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Molecular Modelling Studies of the Nicotinic Acetylcholine Receptor. Shiva Amiri Professor Mark S. P. Sansom and Dr. Philip C. Biggin D. Phil. Symposium, October 6, 2005. Ligand binding domain (LB) core of 10 β -strands, forming a β -sandwich
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Professor Mark S. P. Sansom and Dr. Philip C. Biggin
D. Phil. Symposium, October 6, 2005
Unwin, Journal of Molecular Biology, March, 2005The Nicotinic Acetylcholine Receptor (nAChR)
Coarse-grainGrouping of atoms
Looking at the behaviour of water in the binding pocket
Docking Nicotine and other ligands onto various frames of trajectories
In-house methodsGrouping data to simplify MD output
Generating random structures from a given structure within distant constraints
Gaussian Network Model (GNM)Assessing the flexibility of structures depending on the number of neighbouring residuesMotion Analysis
Covariance matrix showing which part of the protein moves together. The red parts show highest covariance and the blue indicates negative covariance (move in opposite directions)
Porcupine plot showing the nAChR’s two domains rotating in opposite directions. Suggests motions that could be involved in the gating mechanism
http://s12-ap550.biop.ox.ac.uk:8078/dynamite_html/index.html (Barrett et al., 2004)Coarse-grain methods (2)
http://s12-ap550.biop.ox.ac.uk:8078/dynamite_html/index.html (Barrett et al., 2004)Molecular Dynamics Simulations
A simulation of AChBP with Nicotine in all 5 binding sites.
The important residues in the binding pocket are shown. These residues are thought to have key interactions with the ligand.
Two subunits of the nAChR are shown with Nicotine inside the binding pocketThe Binding Pocket
Water molecules which remain in their position in the Binding Pocket
Nicotine docked onto the AChBP binding site
Developed a method to generate protein structures from their separate domains
Automated docking of ligands (Nicotine, acetylcholine, carbamylcholine, insecticides) onto AChBP and nAChR (and its mutants) along a trajectory
Dr. Philip C. Biggin
Dr. Alessandro Grottesi
Dr. Kaihsu Tai
Dr. Zara Sands
Dr. Oliver Beckstein
Dr. Daniele Bemporad
Dr. Jorge Pikunic
Dr. Andy Hung
Dr. Shozeb Haider
Dr. Syma Khalid
Dr. Pete Bond
Dr. Kia Balali-Mood
Dr. Hiunji Kim
Dr. Bing Wu
Chze Ling Wee
CYS 188The Binding Pocket
The important residues in the binding pocket are shown. These residues have been shown to interact with the ligand.