Advertisement

Journal of Biological Physics

, Volume 44, Issue 3, pp 331–344 | Cite as

Exploring conformational states and helical packings in the P2X receptor transmembrane domain by molecular dynamics simulation

  • Guo-Hua Li
Original Paper

Abstract

The P2X receptor is a trimeric transmembrane protein that acts as an ATP-gated ion channel. Its transmembrane domain (TMD) contains only six helices and three of them, the M2 helices, line the ion conduction pathway. Here, using molecular dynamics simulation, I identify four conformational states of the TMD that are associated with four types of packing between M2 helices. Packing in the extracellular half of the M2 helix produces closed conformations, while packing in the intracellular half produces both open and closed conformations. State transition is observed and supports a mechanism where iris-like twisting of the M2 helices switches the location of helical packing between the extracellular and the intracellular halves of the helices. In addition, this twisting motion alters the position and orientation of residue side-chains relative to the pore and therefore influences the pore geometry and possibly ion permeation. Helical packing, on the other hand, may restrict the twisting motion and generate discrete conformational states.

Keywords

Helical packing P2X Ion channel Molecular dynamics Transmembrane helix 

Notes

Acknowledgments

This work was supported by a grant to G.H.L. from the National Natural Science Foundation of China (Grant No. 30972861).

Compliance with ethical standards

Conflict of interest

The author declares no conflict of interest.

Supplementary material

10867_2018_9493_MOESM1_ESM.pse (994 kb)
Supplementary File 1 An example of axial projection of the Cα atoms from a simulation of the TMD-4DW0 model in a POPC bilayer. The file is viewed using PyMol. (PSE 994 kb)
10867_2018_9493_MOESM2_ESM.pse (432 kb)
Supplementary Movie 1 Twisting of M2 helices changes the organization of the M2 bundle. The pore is initially closed in the outer portion of the structure. Twisting of M2 helices increases the outer portion, creating a continuous open pore. In addition, the relative positions of residues are changed, which is important for packing and channel gating. This movie is generated by changing the azimuth angles while the other parameters remain constant. (PSE 431 kb)
10867_2018_9493_MOESM3_ESM.pse (419 kb)
Supplementary Movie 2 Rotation of M2 helices changes the positions and orientations of the residue side-chains. This movie is generated by changing the rotation angles while the other parameters remain constant. (PSE 418 kb)
10867_2018_9493_MOESM4_ESM.png (135 kb)
Supplementary Fig. S1 An example showing the measurements of the stability of MD simulation. The top panel is a plot of RMSD of Cα atoms relative to the start conformation. The bottom panel is a plot of the PH values during the simulation. At about 30 ns, both the RMSD and PH curves reach plateaus. (PNG 134 kb)
10867_2018_9493_MOESM5_ESM.png (90 kb)
Supplementary Fig. S2 A schematic diagram showing the collective changes in residue packing due to axial rotation of the M2 helices. In type 1 packing, L339 side-chain splays outwards and interacts weakly with the downstream M2 helix. In type 2 packing, M2 helices rotate in a clockwise direction (seen from the extracellular end of the M2 helices), this brings L339 closer to the target helices, and shifts the binding sites of A344 and A347 and L348 collectively. The Supplementary Movie 2 also shows how the rotation affect the packing pattern between M2 helices. (PNG 90 kb)
10867_2018_9493_MOESM6_ESM.png (218 kb)
Supplementary Fig. S3 The position of the residue L351 in the C1 state (A), the C2 state (B), the O1 state (C) and the D1 state (D). This example is from a simulation of the TMD-4DW1 model in a POPC bilayer. (PNG 217 kb)

References

  1. 1.
    Chothia, C., Levitt, M., Richardson, D.: Helix to helix packing in proteins. J. Mol. Biol. 145, 215–250 (1981)CrossRefGoogle Scholar
  2. 2.
    Bowie, J.U.: Helix packing in membrane proteins. J. Mol. Biol. 272, 780–789 (1997)CrossRefGoogle Scholar
  3. 3.
    Gimpelev, M., Forrest, L.R., Murray, D., Honig, B.: Helical packing patterns in membrane and soluble proteins. Biophys. J. 87, 4075–4086 (2004)CrossRefGoogle Scholar
  4. 4.
    Walters, R.F., DeGrado, W.F.: Helix-packing motifs in membrane proteins. Proc. Natl. Acad. Sci. U.S.A. 103, 13658–13663 (2006)ADSCrossRefGoogle Scholar
  5. 5.
    Dai, J., Zhou, H.X.: General rules for the arrangements and gating motions of pore-lining helices in homomeric ion channels. Nat. Commun. 5, 4641 (2014)Google Scholar
  6. 6.
    Kawate, T., Michel, J.C., Birdsong, W.T., Gouaux, E.: Crystal structure of the ATP-gated P2X4 ion channel in the closed state. Nature 460, 592–598 (2009)ADSCrossRefGoogle Scholar
  7. 7.
    Hattori, M., Gouaux, E.: Molecular mechanism of ATP binding and ion channel activation in P2X receptors. Nature 485, 207–212 (2012)ADSCrossRefGoogle Scholar
  8. 8.
    Kasuya, G., Fujiwara, Y., Tsukamoto, H., Morinaga, S., Ryu, S., Touhara, K., Ishitani, R., Furutani, Y., Hattori, M., Nureki, O.: Structural insights into the nucleotide base specificity of P2X receptors. Sci. Rep. 7, 45208 (2017)ADSCrossRefGoogle Scholar
  9. 9.
    Karasawa, A., Kawate, T.: Structural basis for subtype-specific inhibition of the P2X7 receptor. eLife 5, e22153 (2016)CrossRefGoogle Scholar
  10. 10.
    Mansoor, S.E., Lü, W., Oosterheert, W., Shekhar, M., Tajkhorshid, E., Gouaux, E.: X-ray structures define human P2X3 receptor gating cycle and antagonist action. Nature 538, 66–71 (2016)ADSCrossRefGoogle Scholar
  11. 11.
    Kasuya, G., Fujiwara, Y., Takemoto, M., Dohmae, N., Nakada-Nakura, Y., Ishitani, R., Hattori, M., Nureki, O.: Structural insights into divalent cation modulations of ATP-gated P2X receptor channels. Cell Rep. 14, 932–944 (2016)CrossRefGoogle Scholar
  12. 12.
    Li, G.H.: Geometric rules of channel gating inferred from computational models of the P2X receptor transmembrane domain. J. Mol. Graph. Model. 61, 107–114 (2015)CrossRefGoogle Scholar
  13. 13.
    Crick, F.H.C.: The packing of α-helices: simple coiled-coils. Acta Cryst. 6, 686–697 (1953)Google Scholar
  14. 14.
    Best, R.B., Zhu, X., Shim, J., Lopes, P.E.M., Mittal, J., Feig, M., MacKerell Jr., A.D.: Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi1 and chi2 dihedral angles. J. Chem. Theor. Comput. 8, 3257–3273 (2012)CrossRefGoogle Scholar
  15. 15.
    Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., Lindahl, E.: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015)ADSCrossRefGoogle Scholar
  16. 16.
    Hess, B., Bekker, H., Berendsen, H.J.C., Fraaije, J.G.E.M.: LINCS: A Linear Constraint Solver for Molecular Simulations. J. Comp. Chem. 18, 1463–1472 (1997)CrossRefGoogle Scholar
  17. 17.
    Darden, T., York, D., Pedersen, L.: Particle mesh Ewald: a N-log(n) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993)ADSCrossRefGoogle Scholar
  18. 18.
    Ho, B.K., Gruswitz, F.: HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures. BMC Struct. Biol. 8, 49 (2008)CrossRefGoogle Scholar
  19. 19.
    Heymann, G., Dai, J., Li, M., Silberberg, S.D., Zhou, H.X., Swartz, K.J.: Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels. Proc. Natl. Acad. Sci. U.S.A. 110, E4045–E4054 (2013)CrossRefGoogle Scholar
  20. 20.
    Pierdominici-Sottile, G., Moffatt, L., Palma, J.: The dynamic behavior of the P2X4 ion channel in the closed conformation. Biophys. J. 111, 2642–2650 (2016)ADSCrossRefGoogle Scholar
  21. 21.
    Kracun, S., Chaptal, V., Abramson, J., Khakh, B.S.: Gated access to the pore of a P2X receptor: structural implications for closed-open transitions. J. Biol. Chem. 285, 10110–10121 (2010)CrossRefGoogle Scholar
  22. 22.
    Li, M., Kawate, T., Silberberg, S.D., Swartz, K.J.: Pore-opening mechanism in trimeric P2X receptor channels. Nat. Commun. 1, 44 (2010)ADSGoogle Scholar
  23. 23.
    Browne, L.E., Nunes, J.P., Sim, J.A., Chudasama, V., Bragg, L., Caddick, S., North, R.A.: Optical control of trimeric P2X receptors and acid-sensing ion channels. Proc. Natl. Acad. Sci. U.S.A. 111, 521–526 (2014)ADSCrossRefGoogle Scholar
  24. 24.
    Habermacher, C., Martz, A., Calimet, N., Lemoine, D., Peverini, L., Specht, A., Cecchini, M., Grutter, T.: Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel. eLife 5, e11050 (2016)CrossRefGoogle Scholar
  25. 25.
    Du, J., Dong, H., Zhou, H.X.: Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations. Proc. Natl. Acad. Sci. U.S.A. 109, 4140–4145 (2012)ADSCrossRefGoogle Scholar
  26. 26.
    Chen, Z., Xu, Y.: Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential. Proteins 62, 539–552 (2006)CrossRefGoogle Scholar
  27. 27.
    Huang, Y.H., Chen, C.: M.: Statistical analyses and computational prediction of helical kinks in membrane proteins. J. Comput. Aided Mol. Des. 26, 1171–1185 (2012)ADSCrossRefGoogle Scholar
  28. 28.
    Mai, T.L., Chen, C.M.: Computational prediction of kink properties of helices in membrane proteins. J. Comput. Aided Mol. Des. 28, 99–109 (2014)ADSCrossRefGoogle Scholar
  29. 29.
    Chen, C.C., Wei, C.C., Sun, Y.C., Chen, C.M.: Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. J. Struct. Biol. 162, 237–247 (2008)CrossRefGoogle Scholar
  30. 30.
    Wu, H.H., Chen, C.C., Chen, C.M.: Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. J. Comput. Aided Mol. Des. 26, 363–374 (2012)ADSCrossRefGoogle Scholar
  31. 31.
    Popot, J.-L., Engelman, D.M.: Membrane protein folding and oligomerization: the two-stage model. Biochemistry 29, 4031–4037 (1990)CrossRefGoogle Scholar
  32. 32.
    Unwin, N., Fujiyoshi, Y.: Gating Movement of Acetylcholine Receptor Caught by Plunge-Freezing. J. Mol. Biol. 422, 617–634 (2012)CrossRefGoogle Scholar
  33. 33.
    Changeux, J.-P., Edelstein, S.: Conformational selection or induced fit? 50 years of debate resolved. F1000. Biol. Rep. 3, 19 (2011)CrossRefGoogle Scholar
  34. 34.
    Vogt, A.D., Cera, E.D.: Conformational Selection Is a Dominant Mechanism of Ligand Binding. Biochemistry 52, 5723–5729 (2013)CrossRefGoogle Scholar
  35. 35.
    Miyazawa, A., Fujiyoshi, Y., Unwin, N.: Structure and gating mechanism of the acetylcholine receptor pore. Nature 423, 949–955 (2003)ADSCrossRefGoogle Scholar
  36. 36.
    Morales-Perez, C.L., Noviello, C.M., Hibbs, R.E.: X-ray structure of the human α4β2 nicotinic receptor. Nature 538, 411–415 (2016)ADSCrossRefGoogle Scholar
  37. 37.
    Mowrey, D.D., Cui, T., Jia, Y., Ma, D., Makhov, A.M., Zhang, P., Tang, P., Xu, Y.: Open-channel structures of the human glycine receptor α1 full-length transmembrane domain. Structure 21, 1897–1904 (2013)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Laboratory of Anesthesiology and Critical Care Medicine, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina

Personalised recommendations