Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Self Assembly Study of the Human GPCR Protein β2-Adrenergic Receptor Using Coarse Grained Molecular Dynamics Technique
Integral membrane proteins roughly constitutes of 25 to 30% to the human genome, of which the G-Protein Coupled Receptors (GPCRs) encode for nearly 3-4% of all the genes, regulating various physiological processes through signal transduction. As a consequence of this, these receptors have become the targets of several modern day drugs. Most of the studies aimed at designing new drugs for targeting GPCRs have assumed that these receptors function in monomeric form. However, this assumption has recently been changed by the description of a number of GPCRs that can be found in oligomeric state within the cellular environment (1). Although many unsolved problems still remain, the idea that GPCRs directly interact to form oligomers, both homomers as well as heteromers, has been gradually accepted. The mechanism of GPCR dimer or oligomer formation, and its effect on receptor function, is not currently well understood.
In the present study, coarse grained molecular dynamics (CGMD) approach was adopted for studying the self-assembly process of the human amine GPCR protein β2-adrenergic receptor (β2-AR), for which several experimental evidences of oligomerization process and its effect on its function are available (2, 3). PDB entry 2RH1 was taken as the starting structure. Since 2RH1 lacks ICL3 (residue 231-262), initially the missing loop was modeled in SYBYL and simulated for 10 ns using restrained MD in order to get a stable conformation. The final structure was then used for further studies. To mimic a cellular environment, 16 copies of β2-AR were inserted into DSPC bilayer at a protein to lipid ratio of 1:104 and then solvated with water. The entire system was represented using the MARTINI CG convention (4), resulting in a total system size of 57296 CG beads. The system was then simulated for 3 µs using the GROMACS package with MARTINI force filed parameters. An increased time-step of 30 femto-second was used which resulted in stable integration. At the end of the simulation period, proper dimers and tetramers of β2-AR were found to be formed through the self-assembly mechanism which were further validated through various analysis methods. The gradual decrease in SASA values calculated with a probe radius of 0.52 nm confirmed that the monomers were indeed coming together to form aggregates. The lipid bilayer analysis also helped to quantify the assembly mechanism. In order to identify the exact residues or domains which are responsible for this oligomerization, a conversion of the CG system back to an all-atom model and simulated annealing simulations are being presently carried out.
Centre for Development of Advanced Computing,
Pune University Campus, Pune – 411 007, India