Bioinformatics and molecular modeling studies of membrane

proteins

Shiva Amiri

Professor Mark S.P. Sansom

June 11, 2004

Membrane proteins

sdfSperelakis, N., Cell Physiology Source Book

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

M2

M3

M4M1

LB

TM

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 domain2.7Å 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

My project

LB

TM

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}

procheck

GROMACS energy minimization

motion analysis:GNM

CONCOORDelectrostatics (Kaihsu Tai)pore dimensions - HOLE

homology models of other LGICs

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

Course grain methods of motion analysis

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

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

Summary

Future work