Computational Sciences and Engineering MS Thesis Defense by Ebru Çetin








Title: Investigation of the intracellular loop 3 and allosteric mechnanisms of β2-Adrenergic among G-protein coupled receptors


Speaker: Ebru Çetin


Time: August 17, 2017, 09:30


Place: ENG 127

Koç University

Rumeli Feneri Yolu

Sariyer, Istanbul

Thesis Committee Members:

Prof. Burak Erman (Advisor, Koc University)

Prof. A.Levent Demirel (Koc University)

Prof. Türkan Haliloğlu (Boğaziçi University)



G-protein coupled receptors are encoded over 700 genes in human genome. They share a common seven transmembrane domain and differing intracellular and extracellular loops. As transmembrane domains, they function as gate-keepers of intercommunication of cells. Thus, their functioning mechanisms are one of most unique ongoing research area. In this study after the introduction of GPCR families, human β2-adrenergic receptor and endogenous ligand epinephrine are investigated. First of all, usually omitted part of β2-Ar intracellular loop 3 and its unbinding energy from inactive to the active state is estimated. Secondly, intracommunications between residues are investigated via correlation matrices.

In allostery analysis two trajectories of β2-Ar embedded in lipid membrane are anaylzed. One of the trajectories is gathered from 1 μs molecular dynamics simulation and second trajectory is gathered from 500 ns molecular dynamics simulation where the ligand binding pocket is restrained to 8 Å in order to mimic ligand binding.

Specifically for β2Ar, experimental measurements show that the distance range of 8Å – 10Å between Asp113 and Ser207 is sufficient for receptor activation.

In 1 μs simulation, it is observed that ICL1 (residues 64 to 66) is in communication with intracellular end of TM6 (Cys265, Lys267). Thr66 of ICL1 is important in protein stabilization in lipid membrane and functions through Tyr123 (TM3) and Ile154 (TM4). Trp99 of ECL1 is correlated to ECL2 (Cys191) and membrane region of TM5 (Ile 214). Phe101 of ECL1 is correlated extracellular end of TM6 and intracellular end of TM5.

In 500 ns simulation, Met98 of ECL1 is correlated to intracellular end of TM1 (Arg53), ICL1 (Phe61), intracellular end of TM2 (Thr68) and cytoplasmic tail (Leu339). Gly102 of ECL1 is correlated to membrane region of TM2 (Glu82), intracellular end of TM3 (Arg131), ICL2 (Ser143) and intracellular end of TM5 (Phe223). Ile135 of TM3 at intracellular region is correlated to extracellular part of TM2 (Ala92), membrane region of TM4 (Val160, Leu163) and membrane region of TM5 (Ala202). These finding imply that ICL1 may be responsible for ligand recognition signals whereas ECL1 is responsible for protein stabilization and recognition of intracellular effectors.

In estimation of required energy for unbinding of intracellular loop 3 is found as 1629 kJ/mol and confirmed with G-protein coupling energy to β2-Ar with the work of -1455 kJ/mol.

Finally, the endogenous ligand epinephrine of β-adrenoceptors is studied in order to estimate critical differences between β1, β2, β3 ligand binding pockets for epinephrine and their selectivity.