Bioinformatics and molecular modeling studies of membrane proteins Shiva Amiri Professor Mark S.P. Sansom June 11, 2004

Membrane proteins sdf Ligand gated ion channels (LGICs) constitute approximately 25% of the genome important drug targets - nerve and muscle excitation - hormonal secretion - sensory transduction - control of salt and water balance etc. malfunctions result in various diseases difficult to get their structures Ligand gated ion channels (LGICs) function is dependent upon the binding of a ligand. examples of LGICs: nAChR, GABAA and GABAC receptors, 5HT3 receptor, Glycine receptor Sperelakis, N., Cell Physiology Source Book sdf

My project to take available structural data and put the pieces together main focus so far: using available information to predict the structure and motions of the α-7 nicotinic acetylcholine receptor (nAChR) we have: 4Å cryo-EM structure of AChR transmembrane domain 2.7Å crystal structure of ligand binding domain homolog task: to combine the separate domains the use of bioinformatics and simulation tools to study functionally relevant motions of LGICs TM LB LB M3 M2 M4 TM M1

The process … homology modelling -Modeller, Procheck 2 PDBs {θmax, zmax} ZAlign termini distances bad contacts ( Unwin distances ) analysis – xfarbe plots make model using chosen {θ, z} GROMACS energy minimization procheck motion analysis: GNM CONCOORD electrostatics (Kaihsu Tai) pore dimensions - HOLE homology models of other LGICs

Course grain methods of motion analysis Gaussian network model (GNM) a course-grained model to approximate fluctuations of residues information on the flexibility and function of the protein produces theoretical B-values CONCOORD LB region spikes rotating to one side and the TM spikes rotating in the opposite direction, suggesting a twisting motion of the receptor

Summary Future work modeling methods for LGICs predicted structure of α-7 nAChR used various methods (GNM, CONCOORD) to look at motions of the predicted structure of α-7 nAChR models of anionic LGICs (GABA and glycine) using current α-7 nAChR structure Future work models of other LGICs motion analysis of other LGICs looking at the hydrophobic girdle (M2) of LGICs to study patterns of conservation and the behaviour of these residues during gating simulation studies of constructed models