Simulations of a protein translocation pore: SecY

Biochemistry

Volumn 45, Issue 43, 2006, Pages 13018-13024

  Haider, Shozeb ^a,b   Hall, Benjamin A ^a   Sansom, Mark S P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; EIGENVALUES AND EIGENFUNCTIONS; IONS; MOLECULAR DYNAMICS; PHOSPHOLIPIDS; POLYPEPTIDES; PRINCIPAL COMPONENT ANALYSIS; X RAY DIFFRACTION;

CENTRAL CHANNEL PROTEINS; CHANNEL GATING; ISOLATED SECY PROTEINS; TRANSLOCATION PORES;

PROTEINS;

ION; PHOSPHOLIPID; SECY PROTEIN; WATER;

ARTICLE; CHANNEL GATING; HYDROPHOBICITY; METHANOCOCCUS JANNASCHII; NONHUMAN; PHOSPHOLIPID BILAYER; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN ISOLATION; SIMULATION; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

ARCHAEAL PROTEINS; COMPUTER SIMULATION; DATABASES, PROTEIN; ION CHANNEL GATING; ION CHANNELS; KINETICS; LIPID BILAYERS; METHANOCOCCUS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PRINCIPAL COMPONENT ANALYSIS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 33751074442     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061013d     Document Type: Article

References (60)

1. Clemons, W. M., Ménétret, J.-F., Akey, C. W., and Rapoport, T. A. (2004) Structural insight into the protein translocation channel, Curr. Opin. Struct. Biol. 14, 390-396.
2. Lemieux, M. J., Huang, Y., and Wang, D. N. (2004) The structural basis of substrate translocation by the Escherichia coli glycerol-3-phosphate transporter: A member of the major facilitator superfamily, Curr. Opin. Struct. Biol. 14, 405-412.
3. Abramson, J., Kaback, H. R., and Iwata, S. (2004) Structural comparison of lactose permease and the glycerol-3-phosphate antiporter: Members of the major facilitator superfamily, Curr. Opin. Struct Biol. 14, 413-419.
4. Pebay-Peyroula, E., and Brandolin, G. (2004) Nucleotide exchange in mitochondria: Insight at a molecular level, Curr. Opin. Struct. Biol. 14, 420-425.
5. Locher, K. P. (2004) Structure and mechanism of ABC transporters, Curr. Opin. Struct. Biol. 14, 426-431.
6. Driessen, A. J., Manting, E. H., and van der Does, C. (2001) The structural basis of protein targeting and translocation in bacteria, Nat. Struct. Biol. 8, 492-498.
7. Gorlich, D., Hartmann, E., Prehn, S., and Rapoport, T. A. (1992) A protein of the endoplasmic reticulum involved early in polypeptide translocation, Nature 357, 47-52.
8. Gorlich, D., Prehn, S., Hartmann, E., Kalies, K. U., and Rapoport, T. A. (1992) A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation, Cell 71, 489-503.
9. Hanada, M., Nishiyama, K. I., Mizushima, S., and Tokuda, H. (1994) Reconstitution of an efficient protein translocation machinery comprising SccA and the three membrane proteins, SecY, SecE, and SecG, J. Biol Chem. 269, 23625-23631.
10. Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks, C. L., Ban, N., and Frank, J. (2005) Structure of the E. coli protein-conducting channel bound to a translating ribosome, Nature 438, 318-324.
11. van den Berg, B., Clemons, W. M., Collinson, I., Modis, Y., Hartmann, E., Harrison, S. C., and Rapoport, T. A. (2004) X-ray structure of a protein-conducting channel, Nature 427, 36-44.
12. Karplus, M. J., and McCammon, J. A. (2002) Molecular dynamics simulations of biomolecules, Nat. Struct. Biol. 9, 646-652.
13. Ash, W. L., Zlomislic, M. R., Oloo, E. O., and Tieleman, D. P. (2004) Computer simulations of membrane proteins, Biochim. Biophys. Acta 1666, 158-189.
14. Gumban, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E., and Schulten, K. (2005) Molecular dynamics simulations of proteins in lipid bilayers, Curr. Opin. Struct. Biol. 15, 423-431.
15. Isralewitz, B., Baudry, J., Gullingsrud, J., Kosztin, D., and Schulten, K. (2001) Steered molecular dynamics investigations of protein function, J. Mol. Graphics Modell. 19, 13-25.
16. Gumbart, J., and Schulten, K. (2006) Molecular dynamics studies of the archael translocon, Biophys. J. 90, 2356-2367.
17. Tian, P., and Andricioaei, I. (2006) Size, motion, and function of the SecY translocon revealed by molecular dynamics simulations with virtual probes, Biophys. J. 90, 2718-2730.
18. Grottesi, A., Domene, C., and Sansom, M. S. P. (2005) Conformational dynamics of M2 helices in KirBac channels: Helix flexibility in relation to gating via molecular dynamics simulations, Biochemistry 44, 14586-14594.
19. Amadei, A., Linssen, A. B. M., and Berendsen, H. J. C. (1993) Essential dynamics of proteins, Proteins: Struct., Funct., Genet. 17, 412-425.
20. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., and Hermans, J. (1981) Intermolecular Forces, Reidel, Dordrecht, The Netherlands.
21. Berendsen, H. J. C., van der Spoel, D., and van Drunen, R. (1995) GROMACS: A message-passing parallel molecular dynamics implementation, Comp. Phys. Commun. 95, 43-56.
22. Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis, J. Mol. Model. 7, 306-317.
23. van Gunsteren, W. F., and Berendsen, H. J. C. (1987) Gromos-87 manual, Biomos BV, Groningen, The Netherlands.
24. Berger, O., Edholm, O., and Jahnig, F. (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidycholine at full hydration, constant pressure and constant temperature, Biophys. J. 72, 2002-2013.
25. Marrink, S. J., Berger, O., Tieleman, D. P., and Jahnig, F. (1998) Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations, Biophys. J. 74, 931-943.
26. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81, 3684-3690.
27. Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems, J. Chem. Phys. 98, 10089-10092.
28. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method, J. Chem. Phys. 103, 8577-8593.
29. Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations, J. Comput. Chem. 18, 1463-1472.
30. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual Molecular Dynamics, J. Mol. Graphics 14, 33-38.
31. Tai, K., Shen, T., Henchman, R. H., Bourne, Y., Marchot, P., and McCammon, J. A. (2002) Mechanism of acetylcholinesterase inhibition by fasciculin: A 5-ns molecular dynamics simulation, J. Am. Chem. Soc. 124, 6153-6161.
32. Tai, K., Shen, T., Börjesson, U., Philippopoulos, M., and McCammon, J. A. (2001) Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase, Biophys. J. 81, 715-724.
33. Barrett, C. P., Hall, B. A., and Noble, M. E. M. (2004) Dynamite: A simple way to gain insight into protein motions, Acta Crystallogr. D60, 2280-2287.
34. Kabseh, W., and Sander, C. (1983) Dictionary of protein secondary structure: Pattern-recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577-2637.
35. Bahar. I., Atilgan, A. R., and Erman, B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Folding Des. 2, 173-181.
36. Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O., and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J. 80, 505-515.
37. Eyal, E., Yang, L., and Bahar, I. (2006) Anisotropic Network Model: Systematic evaluation and a new web interface, Bioinformatics (in press).
38. Law, R. J., Capener, C., Baaden, M., Bond, P. J., Campbell, J., Patargias, G., Arinaminpathy, Y., and Sansom, M. S. P. (2005) Membrane protein structure quality in molecular dynamics simulation, J. Mol. Graphics Modell. 24, 157-165.
39. Garcia, A. E. (1992) Large-amplitude nonlinear motions in proteins, Phys. Rev. Lett. 68, 2696-2699.
40. Faraldo-Gómez, J. D., Forrest, L. R., Baaden, M., Bond, P. J., Domene, C., Patargias, G., Cuthbertson, J., and Sansom, M. S. P. (2004) Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations, Proteins: Struct., Fund., Bioinf. 57, 783-791.
41. Tozzini, V. (2005) Coarse-grained models for proteins, Curr. Opin. Struct. Biol. 15, 144-150.
42. Yang, L. W., Liu, X., Jursa, C. J., Holliman, M., Rader, A. J., Karimi, H. A., and Bahar, I. (2005) iGNM: A database of protein functional motions based on Gaussian Network Model, Bioinformatics 21, 2978-2987.
43. Tirion, M. M. (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett. 77, 1905-1908.
44. Beckstein, O., Biggin, P. C., and Sansom, M. S. P. (2001) A Hydrophobic galins mechanism for nanopores, J. Phys. Chem. B. 105, 12902-12905.
45. Beckstein, O., and Sansom, M. S. P. (2003) Liquid-vapor oscillations of water in hydrophobic nanopores, Proc. Natl. Acad. Sci. U.S.A. 100, 7063-7068.
46. Beckstein, O., Tai, K., and Sansom, M. S. P. (2004) Not ions alone: Barriers to ion permeation in nanopores and channels, J. Am. Chem. Soc 126, 14694-14695.
47. Smart, O. S., Goodfellow, J. M., and Wallace, B. A. (1993) The pore dimensions of gramicidin A, Biophys. J. 65, 2455-2460.
48. White, S. H., and von Heijne, G. (2004) The machinery of membrane protein assembly, Curr. Opin. Struct. Biol. 14, 397-404.
49. Shen, Y. F., Kong, Y. F., and Ma, J. P. (2002) Intrinsic flexibility and gating mechanism of the potassium channel KcsA, Proc. Natl. Acad. Sci. U.S.A. 99, 1949-1953.
50. Shrivastava, I. H., and Bahar, I. (2006) Common mechanism of pore opening shared by five different potassium channels, Biophys. J. 90, 3929-3940.
51. Jiang, Y., Lee, A., Chen, J., Cadene, M., Chait, B. T., and MacKinnon, R. (2002) The open pore conformation of potassium channels, Nature 417, 523-526.
52. Biggin, P. C., and Sansom, M. S. P. (2002) Open-state models of a potassium channel, Biophys. J. 83, 1867-1876.
53. Popot, J. L., and Engelman, D. M. (1990) Membrane protein folding and oligomerization: The two-state model, Biochemistry 29, 4031-4037.
54. Engelman, D. M., Chen, Y., Chin, C., Cumin, R., Dixon, A. M., Dupuy, A., Lee, A., Lehnert, U., Mathews, E., Reshetnyak, Y., Senes, A., and Popot, J. L. (2003) Membrane protein folding: Beyond the two stage model, FEBS Lett. 555, 122-125.
55. Hessa, T., Kim, H., Bihlmaier, K., Lundin, C., Boekel, J., Andersson, H., Nilsson, I., White, S. H., and von Heijne, G. (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon, Nature 433, 377-381.
56. Freites, J. A., Tobias, D. J., von Heijne, G., and White, S. H. (2005) Interlace connections of a transmembrane voltage sensor, Proc. Natl. Acad. Sci. U.S.A. 102, 15059-15064.
57. Bowie, J. U. (2005) Solving the membrane protein folding problem, Nature 438, 581-589.
58. Bond, P. J., and Sansom, M. S. P. (2006) Insertion and assembly of membrane proteins via simulation, J. Am. Chem. Soc. 128, 2697-2704.
59. Keskin, O., Jernigan, R. L., and Bahar, I. (2000) Proteins with similar architecture exhibit similar large-scale dynamic behavior, Biophys. J. 78, 2093-2106.
60. Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A., and Sansom, M. S. P. (1996) HOLE: A program for the analysis of the pore dimensions of ion channel structural models, J. Mol. Graphics 14, 354-360.