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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 between the activated structure (3POG) and the rest of the analyzed structures exceeded the average plus 2.5 times the standard deviation of the values detected across all residues – separate figures for the individual structures are given in Additional file1: Figure S3. 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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Fig10: Three-dimensional representation of the β2AR, showing the residues for which the difference in closeness-centrality between the activated structure (3POG) and the rest of the analyzed structures exceeded the average plus 2.5 times the standard deviation of the values detected across all residues – separate figures for the individual structures are given in Additional file1: Figure S3. 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: Our second level of analysis delved more deeply into the study of the difference in centrality among the seven structures. In particular, for each residue, we studied the difference between the centrality detected for the activated structure (3P0G) and each of the six inactive structures. As the plot shown in Figure 9 reveals, there is one region for which the centrality detected for the active structure is markedly different from that of the corresponding residues in the inactive structure. Mapping on the crystal structures the residues with the most marked differences in centrality – more specifically the residues for which the difference in centrality exceeded cutoff values set to the average plus or minus 2.5 times the standard deviation across all residues (difference in centrality ≥ 0.022 or ≤ −0.026) – reveals that the region in which most of the differences are concentrated is located toward the cytosolic end of TM6 (Figure 10 and Additional file 1: Figure S3). More specifically, residues located in this region show a higher centrality in the inactive structures than in the activated structures. A further region for which differences in centrality were detected is the second intracellular loop, with one residue that features a higher centrality in the inactive than the activated structure (Pro 138) and one that acquires centrality with the activation (Ser 143). Of note, this domain was crystallized in an unstructured conformation in the inactive structures and as a α-helix in the activated structures (see panel c of Figure 2). Moreover the residue located at the extracellular end of TM1 (Trp 321.33), features a marked lower centrality in two of the analyzed structures, namely 3NY9 and 3NYA, than the rest of the analyzed structures – it is worth noting, however, that for the 3NY9 structure the side chain of Trp 321.33 was not solved. The numerical values of the difference in centrality values for the mapped residues are numerically reported in Additional file 1: Table S2.Figure 9


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 between the activated structure (3POG) and the rest of the analyzed structures exceeded the average plus 2.5 times the standard deviation of the values detected across all residues – separate figures for the individual structures are given in Additional file1: Figure S3. 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.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig10: Three-dimensional representation of the β2AR, showing the residues for which the difference in closeness-centrality between the activated structure (3POG) and the rest of the analyzed structures exceeded the average plus 2.5 times the standard deviation of the values detected across all residues – separate figures for the individual structures are given in Additional file1: Figure S3. 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: Our second level of analysis delved more deeply into the study of the difference in centrality among the seven structures. In particular, for each residue, we studied the difference between the centrality detected for the activated structure (3P0G) and each of the six inactive structures. As the plot shown in Figure 9 reveals, there is one region for which the centrality detected for the active structure is markedly different from that of the corresponding residues in the inactive structure. Mapping on the crystal structures the residues with the most marked differences in centrality – more specifically the residues for which the difference in centrality exceeded cutoff values set to the average plus or minus 2.5 times the standard deviation across all residues (difference in centrality ≥ 0.022 or ≤ −0.026) – reveals that the region in which most of the differences are concentrated is located toward the cytosolic end of TM6 (Figure 10 and Additional file 1: Figure S3). More specifically, residues located in this region show a higher centrality in the inactive structures than in the activated structures. A further region for which differences in centrality were detected is the second intracellular loop, with one residue that features a higher centrality in the inactive than the activated structure (Pro 138) and one that acquires centrality with the activation (Ser 143). Of note, this domain was crystallized in an unstructured conformation in the inactive structures and as a α-helix in the activated structures (see panel c of Figure 2). Moreover the residue located at the extracellular end of TM1 (Trp 321.33), features a marked lower centrality in two of the analyzed structures, namely 3NY9 and 3NYA, than the rest of the analyzed structures – it is worth noting, however, that for the 3NY9 structure the side chain of Trp 321.33 was not solved. The numerical values of the difference in centrality values for the mapped residues are numerically reported in Additional file 1: Table S2.Figure 9

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