Abstract
Increasing body of evidence indicate that G protein-coupled receptors (GPCRs) exist as dimers and oligomers in the cell membrane. The goal of this study is to estimate the homodimeric form of beta-2 adrenergic (s2AR) receptor which is a member of the GPCR family, via multiple docking experiments.The transmembrane domain VI (TMVI) of the receptor is suggested to be a significant part of the interface both experimentally and theoretically [1,2]. The amino acid sequence motif, 75LIXXGVXXG83VXXT, which is proposed to be essential for dimerization in glycophorin A is similarly observed on TMVI of s2AR as in LKTLG276IMMG280TFTL284. A peptide is derived from TMVI consisting of residues from 276 to 296, GIIMGTFTLCWLPFFIVNIVH and blindly docked to one conformer of the monomeric structure using a rigid body approach, via AutoDock v4.0 software tool [3]. Bound conformations were then reevaluated with a knowledge-based scoring function called DSXonline v0.88 [4].Docking results shows that the peptide has the highest binding affinity for TMVI which supports the possible role of TMVI at the interface of a dimeric structure. Also, a residue interface propensity data derived from a set of 32 nonhomologous homodimers [5] is able to identify TMVI as the domain which contains the highest number of residues with the highest interface propensity values.
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