Thompson A J, Chau P-L, Chan S L, Lummis S C R
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
Biophys J. 2006 Mar 15;90(6):1979-91. doi: 10.1529/biophysj.105.069385. Epub 2005 Dec 30.
The binding sites of 5-HT3 and other Cys-loop receptors have been extensively studied, but there are no data on the entry and exit routes of ligands for these sites. Here we have used molecular dynamics simulations to predict the pathway for agonists and antagonists exiting from the 5-HT3 receptor binding site. The data suggest that the unbinding pathway follows a tunnel at the interface of two subunits, which is approximately 8 A long and terminates approximately 20 A above the membrane. The exit routes for an agonist (5-HT) and an antagonist (granisetron) were similar, with trajectories toward the membrane and outward from the ligand binding site. 5-HT appears to form many hydrogen bonds with residues in the unbinding pathway, and experiments show that mutating these residues significantly affects function. The location of the pathway is also supported by docking studies of granisetron, which show a potential binding site for granisetron on the unbinding route. We propose that leaving the binding pocket along this tunnel places the ligands close to the membrane and prevents their immediate reentry into the binding pocket. We anticipate similar exit pathways for other members of the Cys-loop receptor family.
5-HT3及其他半胱氨酸环受体的结合位点已得到广泛研究，但关于这些位点配体的进出途径尚无数据。在此，我们利用分子动力学模拟来预测激动剂和拮抗剂从5-HT3受体结合位点的退出途径。数据表明，解离途径沿着两个亚基界面处的一条通道，该通道约8埃长，在膜上方约20埃处终止。激动剂（5-羟色胺）和拮抗剂（格拉司琼）的退出途径相似，均朝着膜并从配体结合位点向外延伸。5-羟色胺似乎与解离途径中的残基形成许多氢键，实验表明，突变这些残基会显著影响功能。通道的位置也得到了格拉司琼对接研究的支持，该研究显示格拉司琼在解离途径上有一个潜在的结合位点。我们认为，沿着这条通道离开结合口袋会使配体靠近膜，并防止它们立即重新进入结合口袋。我们预计半胱氨酸环受体家族的其他成员也有类似的退出途径。
