Hualiang
H
D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009538:Nicotine / Q000737:chemistry*; D013997:Time Factors
C428944:AChBP protein, Lymnaea; D002352:Carrier Proteins; D008024:Ligands; D009538:Nicotine