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Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues.

Sheftel S, Muratore KE, Black M, Costanzi S - In Silico Pharmacol (2013)

Bottom Line: At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures.Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures.Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA.

ABSTRACT

Purpose: G protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β2 adrenergic receptor (β2 AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor.

Methods: Networks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks - or networks in general - to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members.

Results: The residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures.

Conclusions: Our results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers.

No MeSH data available.


Related in: MedlinePlus

Three-dimensional representation of the β2AR, showing the residues for which the difference in closeness-centrality detected when the analyses were performed in the presence or the absence of ligands exceeded the average plus 2.5 times the standard deviation of the values detected across all residues, for all the analyzed blocker-bound structures (panel a), as well as the agonist-bound 3PDS (panel b) and 3POG (panel c). Separate figures for the individual blocker-bound structures are given in Additional file1: Figure S4. The backbone of the receptor is schematically portrayed as a ribbon colored with a continuous spectrum ranging from red at the N-terminus to purple at the C-terminus, with TM1 in red/orange, TM2 in orange, TM3 in yellow, TM4 in yellow/green, TM5 in green, TM6 in blue and TM7 in purple. The non-hydrogen atoms of the shown residues are represented as spheres, colored according to the same scheme illustrated for the backbone.
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Fig12: Three-dimensional representation of the β2AR, showing the residues for which the difference in closeness-centrality detected when the analyses were performed in the presence or the absence of ligands exceeded the average plus 2.5 times the standard deviation of the values detected across all residues, for all the analyzed blocker-bound structures (panel a), as well as the agonist-bound 3PDS (panel b) and 3POG (panel c). Separate figures for the individual blocker-bound structures are given in Additional file1: Figure S4. The backbone of the receptor is schematically portrayed as a ribbon colored with a continuous spectrum ranging from red at the N-terminus to purple at the C-terminus, with TM1 in red/orange, TM2 in orange, TM3 in yellow, TM4 in yellow/green, TM5 in green, TM6 in blue and TM7 in purple. The non-hydrogen atoms of the shown residues are represented as spheres, colored according to the same scheme illustrated for the backbone.

Mentions: In the first level of analysis, the structures were analyzed without the co-crystallized ligands. Thus, in our second level of analysis we studied the change in centrality detected when the structures were analyzed with or without the co-crystallized ligand. Because the ligands in question are small molecules, we treated them as a single residue. As the plot shown in Figure 11 reveals, there is one major region for which the centrality is markedly increased in the presence of the ligands. Mapping on the crystal structures the residues most markedly affected by the ligands – more specifically the residues for which the difference in centrality was equal or higher than a cutoff value set to the average plus 2.5 times the standard deviation across all residues (difference in centrality ≥ 0.015) – reveals that the region in question comprises residues in EL2 and the adjacent half of TM5 (Figure 12 and Additional file 1: Figure S4). A closer examination of Figure 12 and Additional file 1: Table S3 reveals that additional regions that acquire centrality for the blocker-bound structures include TM3, TM6, TM7 and EL3, while additional regions that acquire centrality for the agonist-bound structures include TM1, TM2, TM3, TM6, TM7 and EL1. Despite this partial overlap, the pattern of residues that acquire centrality in the presence of agonists or blockers is rather different. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures. In particular, only two residues are in common between the two agonist-bound structures and some of the blocker-bound structures, namely Cys 191EL2 and Ser 2045.43. Moreover, the inactive structure crystallized with the large, covalently bound, FAUC 50 agonist (3PDS) shares two additional residues in common with some of the blocker-bounds structures, namely Ala 2005.39, Ser 2035.42 (Additional file 1: Table S3).Figure 11


Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues.

Sheftel S, Muratore KE, Black M, Costanzi S - In Silico Pharmacol (2013)

Three-dimensional representation of the β2AR, showing the residues for which the difference in closeness-centrality detected when the analyses were performed in the presence or the absence of ligands exceeded the average plus 2.5 times the standard deviation of the values detected across all residues, for all the analyzed blocker-bound structures (panel a), as well as the agonist-bound 3PDS (panel b) and 3POG (panel c). Separate figures for the individual blocker-bound structures are given in Additional file1: Figure S4. The backbone of the receptor is schematically portrayed as a ribbon colored with a continuous spectrum ranging from red at the N-terminus to purple at the C-terminus, with TM1 in red/orange, TM2 in orange, TM3 in yellow, TM4 in yellow/green, TM5 in green, TM6 in blue and TM7 in purple. The non-hydrogen atoms of the shown residues are represented as spheres, colored according to the same scheme illustrated for the backbone.
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Related In: Results  -  Collection

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Fig12: Three-dimensional representation of the β2AR, showing the residues for which the difference in closeness-centrality detected when the analyses were performed in the presence or the absence of ligands exceeded the average plus 2.5 times the standard deviation of the values detected across all residues, for all the analyzed blocker-bound structures (panel a), as well as the agonist-bound 3PDS (panel b) and 3POG (panel c). Separate figures for the individual blocker-bound structures are given in Additional file1: Figure S4. The backbone of the receptor is schematically portrayed as a ribbon colored with a continuous spectrum ranging from red at the N-terminus to purple at the C-terminus, with TM1 in red/orange, TM2 in orange, TM3 in yellow, TM4 in yellow/green, TM5 in green, TM6 in blue and TM7 in purple. The non-hydrogen atoms of the shown residues are represented as spheres, colored according to the same scheme illustrated for the backbone.
Mentions: In the first level of analysis, the structures were analyzed without the co-crystallized ligands. Thus, in our second level of analysis we studied the change in centrality detected when the structures were analyzed with or without the co-crystallized ligand. Because the ligands in question are small molecules, we treated them as a single residue. As the plot shown in Figure 11 reveals, there is one major region for which the centrality is markedly increased in the presence of the ligands. Mapping on the crystal structures the residues most markedly affected by the ligands – more specifically the residues for which the difference in centrality was equal or higher than a cutoff value set to the average plus 2.5 times the standard deviation across all residues (difference in centrality ≥ 0.015) – reveals that the region in question comprises residues in EL2 and the adjacent half of TM5 (Figure 12 and Additional file 1: Figure S4). A closer examination of Figure 12 and Additional file 1: Table S3 reveals that additional regions that acquire centrality for the blocker-bound structures include TM3, TM6, TM7 and EL3, while additional regions that acquire centrality for the agonist-bound structures include TM1, TM2, TM3, TM6, TM7 and EL1. Despite this partial overlap, the pattern of residues that acquire centrality in the presence of agonists or blockers is rather different. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures. In particular, only two residues are in common between the two agonist-bound structures and some of the blocker-bound structures, namely Cys 191EL2 and Ser 2045.43. Moreover, the inactive structure crystallized with the large, covalently bound, FAUC 50 agonist (3PDS) shares two additional residues in common with some of the blocker-bounds structures, namely Ala 2005.39, Ser 2035.42 (Additional file 1: Table S3).Figure 11

Bottom Line: At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures.Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures.Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA.

ABSTRACT

Purpose: G protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β2 adrenergic receptor (β2 AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor.

Methods: Networks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks - or networks in general - to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members.

Results: The residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures.

Conclusions: Our results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers.

No MeSH data available.


Related in: MedlinePlus