selectively activate specific signaling cascades (biased agonists), and
abolish activity of other ligands (antagonists). Co-crystallization of
the GPCR with such ligands reveals distinct structural changes that
occur upon GPCR activation.
2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]5-hydroxy-2H-1,4-benzoxazin-3(4H)-one), active state of β 2 -Adrenergic Receptor (β 2 AR) bound to a nucleotide-free G s -protein heterotrimer provides the first high-resolution view of the ternary complex of
GPCR activation (PDB ID: 3SN6, hereafter referred to as β 2 AR-G s ).
Here we revisit this classical complex [38] and analyze it in terms of
weighted PSNs. Additionally, we also consider an antagonist
alprenolol-bound inactive state β 2 AR [39] (PDB ID: 3NYA, hereafter
referred to as β 2 AR-anta) for elucidating ligand-induced conformational changes at side-chain levels. Being one of the first GPCRs to be
biophysically characterized, cloned [40] and structurally determined
by means of X-ray crystallography [41], the β 2 -Adrenergic Receptor
serves as a classical system for understanding cell signaling. β 2 AR
functions by binding to hormone and neurotransmitter adrenaline
(also known as epinephrine) and inducing physiological responses
like smooth muscle relaxation and bronchodilation via the agency of
L-type Calcium channels [38]. A schematic representation of the
ternary complex of GPCR, G-protein and ligand is depicted in Fig. 2.
With a view to understand ligand-induced complex formation
between GPCR and G-protein, we investigate agonist and
antagonist-bound GPCR complexes in terms of weighted sidechain edges and bring to light distinct clustering patterns that
delineate ligand-induced conformational changes. We adopt the
weighted PSN methodology to understand the propagation of
information across the 7TM architecture in terms of non-covalent
side-chain interactions. In this section we investigate the following:
(1) ligand-protein contacts in β 2 AR-G s and β 2 AR-anta; (2) consequence of ligand binding on redistribution of interactions in
GPCR-G-protein bound systems, and (3) manifestation of these
perturbations on the local and global re-wiring of GPCRs in terms
of residue (node) clustering.
5.1 Binding Site
Comparison
of β 2 AR-G s
and β 2 AR-Anta
Complexes
Comparison of the ligand binding pocket in β 2 AR-G s and β 2 ARanta complexes reveals crucial information about the role of TM
helices in maintaining ligand-protein contacts. In particular, the
high-affinity agonist P0G (or BI-167107) in β 2 AR-G s is housed
in the binding pocket by means of strong hydrogen bonds
mediated by residues Asp113
3.32
, Asn312
7.39
, Ser203
5.42
, and
Ser207
5.46 (Fig. 3 panel a, superscripts indicate BallesterosWeinstein numbering Scheme [42] in which the first digit in superscript indicates helix number and digits in superscript following
decimal point indicate residue number relative to the most conserved residue in that particular TM helix which is numbered as
98
Vasundhara Gadiyaram et al.
abolish activity of other ligands (antagonists). Co-crystallization of
the GPCR with such ligands reveals distinct structural changes that
occur upon GPCR activation.
2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]5-hydroxy-2H-1,4-benzoxazin-3(4H)-one), active state of β 2 -Adrenergic Receptor (β 2 AR) bound to a nucleotide-free G s -protein heterotrimer provides the first high-resolution view of the ternary complex of
GPCR activation (PDB ID: 3SN6, hereafter referred to as β 2 AR-G s ).
Here we revisit this classical complex [38] and analyze it in terms of
weighted PSNs. Additionally, we also consider an antagonist
alprenolol-bound inactive state β 2 AR [39] (PDB ID: 3NYA, hereafter
referred to as β 2 AR-anta) for elucidating ligand-induced conformational changes at side-chain levels. Being one of the first GPCRs to be
biophysically characterized, cloned [40] and structurally determined
by means of X-ray crystallography [41], the β 2 -Adrenergic Receptor
serves as a classical system for understanding cell signaling. β 2 AR
functions by binding to hormone and neurotransmitter adrenaline
(also known as epinephrine) and inducing physiological responses
like smooth muscle relaxation and bronchodilation via the agency of
L-type Calcium channels [38]. A schematic representation of the
ternary complex of GPCR, G-protein and ligand is depicted in Fig. 2.
With a view to understand ligand-induced complex formation
between GPCR and G-protein, we investigate agonist and
antagonist-bound GPCR complexes in terms of weighted sidechain edges and bring to light distinct clustering patterns that
delineate ligand-induced conformational changes. We adopt the
weighted PSN methodology to understand the propagation of
information across the 7TM architecture in terms of non-covalent
side-chain interactions. In this section we investigate the following:
(1) ligand-protein contacts in β 2 AR-G s and β 2 AR-anta; (2) consequence of ligand binding on redistribution of interactions in
GPCR-G-protein bound systems, and (3) manifestation of these
perturbations on the local and global re-wiring of GPCRs in terms
of residue (node) clustering.
5.1 Binding Site
Comparison
of β 2 AR-G s
and β 2 AR-Anta
Complexes
Comparison of the ligand binding pocket in β 2 AR-G s and β 2 ARanta complexes reveals crucial information about the role of TM
helices in maintaining ligand-protein contacts. In particular, the
high-affinity agonist P0G (or BI-167107) in β 2 AR-G s is housed
in the binding pocket by means of strong hydrogen bonds
mediated by residues Asp113
3.32
, Asn312
7.39
, Ser203
5.42
, and
Ser207
5.46 (Fig. 3 panel a, superscripts indicate BallesterosWeinstein numbering Scheme [42] in which the first digit in superscript indicates helix number and digits in superscript following
decimal point indicate residue number relative to the most conserved residue in that particular TM helix which is numbered as
98
Vasundhara Gadiyaram et al.