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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

View of the “knot region” of the β2AR, with the P-I-F motif highlighted: a) The carazolol-bound inactive structure (2RH1); b) the active structure (3P0G). The residues that belong to the P-I-F motif are shown as balls and sticks, all the others are shown as thin tubes. The color of the carbon atoms reflects the sequence position of the residues and goes 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 ligands co-crystallized with the receptors are also shown as balls and sticks, with their carbon atoms colored in gray.
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Fig5: View of the “knot region” of the β2AR, with the P-I-F motif highlighted: a) The carazolol-bound inactive structure (2RH1); b) the active structure (3P0G). The residues that belong to the P-I-F motif are shown as balls and sticks, all the others are shown as thin tubes. The color of the carbon atoms reflects the sequence position of the residues and goes 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 ligands co-crystallized with the receptors are also shown as balls and sticks, with their carbon atoms colored in gray.

Mentions: The identification of the non-covalent interactions did not require the addition of hydrogen atoms to the crystal structures, since CSU has been expressly designed to implicitly account their presence. However, for the preparation of Figures 1, 3, 4 and 5, we added hydrogen atoms with the “protein preparation wizard” workflow of the Schrödinger suite, to add hydrogen atoms and calculate the protonation states of ionizable groups at pH 7. The workflow also optimized the orientation of hydroxyl groups, as well as Asn, Gln and His residues (Schrödinger Suite 2012; Sastry et al. 2013).Figure 3


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)

View of the “knot region” of the β2AR, with the P-I-F motif highlighted: a) The carazolol-bound inactive structure (2RH1); b) the active structure (3P0G). The residues that belong to the P-I-F motif are shown as balls and sticks, all the others are shown as thin tubes. The color of the carbon atoms reflects the sequence position of the residues and goes 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 ligands co-crystallized with the receptors are also shown as balls and sticks, with their carbon atoms colored in gray.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230308&req=5

Fig5: View of the “knot region” of the β2AR, with the P-I-F motif highlighted: a) The carazolol-bound inactive structure (2RH1); b) the active structure (3P0G). The residues that belong to the P-I-F motif are shown as balls and sticks, all the others are shown as thin tubes. The color of the carbon atoms reflects the sequence position of the residues and goes 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 ligands co-crystallized with the receptors are also shown as balls and sticks, with their carbon atoms colored in gray.
Mentions: The identification of the non-covalent interactions did not require the addition of hydrogen atoms to the crystal structures, since CSU has been expressly designed to implicitly account their presence. However, for the preparation of Figures 1, 3, 4 and 5, we added hydrogen atoms with the “protein preparation wizard” workflow of the Schrödinger suite, to add hydrogen atoms and calculate the protonation states of ionizable groups at pH 7. The workflow also optimized the orientation of hydroxyl groups, as well as Asn, Gln and His residues (Schrödinger Suite 2012; Sastry et al. 2013).Figure 3

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