Probing the environment of signal-anchor sequences during topogenesis in the endoplasmic reticulum

Biochemistry

Volumn 44, Issue 6, 2005, Pages 2039-2047

  Higy, Marie ^a   Gander, Stefan ^a   Spiess, Martin ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CARBON; HYDROPHOBICITY; MATHEMATICAL MODELS; MEMBRANES; NITROGEN; TOPOLOGY;

FLANKING CHARGES; HYDROPHOBIC RESIDUES; LIPID BILAYER; TOPOGENESIS;

PROTEINS;

ALANINE; AROMATIC AMINO ACID; COMPLEMENTARY DNA; PHENYLALANINE; PROTEINASE; TYROSINE; VALINE;

ANIMAL CELL; ARTICLE; CELL STRAIN COS7; ENDOPLASMIC RETICULUM; ENZYME ASSAY; GLYCOSYLATION; HYDROPHOBICITY; LIPID BILAYER; MEMBRANE TRANSPORT; NONHUMAN; PRIORITY JOURNAL;

ALANINE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; CERCOPITHECUS AETHIOPS; COS CELLS; ENDOPLASMIC RETICULUM; GENETIC VECTORS; HYDROPHOBICITY; INTRACELLULAR MEMBRANES; LEUCINE; LIPID BILAYERS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PHENYLALANINE; PROTEIN SORTING SIGNALS; PROTEIN TRANSPORT; TRANSFECTION; TRYPTOPHAN; VALINE;

MAMMALIA;

EID: 13544259578     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047976z     Document Type: Article

References (39)

1. Walter, P., and Johnson, A. E. (1994) Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane, Annu. Rev. Cell Biol. 10, 87-119.
2. Rapoport, T. A., Jungnickel, B., and Kutay, U. (1996) Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes, Annu. Rev. Biochem. 65, 271-303.
3. Johnson, A. E., and van Waes, M. A. (1999) The translocon: a dynamic gateway at the ER membrane, Annu. Rev. Cell Dev. Biol. 15, 799-842.
4. Keenan, R. J., Freymann, D. M., Stroud, R. M., and Walter, P. (2001) The signal recognition particle, Annu. Rev. Biochem. 70, 755-775.
5. Goder, V., and Spiess, M. (2001) Topogenesis of membrane proteins: determinants and dynamics, FEBS Lett. 504, 87-93.
6. von Heijne, G. (1986) The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology, EMBO J. 5, 3021-3027.
7. Hartmann, E., Rapoport, T. A., and Lodish, H. F. (1989) Predicting the orientation of eukaryotic membrane-spanning proteins, Proc. Natl. Acad. Sci. U.S.A. 86, 5786-5790.
8. Beltzer, J. P., Fiedler, K., Fuhrer, C., Geffen, I., Handschin, C., Wessels, H. P., and Spiess, M. (1991) Charged residues are major determinants of the transmembrane orientation of a signal-anchor sequence, J. Biol. Chem. 266, 973-978.
9. Parks, G. D., and Lamb, R. A. (1991) Topology of eukaryotic type-II membrane proteins: Importance of N-terminal positively charged residues flanking the hydrophobic domain, Cell 64, 777-787.
10. Goder, V., Junne, T., and Spiess, M. (2004) Sec61p contributes to signal sequence orientation according to the positive-inside rule, Mol. Biol. Cell 15, 1470-1478.
11. Denzer, A. J., Nabholz, C. E., and Spiess, M. (1995) Transmembrane orientation of signal-anchor proteins is affected by the folding state but not the size of the aminoterminal domain, EMBO J. 74, 6311-6317.
12. Sakaguchi, M., Tomiyoshi, R., Kuroiwa, T., Mihara, K., and Omura, T. (1992) Functions of signal and signal-anchor sequences are determined by the balance between the hydrophobic segment and the N-terminal charge, Proc. Natl. Acad. Sci. U.S.A. 89, 16-19.
13. Wahlberg, J. M., and Spiess, M. (1997) Multiple determinants direct the orientation of signal-anchor proteins: The topogenic role of the hydrophobic signal domain., J. Cell Biol. 137, 555-562.
14. Rösch, K., Naeher, D., Laird, V., Goder, V., and Spiess, M. (2000) The topogenic contribution of uncharged amino acids on signal sequence orientation in the endoplasmic reticulum, J. Biol. Chem. 275, 14916-14922,
15. Goder, V., and Spiess, M. (2003) Molecular mechanism of signal sequence orientation in the endoplasmic reticulum, EMBO J. 22, 3645-3653.
16. Ellis, L., Clauser, E., Morgan, D. O., Edery, M., Roth, R. A., and Rutter, W. J. (1986) Replacement of insulin receptor tyrosine residues 1162 and 1163 compromises insulin-stimulated kinase activity and uptake of 2- deoxyglucose, Cell 45, 721-732.
17. Wessels, H. P., Beltzer, J. P., and Spiess, M. (1991) Analysis of protein topology in the endoplasmic reticulum, Methods Cell Biol. 34, 287-302.
18. Schmid, S. R., and Spiess, M. (1988) Deletion of the amino-terminal domain of asialoglycoprotein receptor H1 allows cleavage of the internal signal sequence, J. Biol. Chem. 263, 16886-16891.
19. Nilsson, I. M., and von Heijne, G. (1993) Determination of the distance between the oligosaccharyltransferase active site and the endoplasmic reticulum membrane, J. Biol. Chem. 268, 5798-5801.
20. Hershey, J. W. B. (1991) Translational control in mammalian cells, Annu. Rev. Biochem. 60, 717-755.
21. Zopf, D., Bernstein, H. D., Johnson, A. E., and Walter, P. (1990) The methionine-rich domain of the 54 kDa protein subunit of the signal recognition particle contains an RNA binding site and can be cross-linked to a signal sequence, EMBO J. 9, 4511-4517.
22. Lutcke, H., High, S., Romisch, K., Ashford, A. J., and Dobberstein, B. (1992) The methionine-rich domain of the 54 kDa subunit of signal recognition particle is sufficient for the interaction with signal sequences, EMBO J. 11, 1543-1551.
23. Keenan, R. J., Freymann, D. M., Walter, P., and Stroud, R. M. (1998) Crystal structure of the signal sequence binding subunit of the signal recognition particle, Cell 94, 181-191.
24. Do, H., Falcone, D., Lin, J., Andrews, D. W., and Johnson, A. E. (1996) The cotranslational integration of membrane proteins into the phospholipid bilayer is a multistep process, Cell 85, 369-378.
25. McCormick, P. J., Miao, Y., Shao, Y., Lin, J., and Johnson, A. E. (2003) Cotranslational protein integration into the ER membrane is mediated by the binding of nascent chains to translocon proteins, Mol. Cell 12, 329-341.
26. Mothes, W., Jungnickel, B., Brunner, J., and Rapoport, T. A. (1998) Signal sequence recognition in cotranslational translocation by protein components of the endoplasmic reticulum membrane, J. Cell Biol. 142, 355-364.
27. Wimley, W. C., and White, S. H. (1996) Experimentally determined hydrophobicity scale for proteins at membrane interfaces, Nat. Struct. Biol. 3, 842-848.
28. Landolt-Marticorena, C., Williams, K. A., Deber, C. M., and Reithmeier, R. A. (1993) Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins, J. Mol. Biol. 229, 602-608.
29. Arkin, I. T., and Brunger, A. T. (1998) Statistical analysis of predicted transmembrane α-helices, Biochim. Biophys. Acta 1429, 113-128.
30. Weiss, M. S., Abele, U., Weckesser, J., Welte, W., Schiltz, E., and Schulz, G. E. (1991) Molecular architecture and electrostatic properties of a bacterial porin, Science 254, 1627-1630.
31. Schirmer, T., Keller, T. A., Wang, Y. F., and Rosenbusch, J. P. (1995) Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution, Science 267, 512-514.
32. Killian, J. A., and von Heijne, G. (2000) How proteins adapt to a membrane-water interface, Trends Biochem. Sci. 25, 429-434.
33. Braun, P., and von Heijne, G. (1999) The aromatic residues Tip and Phe have different effects on the positioning of a transmembrane helix in the microsomal membrane, Biochemistry 38, 9778-9782.
34. Martoglio, B., Hofmann, M. W., Brunner, J., and Dobberstein, B. (1995) The protein-conducting channel in the membrane of the endoplasmic reticulum is open laterally toward the lipid bilayer, Cell 81, 207-214.
35. van den Berg, B., demons, W. M., Jr., 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.
36. Beckmann, R., Spahn, C. M., Eswar, N., Helmers, J., Penczek, P. A., Sali, A., Frank, J., and Blobel, G. (2001) Architecture of the protein-conducting channel associated with the translating 80S ribosome, Cell 107, 361-372.
37. Menetret, J. F., Neuhof, A., Morgan, D. G., Plath, K., Radermacher, M., Rapoport, T. A., and Akey, C. W. (2000) The structure of ribosome-channel complexes engaged in protein translocation, Mol. Cell 6, 1219-1232.
38. Hamman, B. D., Chen, J. C., Johnson, E. E., and Johnson, A. E. (1997) The aqueous pore through the translocon has a diameter of 40-60 Å during cotranslational protein translocation at the ER membrane, Cell 89, 535-544.
39. Lyubartsev, A. P., and Laaksonen, A. (2000) M.DynaMix: A scalable portable parallel MD simulation package for arbitrary molecular mixtures, Comput. Phys. Commun. 128, 565-589.