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Communication over the network of binary switches regulates the activation of A2A adenosine receptor - PubMed

  • ️Thu Jan 01 2015

Communication over the network of binary switches regulates the activation of A2A adenosine receptor

Yoonji Lee et al. PLoS Comput Biol. 2015.

Abstract

Dynamics and functions of G-protein coupled receptors (GPCRs) are accurately regulated by the type of ligands that bind to the orthosteric or allosteric binding sites. To glean the structural and dynamical origin of ligand-dependent modulation of GPCR activity, we performed total ~ 5 μsec molecular dynamics simulations of A2A adenosine receptor (A2AAR) in its apo, antagonist-bound, and agonist-bound forms in an explicit water and membrane environment, and examined the corresponding dynamics and correlation between the 10 key structural motifs that serve as the allosteric hotspots in intramolecular signaling network. We dubbed these 10 structural motifs "binary switches" as they display molecular interactions that switch between two distinct states. By projecting the receptor dynamics on these binary switches that yield 2(10) microstates, we show that (i) the receptors in apo, antagonist-bound, and agonist-bound states explore vastly different conformational space; (ii) among the three receptor states the apo state explores the broadest range of microstates; (iii) in the presence of the agonist, the active conformation is maintained through coherent couplings among the binary switches; and (iv) to be most specific, our analysis shows that W246, located deep inside the binding cleft, can serve as both an agonist sensor and actuator of ensuing intramolecular signaling for the receptor activation. Finally, our analysis of multiple trajectories generated by inserting an agonist to the apo state underscores that the transition of the receptor from inactive to active form requires the disruption of ionic-lock in the DRY motif.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. 1 and 2 at the interface between TM1, TM2, and TM7 for the antagonist-bound, apo, and agonist-bound forms.

(a) H-bonding network of the microswitch residues. (b) Diagram of the H-bond network in the three receptor states.

Figure 2
Figure 2. 3 and 4 defined in the DRY motif and ionic-lock.

(a) Configurations of the DRY motif and ionic-lock in the three receptor states. (b) The distances of R102Cζ-E228Cδ (left, top) and L110Cα-A221Cα (left, bottom) are colored in black, blue, and red for the apo, antagonist-bound, and agonist-bound states, respectively, and their histograms are shown on the right side of the plots. On the right panel, scattered plot using the distances of R102-E228 and L110-A221 is shown with the yellow arrow depicting the conformational transition between three ligand forms. (c) Diagram of the H-bond network in the three receptor states.

Figure 3
Figure 3. 5 to 10 defined from the rotameric switches in TM4, TM5, TM6, and TM7.

Rotameric states of (a) W129, (b) Y197, (c) CWxP motif, and (d) NPxxY motif are compared for the apo (white), antagonist-bound (cyan), and agonist-bound (pink) forms. (e) Helix bending in TM7. The helix bending angle (bendix) of TM7 was calculated using bendix program [45]. The helix is displayed as a cylinder marked with the heatmap ranging from 0o to 20o. The scatter plot on right side depicts the relationship between H-bond of N280-S281 and the bending angle of the TM7 helix (apo: black, antagonist-bound: blue, agonist-bound states: red). The average bending angles are annotated with the symbols, X.

Figure 4
Figure 4. Ten binary switches.

The time traces of the apo, antagonist-bound, and agonist-bound forms are colored by black, blue, and red, respectively, and their histograms are shown on the right side of the panels. From formula image4 to formula image10, the values separating the on and off states are marked in red circles.

Figure 5
Figure 5. Dynamics of A2AAR in 10-binary switch representation.

(a) Simulation trajectories of antagonist (blue), apo (black), agonist (red) form represented in terms of the ON/OFF state of 10 switches. The lines denote the ON states, and the trajectories evolve from the top to bottom. (b) Mean value of each switch with error bar denoting the standard deviation. (c) Time traces of the microstates represented by the decimal numbers from 0 to 1023 in the apo (black), antagonist-bound (blue), and agonist-bound (red) forms. (d) Corresponding population of the microstates. (e) A schematic of similarity between three receptor states in terms of Hamming distance d αβ with the measure of complexity, I (Eq. 2), illustrated with polygons.

Figure 6
Figure 6. Microstates observed during the MD simulation and their occupancies.

For each microstate, the switches in the ON state (s i = 1) are marked with colored boxes.

Figure 7
Figure 7. Cross-correlations among binary switches.

(a) Cross-correlation matrices between the changes in 10 ON/OFF switches for three distinct receptor states calculated by using Fig. 3. The symbols “P” in the matrix elements are for the postive correlatin (C ij > 0.25); “N” is for the negative correlation (C ij < −0.25). (b) Diagram of the cross-correlation between the switches. TM1 to TM7 helices are displayed in gray circles, and the ten switches are specified with the boxes. The positive and negative correlations are depicted using red and blue lines, respectively. (c) Coordination of the antagonist and agonist to formula image7 (W246). W246 and the bound ligands are depicted in the left and right figures. The graph in the middle shows the distances between the center of mass of the W246 (indole 6-ring) and the center of mass of the furan ring (ZM-241385, blue) and ethyl group (UK-432097, red).

Figure 8
Figure 8. Agonist inserted to apo form.

(a) Time traces from the case 1 to case 4. In the cases 1 and 2, the agonist was inserted into the apo form when the ionic-lock was intact; whereas in the cases 3 and 4, the agonist was inserted when the ionic-lock was disrupted. (b) Average values of switch from formula image1 to formula image10 for the case 1 through 4. (c) Population of microstates sampled after the insertion of agonist. (d) Hamming distance and complexity calculated for cases 1–4. (e) The stars are the locations of the cases from 1 to 4, calculated in terms of Hamming distance relative to the apo, antagonist, and agonist forms.

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References

    1. Rosenbaum D, Rasmussen S, Kobilka B (2009) The structure and function of G-protein-coupled receptors. Nature 459: 356–363. 10.1038/nature08144 - DOI - PMC - PubMed
    1. Jaakola V, Griffith M, Hanson M, Cherezov V, Chien E, et al. (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322: 1211–1217. 10.1126/science.1164772 - DOI - PMC - PubMed
    1. Rasmussen S, DeVree B, Zou Y, Kruse A, Chung K, et al. (2011) Crystal structure of the β2 adrenergic receptor-gs protein complex. Nature 477: 549–555. 10.1038/nature10361 - DOI - PMC - PubMed
    1. Lebon G, Warne T, Edwards P, Bennett K, Langmead C, et al. (2011) Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation. Nature 474: 521–525. 10.1038/nature10136 - DOI - PMC - PubMed
    1. Nygaard R, Frimurer T, Holst B, Rosenkilde M, Schwartz T (2009) Ligand binding and micro-switches in 7TM receptor structures. Trends Pharmacol Sci 30: 249–259. 10.1016/j.tips.2009.02.006 - DOI - PubMed

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Grants and funding

This work was partly supported by the grant from the Basic Science Research Program (Grant number 2013R1A6A3A01066055) (to YL) and the National Leading Research Lab (NLRL) program (2011-0028885) (to SC) funded by the Ministry of Science, ICT \& Future Planning (MSIP) and the National Research Foundation of Korea (NRF). CH thanks the KITP at the University of California, Santa Barbara, for support during the preparation of the manuscript (NSF PHY11-25915). We thank KIAS and KISTI Supercomputing Center for providing computing resources.

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