Abstract:
G protein-coupled receptors (GPCRs) represent the single largest family of cell surface receptors involved in signal transduction. It is estimated that several hundred distinct members of this receptor family in humans direct responses to a wide variety of chemical transmitters, including biogenic amines, amino acids, peptides, lipids, nucleosides, and large polypeptides. These transmembrane receptors are key controllers of such diverse physiological processes as neurotransmission, cellular metabolism, secretion, cellular differentiation, and growth as well as inflammatory and immune responses. GPCRs therefore represent major targets for the development of new drug candidates with potential application in all clinical fields. In this thesis, the crystal structure of a human β2- adrenergic receptor (β2AR) complexed with a partial inverse agonist carazolol was used as a starting conformation (PDB ID: 2rh1). The missing intracellular loop III (ICL3), which plays an essential role in G protein recognition, was estimated via homology modelling. An alternative model of the receptor with missing loop, which called as "clipped" model, was also used in order to understand the effect of the loop on the dynamics. The purpose of this study is to explore the dynamics of the receptor and the effect of the generated loop on the whole structure the shed light on the results of MD simulations. Here we characterize 0.8 μs and 0.5 μs all-atom MD simulation of an apo-β2AR for looped and clipped model respectively. Also Asn187 residue has been replaced with Glu187 to facilitate crystallization for the clipped model. Though it is estimated that a single residue will not affect the dynamics of the system significantly, to obtain a definite outcome, the system, undergoing no mutation, has been formed with its natural contents, and being placed within cell membrane, it has been exposed to a 0.5 μs all-atom MD simulation of an apo- β2AR. From MD studies, it was shown that the global orientation of the loop region (ICL3) changed considerably with respect to the core structure. The maximum mobility was observed for ICL3 and short loops ICL2, ECL2 and ECL3 connecting the transmembrane helices.
