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

2. 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

3. 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

4. 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

5. 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

6. 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