A molecular modeling study of the interaction between SRP-receptor complex and peptide translocon

Biochemical and Biophysical Research Communications

Volumn 377, Issue 2, 2008, Pages 346-350

  Chen, Shifei ^a   Fan, Yi ^a   Shen, Xueling ^a   Sun, Peng ^b   Jiang, Guosong ^c   Shen, Yi ^c   Xue, Wenfei ^a   Li, Yongquan ^a   Chen, Xin ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c HANGZHOU VOCATIONAL AND TECHNICAL COLLEGE   (China)

Author keywords

Molecular interaction; Molecular modeling; Peptide translocon; Signal recognition particle

Indexed keywords

DOCKING PROTEIN; FFH PROTEIN; FTSY PROTEIN; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANOSINE TRIPHOSPHATE; SIGNAL RECOGNITION PARTICLE; TRANSLOCON; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CYTOPLASM; HYDROLYSIS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REGULATORY MECHANISM;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CALCIUM-BINDING PROTEINS; COMPUTER SIMULATION; ESCHERICHIA COLI PROTEINS; MEMBRANE GLYCOPROTEINS; MODELS, MOLECULAR; MUTATION; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RECEPTORS, PEPTIDE; SIGNAL RECOGNITION PARTICLE;

EID: 55549094402     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.09.119     Document Type: Article

References (29)

1. Doudna J.A., and Batey R.T. Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73 (2004) 539-557
2. Egea P.F., Shan S.O., Napetschnig J., Savage D.F., Walter P., and Stroud R.M. Substrate twinning activates the signal recognition particle and its receptor. Nature 427 (2004) 215-221
3. Mitra K., Schaffitzel C., Shaikh T., Tama F., Jenni S., Brooks III C.L., Ban N., and Frank J. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438 (2005) 318-324
4. Halic M., Blau M., Becker T., Mielke T., Pool M.R., Wild K., Sinning I., and Beckmann R. Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Nature 444 (2006) 507-511
5. Parlitz R., Eitan A., Stjepanovic G., Bahari L., Bange G., Bibi E., and Sinning I. Escherichia coli signal recognition particle receptor FtsY contains an essential and autonomous membrane-binding amphipathic helix. J. Biol. Chem. 282 (2007) 32176-32184
6. Angelini S., Deitermann S., and Koch H.G. FtsY, the bacterial signal-recognition particle receptor, interacts functionally and physically with the SecYEG translocon. EMBO Rep. 6 (2005) 476-481
7. Mendez R., Leplae R., Lensink M.F., and Wodak S.J. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60 (2005) 150-169
8. Wiehe K., Pierce B., Mintseris J., Tong W.W., Anderson R., Chen R., and Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins 60 (2005) 207-213
9. Chu F., Shan S.O., Moustakas D.T., Alber F., Egea P.F., Stroud R.M., Walter P., and Burlingame A.L. Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 101 (2004) 16454-16459
10. Buskiewicz I., Kubarenko A., Peske F., Rodnina M.V., and Wintermeyer W. Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY. RNA 11 (2005) 947-957
11. Herskovits A.A., Seluanov A., Rajsbaum R., ten Hagen-Jongman C.M., Henrichs T., Bochkareva E.S., Phillips G.J., Probst F.J., Nakae T., Ehrmann M., Luirink J., and Bibi E. Evidence for coupling of membrane targeting and function of the signal recognition particle (SRP) receptor FtsY. EMBO Rep. 2 (2001) 1040-1046
12. Eitan A., and Bibi E. The core Escherichia coli signal recognition particle receptor contains only the N and G domains of FtsY. J. Bacteriol. 186 (2004) 2492-2494
13. Kim D.E., Chivian D., and Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32 (2004) W526-W531
14. Gu S.Q., Peske F., Wieden H.J., Rodnina M.V., and Wintermeyer W. The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA 9 (2003) 566-573
15. Ponder J.W., and Case D.A. Force fields for protein simulations. Adv. Protein Chem. 66 (2003) 27-85
16. Manting E.H., van Der Does C., Remigy H., Engel A., and Driessen A.J. SecYEG assembles into a tetramer to form the active protein translocation channel. EMBO J. 19 (2000) 852-861
17. De Keyzer J., Van Der Does C., and Driessen A.J. Kinetic analysis of the translocation of fluorescent precursor proteins into Escherichia coli membrane vesicles. J. Biol. Chem. 277 (2002) 46059-46065
18. de Leeuw E., te Kaat K., Moser C., Menestrina G., Demel R., de Kruijff B., Oudega B., Luirink J., and Sinning I. Anionic phospholipids are involved in membrane association of FtsY and stimulate its GTPase activity. EMBO J. 19 (2000) 531-541
19. Millman J.S., and Andrews D.W. A site-specific, membrane-dependent cleavage event defines the membrane binding domain of FtsY. J. Biol. Chem. 274 (1999) 33227-33234
20. Zelazny A., Seluanov A., Cooper A., and Bibi E. The NG domain of the prokaryotic signal recognition particle receptor, FtsY, is fully functional when fused to an unrelated integral membrane polypeptide. Proc. Natl. Acad. Sci. USA 94 (1997) 6025-6029
21. Millman J.S., Qi H.Y., Vulcu F., Bernstein H.D., and Andrews D.W. FtsY binds to the Escherichia coli inner membrane via interactions with phosphatidylethanolamine and membrane proteins. J. Biol. Chem. 276 (2001) 25982-25989
22. Kholodenko B.N., Hoek J.B., and Westerhoff H.V. Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends Cell Biol. 10 (2000) 173-178
23. Gariani T., Samuelsson T., and Sauer-Eriksson A.E. Conformational variability of the GTPase domain of the signal recognition particle receptor FtsY. J. Struct. Biol. 153 (2006) 85-96
24. Mishra V.K., and Palgunachari M.N. Interaction of model class A1, class A2, and class Y amphipathic helical peptides with membranes. Biochemistry 35 (1996) 11210-11220
25. Segrest J.P., De Loof H., Dohlman J.G., Brouillette C.G., and Anantharamaiah G.M. Amphipathic helix motif: classes and properties. Proteins 8 (1990) 103-117
26. Kortemme T., Kim D.E., and Baker D. Computational alanine scanning of protein-protein interfaces. Sci. STKE 2004 (2004) pl2
27. Baba T., Jacq A., Brickman E., Beckwith J., Taura T., Ueguchi C., Akiyama Y., and Ito K. Characterization of cold-sensitive secY mutants of Escherichia coli. J. Bacteriol. 172 (1990) 7005-7010
28. Freymann D.M., Keenan R.J., Stroud R.M., and Walter P. Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP. Nat. Struct. Biol. 6 (1999) 793-801
29. Freymann D.M., Keenan R.J., Stroud R.M., and Walter P. Structure of the conserved GTPase domain of the signal recognition particle. Nature 385 (1997) 361-364