Hydrophobicity of transmembrane proteins: Spatially profiling the distribution

Protein Science

Volumn 12, Issue 3, 2003, Pages 586-599

  Silverman, B David ^a,b  

^a IBM T J WATSON RESEARCH CENTER   (United States)

^b IBM   (United States)

Author keywords

Helical bundles; Hydrophobicity; Spatial profiling; Transmembrane proteins; Zero order moment

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN;

ALPHA HELIX; ARTICLE; CALCULATION; HYDROPHOBICITY; LIPID BILAYER; PRIORITY JOURNAL; PROTEIN TERTIARY STRUCTURE;

ANIMALS; HUMANS; HYDROPHOBICITY; LIPID BILAYERS; MEMBRANE PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 0037370648     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0214903     Document Type: Article

References (40)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Boume, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 236-242.
2. Bonneau, R., Strauss, C.E.M., and Baker, D. 2001. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins: Struct. Funct. Genet. 43: 1-11.
3. Chang, G., Spencer, R.H., Lee, A.T., Barclay, M.T., and Rees, D.C. 1998. Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science 282: 2220-2226.
4. Eisenberg, D., Weiss, R.M., Terwilliger, T.C., and Wilcox, W. 1982. Hydrophobic moments of protein structure. Faraday Symp. Chem. Soc. 17: 109-120.
5. Engelman, D.M. and Zaccai, G. 1980. Bacteriorhodopsin is an inside-out protein. Proc. Natl. Acad. Sci. 77: 5894-5898.
6. Engelman, D.M., Steitz, T.A., and Goldman, A. 1986. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Ann. Rev. Biophys. Hem. 15: 321-353.
7. Ermler, U., Fritzsch, G., Buchanan, S.K., and Michel, H. 1994. Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 Å resolution: Cofactors and protein-cofactor interactions. Structure 2: 925-936.
8. Holm, H. and Sander, C. 1992. Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225: 93-105.
9. Huang, E.S., Subbiah, S., and Levitt, M. 1995. Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol. 252: 709-720.
10. Iverson, T.M., Luna-Chavez, C., Croal, L.R., Cecchini, G., and Rees, D.C. 2002. Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J. Biol. Chem. 277: 16124-16130.
11. Iwata, S., Lee, J.W., Okada, K., Lee, J.K., Iwata, M., Rasmussen, B., Link, T.A., Ramaswamy, S., and Jap, B.K. 1998. Complete structure of the 11-subunit bovine mitochondrial cytochrome bcl complex. Science 281: 64-71.
12. Jordan, P., Fromme, P., Witt, H.T., Klukas, O., Saenger, W., and Krauss, N. 2001. Three-dimensional structure of cyanobacterial Photosystem I at 2.5 Å resolution. Nature 411: 909-917.
13. Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14: 1-63.
14. Kidera, A., Konishi, Y., Ooi, T., and Scheraga, H.A. 1985. Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acids. J. Protein Chem. 5: 265-297.
15. Kytte, J. and Doolittle, R.F. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132.
16. Lee, J. and Shin, S.M. 2001. Understanding β-hairpin formation by molecular dynamics simulations of unfolding. Biophys. J. 81: 2507-2516.
17. Locher, K.P., Lee, A.T., and Rees, D.C. 2002. The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism. Science 296: 1091-1098.
18. Luecke, H., Schobert, B., Richter, H.T., Cartailler, J.P., and Lanyi, J.K. 1999. Structure of bacteriorhodopsin at 1.55 Å resolution. J. Mol. Biol. 291: 899-911.
19. Meirovitch, H. and Scheraga, H.A. 1981. Empirical studies of hydrophobicity. 3. Radial distribution of clusters of hydrophobic and hydrophilic amino acids. Macromolecules 14: 340-345.
20. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540. (1J4N, 1L7V, and 1KF6 have not been listed).
21. Novotny, J., Rashin, A.A., and Bruccoleri, R.E. 1988. Criteria that discriminate between native proteins and incorrectly folded models. Proteins: Struct. Funct. Genet. 4: 19-30.
22. Perutz, M.F., Kendrew, J.C., and Watson, H.C. 1965. Structure and function of haemoglobin. J. Mol. Biol. 13: 669-678.
23. Rastogi, V.K. and Girvin, M.E. 1999. Structural changes linked to proton translocation by subunit C of the ATP synthase. Nature 402: 263-268.
24. Rees, D.C. and Eisenberg, D. 2000. Turning a reference inside-out: Commentary on an article by Stevens and Arkin entitled: "Are membrane proteins 'inside-out' proteins?" Proteins: Struct. Funct. Genet. 38: 121-122.
25. Rees, D.C., DeAntonio, L., and Eisenberg, D. 1989. Hydrophobic organization of membrane proteins. Science 245: 510-513.
26. Rose, G. 1978. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature 272: 586-590.
27. Rose, G.D. and Roy, S. 1980. Hydrophobic basis of packing in globular proteins. Proc. Natl. Acad. Sci. 77: 4643-4647.
28. Silverman, B.D. 2001. Hydrophobic moments of protein structures: Spatially profiling the distribution. Proc. Nat. Acad. Sci. 98: 4996-5001.
29. Soulimane, T., Buse, J., Bourenkov, G.P., Bartunik, H.D., Huber, R., and Than, M.E. 2000. Structure and mechanism of the aberrant Ba3-cytochrome C oxidase from Thermus thermophilus. EMBO J. 19: 1766-1776.
30. Stevens, T.J. and Arkin, I.T. 1999. Are membrane proteins "inside-out" proteins? Proteins: Struct. Funct. Genet. 36: 135-143.
31. -. 2000. Turning an opinion inside-out: Rees and Eisenberg's commentary (2000. Proteins 38: 121-122) on "Are membrane proteins 'inside-out' proteins?" (1999. Proteins 36: 135-143). Proteins: Struct. Funct. and Genet. 40: 463-464.
32. -. 2000. Turning an opinion inside-out: Rees and Eisenberg's commentary (2000. Proteins 38: 121-122) on "Are membrane proteins 'inside-out' proteins?" (1999. Proteins 36: 135-143). Proteins: Struct. Funct. and Genet. 40: 463-464.
33. -. 2000. Turning an opinion inside-out: Rees and Eisenberg's commentary (2000. Proteins 38: 121-122) on "Are membrane proteins 'inside-out' proteins?" (1999. Proteins 36: 135-143). Proteins: Struct. Funct. and Genet. 40: 463-464.
34. -. 2000. Turning an opinion inside-out: Rees and Eisenberg's commentary (2000. Proteins 38: 121-122) on "Are membrane proteins 'inside-out' proteins?" (1999. Proteins 36: 135-143). Proteins: Struct. Funct. and Genet. 40: 463-464.
35. Sui, H., Han, B.G., Lee, J.K., Walian, P., and Jap, B.K. 2001. Structural basis of water-specific transport through the AQPI water channel. Nature 414: 872-878.
36. Wallin, E., Tsukihara, T., Yoshikawa, S., Von Heijne, G., and Elofsson, A. 1997. Architecture of helix membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci. 6: 808-815.
37. White, S.H. and Wimley, W.C. 1999. Membrane protein folding and stability: Physical principles. Annu. Rev. Biophys. Biomolec. Struct. 28: 319-365.
38. Zagrovic, B., Sorin, E.J., and Pande, V. 2001. β-Hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313: 151-169.
39. Zhou, R., Beme, B.J., and Germain, R. 2001. The free energy landscape for β hairpin folding in explicit water. Proc. Natl. Acad. Sci. 98: 14931-14936.
40. + channel-FAB complex at 2.0 Å resolution. Nature 414: 43-48.