Investigation of allosteric coupling in beta-2 adrenergic receptor through molecular dynamics simulations

Abstract

The purpose of this thesis is to investigate the allosteric coupling between intra- and extracellular parts of G-protein coupled human β2 adrenergic receptor (β2AR) in the presence of intracellular loop ICL3, which is missing in all crystallographic structures. In a recent study, a 1 μs MD run showed that closure of the G-protein binding site due to tight packing and closure of ICL3 under the receptor was coupled with the expansion of the ligand binding site. In this study, two independent 500 ns runs, which started from the final snapshot of the original 1 μs MD run with closed ICL3, showed that ICL3 stayed mostly in closed position, pointing out that it is a stable state blocking the binding cavity of G-protein. This allosteric coupling between ICL3 opening/closure and ligand binding site compression/expansion was further investigated by imposing specific distance constraints on the ligand binding site of the receptor. A total of seven constraints were applied between the residues on helices 3, 5, 6 and 7 that form the binding pocket. Specifically, these constraints were between residue couples Ser203Oγ-Asp113Cγ, Ser204Oγ-Asp113Cγ, Ser207Oγ-Asp113Cγ, Asn293Cβ-Asp113Cβ, Phe289Cβ-Asp113Cβ, Asn312Cβ-Asp113Cβ, and Phe289Cβ-Asp312Cβ. Constraining the binding site to an open position forced ICL3 to close from its fully open position. Constraining the binding site to a relatively closed position kept ICL3 around its open form. Using one extra constraint on backbone atoms (between residues Ser207Cα-Asp113Cα of helices 5 and 3) facilitated the opening of the binding site, and thus accelerated the closure of ICL3 from a relatively open position. However, attempting to compress the binding pocket did not lead to a fully open ICL3. Through this work, the allosteric coupling between the ligand binding regions in the extracellular parts of H5 and H6 and the intracellular part of the receptor including ICL3