Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 1997 Sep;73(3):1364–1381. doi: 10.1016/S0006-3495(97)78169-4

Molecular dynamics study of water and Na+ ions in models of the pore region of the nicotinic acetylcholine receptor.

G R Smith 1, M S Sansom 1
PMCID: PMC1181036  PMID: 9284304

Abstract

The nicotinic acetylcholine receptor (nAChR) is an integral membrane protein that forms ligand-gated and cation-selective channels. The central pore is lined by a bundle of five approximately parallel M2 helices, one from each subunit. Candidate model structures of the solvated pore region of a homopentameric (alpha7)5 nAChR channel in the open state, and in two possible forms of the closed state, have been studied using molecular dynamics simulations with restraining potentials. It is found that the mobility of the water is substantially lower within the pore than in bulk, and the water molecules become aligned with the M2 helix dipoles. Hydrogen-bonding patterns in the pore, especially around pore-lining charged and hydrophilic residues, and around exposed regions of the helix backbone, have been determined. Initial studies of systems containing both water and sodium ions together within the pore region have also been conducted. A sodium ion has been introduced into the solvated models at various points along the pore axis and its energy profile evaluated. It is found that the ion causes only a local perturbation of the water structure. The results of these calculations have been used to examine the effectiveness of the central ring of leucines as a component of a gate in the closed-channel model.

Full text

PDF
1364

Images in this article

1366FIGURE 1
on p.1366

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akabas M. H., Kaufmann C., Archdeacon P., Karlin A. Identification of acetylcholine receptor channel-lining residues in the entire M2 segment of the alpha subunit. Neuron. 1994 Oct;13(4):919–927. doi: 10.1016/0896-6273(94)90257-7. [DOI] [PubMed] [Google Scholar]
  2. Akabas M. H., Stauffer D. A., Xu M., Karlin A. Acetylcholine receptor channel structure probed in cysteine-substitution mutants. Science. 1992 Oct 9;258(5080):307–310. doi: 10.1126/science.1384130. [DOI] [PubMed] [Google Scholar]
  3. Bertrand D., Galzi J. L., Devillers-Thiéry A., Bertrand S., Changeux J. P. Mutations at two distinct sites within the channel domain M2 alter calcium permeability of neuronal alpha 7 nicotinic receptor. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):6971–6975. doi: 10.1073/pnas.90.15.6971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bertrand D., Galzi J. L., Devillers-Thiéry A., Bertrand S., Changeux J. P. Stratification of the channel domain in neurotransmitter receptors. Curr Opin Cell Biol. 1993 Aug;5(4):688–693. doi: 10.1016/0955-0674(93)90141-c. [DOI] [PubMed] [Google Scholar]
  5. Breed J., Sankararamakrishnan R., Kerr I. D., Sansom M. S. Molecular dynamics simulations of water within models of ion channels. Biophys J. 1996 Apr;70(4):1643–1661. doi: 10.1016/S0006-3495(96)79727-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Changeux J. P., Galzi J. L., Devillers-Thiéry A., Bertrand D. The functional architecture of the acetylcholine nicotinic receptor explored by affinity labelling and site-directed mutagenesis. Q Rev Biophys. 1992 Nov;25(4):395–432. doi: 10.1017/s0033583500004352. [DOI] [PubMed] [Google Scholar]
  7. Charnet P., Labarca C., Leonard R. J., Vogelaar N. J., Czyzyk L., Gouin A., Davidson N., Lester H. A. An open-channel blocker interacts with adjacent turns of alpha-helices in the nicotinic acetylcholine receptor. Neuron. 1990 Jan;4(1):87–95. doi: 10.1016/0896-6273(90)90445-l. [DOI] [PubMed] [Google Scholar]
  8. Cohen B. N., Labarca C., Czyzyk L., Davidson N., Lester H. A. Tris+/Na+ permeability ratios of nicotinic acetylcholine receptors are reduced by mutations near the intracellular end of the M2 region. J Gen Physiol. 1992 Apr;99(4):545–572. doi: 10.1085/jgp.99.4.545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dwyer T. M., Adams D. J., Hille B. The permeability of the endplate channel to organic cations in frog muscle. J Gen Physiol. 1980 May;75(5):469–492. doi: 10.1085/jgp.75.5.469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Galzi J. L., Devillers-Thiéry A., Hussy N., Bertrand S., Changeux J. P., Bertrand D. Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic. Nature. 1992 Oct 8;359(6395):500–505. doi: 10.1038/359500a0. [DOI] [PubMed] [Google Scholar]
  11. Giraudat J., Dennis M., Heidmann T., Haumont P. Y., Lederer F., Changeux J. P. Structure of the high-affinity binding site for noncompetitive blockers of the acetylcholine receptor: [3H]chlorpromazine labels homologous residues in the beta and delta chains. Biochemistry. 1987 May 5;26(9):2410–2418. doi: 10.1021/bi00383a003. [DOI] [PubMed] [Google Scholar]
  12. Hucho F., Görne-Tschelnokow U., Strecker A. Beta-structure in the membrane-spanning part of the nicotinic acetylcholine receptor (or how helical are transmembrane helices?). Trends Biochem Sci. 1994 Sep;19(9):383–387. doi: 10.1016/0968-0004(94)90116-3. [DOI] [PubMed] [Google Scholar]
  13. Hucho F., Hilgenfeld R. The selectivity filter of a ligand-gated ion channel. The helix-M2 model of the ion channel of the nicotinic acetylcholine receptor. FEBS Lett. 1989 Oct 23;257(1):17–23. doi: 10.1016/0014-5793(89)81775-2. [DOI] [PubMed] [Google Scholar]
  14. Hucho F., Oberthür W., Lottspeich F. The ion channel of the nicotinic acetylcholine receptor is formed by the homologous helices M II of the receptor subunits. FEBS Lett. 1986 Sep 1;205(1):137–142. doi: 10.1016/0014-5793(86)80881-x. [DOI] [PubMed] [Google Scholar]
  15. Hucho F., Tsetlin V. I., Machold J. The emerging three-dimensional structure of a receptor. The nicotinic acetylcholine receptor. Eur J Biochem. 1996 Aug 1;239(3):539–557. doi: 10.1111/j.1432-1033.1996.0539u.x. [DOI] [PubMed] [Google Scholar]
  16. Hummer G., Garde S., García A. E., Pohorille A., Pratt L. R. An information theory model of hydrophobic interactions. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8951–8955. doi: 10.1073/pnas.93.17.8951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Imoto K., Busch C., Sakmann B., Mishina M., Konno T., Nakai J., Bujo H., Mori Y., Fukuda K., Numa S. Rings of negatively charged amino acids determine the acetylcholine receptor channel conductance. Nature. 1988 Oct 13;335(6191):645–648. doi: 10.1038/335645a0. [DOI] [PubMed] [Google Scholar]
  18. Karlin A., Akabas M. H. Toward a structural basis for the function of nicotinic acetylcholine receptors and their cousins. Neuron. 1995 Dec;15(6):1231–1244. doi: 10.1016/0896-6273(95)90004-7. [DOI] [PubMed] [Google Scholar]
  19. Kearney P. C., Zhang H., Zhong W., Dougherty D. A., Lester H. A. Determinants of nicotinic receptor gating in natural and unnatural side chain structures at the M2 9' position. Neuron. 1996 Dec;17(6):1221–1229. doi: 10.1016/s0896-6273(00)80252-4. [DOI] [PubMed] [Google Scholar]
  20. Kerr I. D., Sankararamakrishnan R., Smart O. S., Sansom M. S. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophys J. 1994 Oct;67(4):1501–1515. doi: 10.1016/S0006-3495(94)80624-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kuyucak S., Chung S. H. Temperature dependence of conductivity in electrolyte solutions and ionic channels of biological membranes. Biophys Chem. 1994 Sep;52(1):15–24. doi: 10.1016/0301-4622(94)00034-4. [DOI] [PubMed] [Google Scholar]
  22. Labarca C., Nowak M. W., Zhang H., Tang L., Deshpande P., Lester H. A. Channel gating governed symmetrically by conserved leucine residues in the M2 domain of nicotinic receptors. Nature. 1995 Aug 10;376(6540):514–516. doi: 10.1038/376514a0. [DOI] [PubMed] [Google Scholar]
  23. Leonard R. J., Labarca C. G., Charnet P., Davidson N., Lester H. A. Evidence that the M2 membrane-spanning region lines the ion channel pore of the nicotinic receptor. Science. 1988 Dec 16;242(4885):1578–1581. doi: 10.1126/science.2462281. [DOI] [PubMed] [Google Scholar]
  24. Lester H. A. The permeation pathway of neurotransmitter-gated ion channels. Annu Rev Biophys Biomol Struct. 1992;21:267–292. doi: 10.1146/annurev.bb.21.060192.001411. [DOI] [PubMed] [Google Scholar]
  25. Levitt D. G. General continuum theory for multiion channel. I. Theory. Biophys J. 1991 Feb;59(2):271–277. doi: 10.1016/S0006-3495(91)82220-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Montal M. Design of molecular function: channels of communication. Annu Rev Biophys Biomol Struct. 1995;24:31–57. doi: 10.1146/annurev.bb.24.060195.000335. [DOI] [PubMed] [Google Scholar]
  27. Nutter T. J., Adams D. J. Monovalent and divalent cation permeability and block of neuronal nicotinic receptor channels in rat parasympathetic ganglia. J Gen Physiol. 1995 Jun;105(6):701–723. doi: 10.1085/jgp.105.6.701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Oiki S., Danho W., Madison V., Montal M. M2 delta, a candidate for the structure lining the ionic channel of the nicotinic cholinergic receptor. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8703–8707. doi: 10.1073/pnas.85.22.8703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ortells M. O., Lunt G. G. A mixed helix-beta-sheet model of the transmembrane region of the nicotinic acetylcholine receptor. Protein Eng. 1996 Jan;9(1):51–59. doi: 10.1093/protein/9.1.51. [DOI] [PubMed] [Google Scholar]
  30. Revah F., Bertrand D., Galzi J. L., Devillers-Thiéry A., Mulle C., Hussy N., Bertrand S., Ballivet M., Changeux J. P. Mutations in the channel domain alter desensitization of a neuronal nicotinic receptor. Nature. 1991 Oct 31;353(6347):846–849. doi: 10.1038/353846a0. [DOI] [PubMed] [Google Scholar]
  31. Role L. W., Berg D. K. Nicotinic receptors in the development and modulation of CNS synapses. Neuron. 1996 Jun;16(6):1077–1085. doi: 10.1016/s0896-6273(00)80134-8. [DOI] [PubMed] [Google Scholar]
  32. Roux B., Karplus M. Molecular dynamics simulations of the gramicidin channel. Annu Rev Biophys Biomol Struct. 1994;23:731–761. doi: 10.1146/annurev.bb.23.060194.003503. [DOI] [PubMed] [Google Scholar]
  33. Roux B., Prod'hom B., Karplus M. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys J. 1995 Mar;68(3):876–892. doi: 10.1016/S0006-3495(95)80264-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sankararamakrishnan R., Adcock C., Sansom M. S. The pore domain of the nicotinic acetylcholine receptor: molecular modeling, pore dimensions, and electrostatics. Biophys J. 1996 Oct;71(4):1659–1671. doi: 10.1016/S0006-3495(96)79370-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sankararamakrishnan R., Samsom M. S. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study. Biopolymers. 1994 Dec;34(12):1647–1657. doi: 10.1002/bip.360341209. [DOI] [PubMed] [Google Scholar]
  36. Sankararamakrishnan R., Sansom M. S. Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices. Biochim Biophys Acta. 1995 Nov 1;1239(2):122–132. doi: 10.1016/0005-2736(95)00165-y. [DOI] [PubMed] [Google Scholar]
  37. Sankararamakrishnan R., Sansom M. S. Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies. Biophys Chem. 1995 Aug;55(3):215–230. doi: 10.1016/0301-4622(95)00006-j. [DOI] [PubMed] [Google Scholar]
  38. Sankararamakrishnan R., Sansom M. S. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study. FEBS Lett. 1995 Dec 27;377(3):377–382. doi: 10.1016/0014-5793(95)01376-8. [DOI] [PubMed] [Google Scholar]
  39. Sansom M. S., Kerr I. D., Breed J., Sankararamakrishnan R. Water in channel-like cavities: structure and dynamics. Biophys J. 1996 Feb;70(2):693–702. doi: 10.1016/S0006-3495(96)79609-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sansom M. S., Sankararamakrishnan R., Kerr I. D. Modelling membrane proteins using structural restraints. Nat Struct Biol. 1995 Aug;2(8):624–631. doi: 10.1038/nsb0895-624. [DOI] [PubMed] [Google Scholar]
  41. Singh C., Sankararamakrishnan R., Subramaniam S., Jakobsson E. Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel. Biophys J. 1996 Nov;71(5):2276–2288. doi: 10.1016/S0006-3495(96)79438-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Smart O. S., Breed J., Smith G. R., Sansom M. S. A novel method for structure-based prediction of ion channel conductance properties. Biophys J. 1997 Mar;72(3):1109–1126. doi: 10.1016/S0006-3495(97)78760-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Smart O. S., Goodfellow J. M., Wallace B. A. The pore dimensions of gramicidin A. Biophys J. 1993 Dec;65(6):2455–2460. doi: 10.1016/S0006-3495(93)81293-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Stroud R. M., McCarthy M. P., Shuster M. Nicotinic acetylcholine receptor superfamily of ligand-gated ion channels. Biochemistry. 1990 Dec 18;29(50):11009–11023. doi: 10.1021/bi00502a001. [DOI] [PubMed] [Google Scholar]
  45. Tierney M. L., Birnir B., Pillai N. P., Clements J. D., Howitt S. M., Cox G. B., Gage P. W. Effects of mutating leucine to threonine in the M2 segment of alpha1 and beta1 subunits of GABAA alpha1beta1 receptors. J Membr Biol. 1996 Nov;154(1):11–21. doi: 10.1007/s002329900128. [DOI] [PubMed] [Google Scholar]
  46. Unwin N. Acetylcholine receptor channel imaged in the open state. Nature. 1995 Jan 5;373(6509):37–43. doi: 10.1038/373037a0. [DOI] [PubMed] [Google Scholar]
  47. Unwin N. Nicotinic acetylcholine receptor at 9 A resolution. J Mol Biol. 1993 Feb 20;229(4):1101–1124. doi: 10.1006/jmbi.1993.1107. [DOI] [PubMed] [Google Scholar]
  48. Unwin N. Projection structure of the nicotinic acetylcholine receptor: distinct conformations of the alpha subunits. J Mol Biol. 1996 Apr 5;257(3):586–596. doi: 10.1006/jmbi.1996.0187. [DOI] [PubMed] [Google Scholar]
  49. Villarroel A., Herlitze S., Koenen M., Sakmann B. Location of a threonine residue in the alpha-subunit M2 transmembrane segment that determines the ion flow through the acetylcholine receptor channel. Proc Biol Sci. 1991 Jan 22;243(1306):69–74. doi: 10.1098/rspb.1991.0012. [DOI] [PubMed] [Google Scholar]
  50. Wang F., Imoto K. Pore size and negative charge as structural determinants of permeability in the Torpedo nicotinic acetylcholine receptor channel. Proc Biol Sci. 1992 Oct 22;250(1327):11–17. doi: 10.1098/rspb.1992.0124. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES