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Modelling membrane proteins using structural restraints

Nature Structural Biology volume 2, pages 624–631 (1995)Cite this article

Abstract

Here we present a procedure for modelling membrane proteins which employs molecular dynamics simulations incorporating target restraints derived from low-resolution structures alongside distance restraints derived from mutagenesis data. The application of the modelling procedure to the closed conformation of the pore domain of the nicotinic acetylcholine receptor is described. This domain is formed by a parallel bundle of five M2 helices. Each M2 helix is kinked due to cumulative distortions of backbone (φ,ψ) values. The central region of M2 may adopt a more distorted conformation. This would enable a ring of conserved leucine residues (one from each M2 helix) to pack together, occluding the central pore and thus preventing ion permeation. Molecular dynamics simulations on isolated helices that kink formation is not an inherent property of M2.

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References

  1. Sansom, M.S.P. & Kerr, I.D., Principles of membrane protein structure. Biomembranes, (Ed. A.G. Lee) 29–78 (JAI Press Inc; 1995).

    Google Scholar 

  2. Popot, J.L. & Engelman, D.M. Membrane protein folding and oligomerization: the two-state model. Biochemistry 29, 4034–4037 (1990).

    Article  Google Scholar 

  3. Popot, J.L. Integral membrane protein structure: transmembrane a helices as autonomous folding domains. Curr. Opin. Struc. Biol. 3, 532–540 (1993).

    Article  CAS  Google Scholar 

  4. Hucho, F., Görne-Tschelnokow, U. & Strecker, A. Structure in the membrane-spanning part of the nicotinic acetylcholine receptor (or how helical are transmembrane helices?). Trends Biochem. Sci. 19, 383–387 (1994).

    Article  CAS  Google Scholar 

  5. Stroud, R.M., McCarthy, M.P. & Shuster, M. Nicotinic acetylcholine receptor superfamily of ligand gated ion channels. Biochemistry 50, 1107–11023 (1990).

    Google Scholar 

  6. Changeux, J.P., Galzi, J.I., Devillers-Thiéry, A. & Bertrand, D. The functional architecture of the acetylcholine nicotinic receptor explored by affinity labelling and site-directed mutagenesis. Quart. Rev. Biophys. 25, 395–432 (1992).

    Article  CAS  Google Scholar 

  7. 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 242, 1578–1581 (1988).

    Article  CAS  Google Scholar 

  8. Villarroel, A., Herlitze, S., Koenen, M. & Sakmann, B. Location of a threonine residue in the α-subunit M2 transmembrane segment that determines the ion flow through the acetylcholine receptor channel. Proc. R. Soc. Lond. B 243, 69–74 (1991).

    Article  CAS  Google Scholar 

  9. Unwin, N. Nicotinic acetylcholine receptor at 9 Å resolution. J. molec. Biol. 229, 1101–1124 (1993).

    Article  CAS  Google Scholar 

  10. Unwin, N. Acetylcholine receptor channel imaged in the open state. Nature 373, 37–43 (1995).

    Article  CAS  Google Scholar 

  11. Breed, J., Kerr, I.D., Sankararamakrishnan, R. & Sansom, M.S.P. Packing interactions of Aib-containing helices: molecular modelling of parallel dimers of simple hydrophobic helices and of alamethicin. Biopolymers 35, 639–655 (1995).

    Article  CAS  Google Scholar 

  12. Sansom, M.S.P., Son, H.S., Sankararamakrishnan, R., Kerr, I.D. & Breed, J. Seven-helix bundles: molecular modelling via restrained molecular dynamics. Biophys. J. 68, 1295–1310 (1995).

    Article  CAS  Google Scholar 

  13. Gazit, E. et al. The α5 segment of Bacillus thuringiensis δ-endotoxin: in vitro toxicity, ion channel formation and molecular modelling. Biochemical Journal 304, 895–902 (1994).

    Article  CAS  Google Scholar 

  14. Kerr, I.D., Sankararamakrishnan, R., Smart, O.S. & Sansom, M.S.P. Parallel helix bundles and ion channels: molecular modelling via simulated annealing and restrained molecular dynamics. Biophys. J. 67, 1501–1515 (1994).

    Article  CAS  Google Scholar 

  15. 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. 5, 688–693 (1993).

    Article  CAS  Google Scholar 

  16. Kerr, I.D. & Sansom, M.S.P. Hydrophilic surface maps of α-helical channel-forming peptides. Eur. Biophys. J. 22, 269–277 (1993).

    Article  CAS  Google Scholar 

  17. Sankararamakrishnan, R. & Sansom, M.S.P. Structural features of isolated M2 helices of nicotinic receptors Simulated annealing via molecular dynamics studies. Biophys. Chem. 53, 215–230 (1995).

    Article  Google Scholar 

  18. Akabas, M.H., Kauffmann, C., Archdeacon, P. & Karlin, A. Identification of acetylcholine receptor channel-lining residues in the entire M2 segment of the a subunit. Neuron 13, 919–927 (1994).

    Article  CAS  Google Scholar 

  19. Revah, F. et al. Mutations in the channel domain alter desensitization of a neuronal nicotinic receptor. Nature 353, 846–849 (1991).

    Article  CAS  Google Scholar 

  20. Labarca, C. et al. Leucine residues at the 9 position of the M2 domain in AChR govern EC50 independently and symmetrically. Biophys. J. 68, A233 (1995).

    Google Scholar 

  21. O'Shea, E.K., Klemm, J.D., Kim, P.S. & Alber, T. X-ray structure of the GCN4 leucine zipper, a two stranded parallel coiled coil. Science 254, 539–544 (1991).

    Article  CAS  Google Scholar 

  22. Barlow, D.J. & Thornton, J.M. Helix geometry in proteins. J. molec. Biol. 201, 601–619 (1988).

    Article  CAS  Google Scholar 

  23. Sankararamakrishnan, R. & Sansom, M.S.P. Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study. Biopolymers 34, 1647–1657 (1994).

    Article  CAS  Google Scholar 

  24. Gray, T.M. & Matthews, B.M. Intrahelical hydrogen bonding of serine, threonine and cysteine residues within α-helices and its relevance to membrane-bound proteins. J. molec. Biol. 175, 75–81 (1984).

    Article  CAS  Google Scholar 

  25. Wilmot, C.M. & Thornton, J.M. β-Turns and their distortions: a proposed new nomenclature. Prot. Engng. 3, 479–493 (1990).

    Article  CAS  Google Scholar 

  26. Hille, B. Ionic Channels of Excitable Membranes (2nd. edn.) Sunderland, Mass.: Sinauer Associates Inc., (1992).

    Google Scholar 

  27. Hucho, F., Oberthur, W. & Lottspeich, F. The ion channel of the nicotinic acetylcholine receptor is formed by the homologous helices MII of the receptor subunits. FEBS Lett. 205, 137–142 (1986).

    Article  CAS  Google Scholar 

  28. Guy, H.R. & Hucho, F. The ion chnnel of the nicotinic acetylcholine receptor. Trends Neurosci. 10, 318–321 (1987).

    Article  CAS  Google Scholar 

  29. Furois-Corbin, S. & Pullman, A. A possible model for the inner wall of the acetylcholine receptor channel. Biochim biophis. Acta 984, 339–350 (1989).

    Article  CAS  Google Scholar 

  30. Montal, M.O., Iwamoto, T., Tomich, J.M. & Montal, M. Design, synthesis, and functional characterisation of a pentameric channel protein that mimics the presumed pre structure of the nicotinic cholinergic receptor. FEBS Lett. 320, 261–266 (1993).

    Article  CAS  Google Scholar 

  31. Ortells, M.O. & Lunt, G.G. The transmembrane region of the nicotinic acetylcholine receptor: is it an all-helix bundle? Recept. Chann. 2, 53–59 (1994).

    CAS  Google Scholar 

  32. Sansom, M.S.P. Twist to open. Curr. Biol. 5, 373–375 (1995).

    Article  CAS  Google Scholar 

  33. Unger, V.M. & Schertler, G.F.X. Low resolution structure of bovine rhodopsin determined by electron cryo-microscopy. Biophys. J. 68, 1776–1786 (1995).

    Article  CAS  Google Scholar 

  34. Baldwin, J.M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J. 12, 1693–1703 (1993).

    Article  CAS  Google Scholar 

  35. Brünger, A.T. X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. Ct.: Yale University Press (1992).

    Google Scholar 

  36. Brooks, B.R. et al. CHARMM: A program for macromolecular energy, minimisation, and dynamics calculations. J. Comp. Chem. 4, 187–217 (1983).

    Article  CAS  Google Scholar 

  37. Baker, E.N. & Hubbard, R.E. Hydrogen bonding in globular proteins. Prog. Biophys. molec. Biol. 44, 97–179 (1984).

    Article  CAS  Google Scholar 

  38. Smart, O.S., Goodfellow, J.M. & Wallace, B.A. The pore dimensions of gramicidin. A. Biophys. J. 65, 2455–2460 (1993).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Laboratory of Molecular Biophysics, The Rex Richards Building, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK

    M.S.P. Sansom, R. Sankararamakrishnan & I.D. Kerr

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  1. M.S.P. Sansom
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  2. R. Sankararamakrishnan
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  3. I.D. Kerr
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Sansom, M., Sankararamakrishnan, R. & Kerr, I. Modelling membrane proteins using structural restraints. Nat Struct Mol Biol 2, 624–631 (1995). https://doi.org/10.1038/nsb0895-624

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