An experimentally based computer search identifies unstructured membrane-binding sites in proteins: Application to class I myosins, PAKs, and CARMIL

Journal of Biological Chemistry

Volumn 285, Issue 8, 2010, Pages 5738-5747

  Brzeska, Hanna ^a   Guag, Jake ^a   Remmert, Kirsten ^a   Chacko, Susan ^b   Korn, Edward D ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACANTHAMOEBA; ACIDIC PHOSPHOLIPIDS; BINDING DOMAIN; CAPPING PROTEINS; CLASS I; COMPUTER SEARCH; CYTOSKELETAL PROTEINS; CYTOSKELETAL SCAFFOLD PROTEINS; GTP-BINDING PROTEINS; HYDROPHOBIC AMINO ACIDS; HYDROPHOBIC REGIONS; HYDROPHOBICITY SCALE; IN-VITRO; LIPID BINDING; MEMBRANE-ASSOCIATED PROTEINS; PROTEIN DOMAINS; PROTEIN SEQUENCES; SEARCH ALGORITHMS; SYNTHETIC PEPTIDE; TERTIARY STRUCTURES;

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; COMPUTER TESTING; HYDROPHOBICITY; LEARNING ALGORITHMS; LIPOSOMES; MEMBRANES; ORGANIC ACIDS; PEPTIDES; PHOSPHOLIPIDS;

BINDING SITES;

ACTIN RELATED PROTEIN 2-3 COMPLEX; AMINO ACID DERIVATIVE; ARGININE; CYTOSKELETON PROTEIN; LYSINE; MYOSIN; PEPTIDE DERIVATIVE; PHOSPHOLIPID; SCAFFOLD PROTEIN; CARRIER PROTEIN; PEPTIDE; PROTOZOAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CELL VACUOLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; MEMBRANE BINDING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN LIPID INTERACTION; ACANTHAMOEBA; ALGORITHM; ANIMAL; CELL MEMBRANE; CHEMISTRY; GENETICS; HYDROPHOBICITY; METABOLISM; MOUSE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

ACANTHAMOEBA;

ACANTHAMOEBA; ALGORITHMS; ANIMALS; BINDING SITES; CARRIER PROTEINS; CELL MEMBRANE; HYDROPHOBICITY; MICE; MYOSINS; PEPTIDES; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 77949319432     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.066910     Document Type: Article

References (56)

1. Lemmon, M. A. (2008) Nat. Rev. Mol. Cell Biol. 9, 99-111
2. Niggli, V. (2001) Trends Biochem. Sci. 26, 604-611
3. Brzeska, H., Hwang, K. J., and Korn, E. D. (2008) J. Biol. Chem. 283, 32014-32023
4. Lynch, T. J., Brzeska, H., Miyata, H., and Korn, E. D. (1989) J. Biol. Chem. 264, 19333-19339
5. Doberstein, S. K., and Pollard, T. D. (1992) J. Cell Biol. 117, 1241-1249
6. Wang, Z. Y., Brzeska, H., Baines, I. C., and Korn, E. D. (1995) J. Biol. Chem. 270, 27969-27976
7. Baines, I. C., and Korn, E. D. (1990) J. Cell Biol. 111, 1895-1904
8. Baines, I. C., Brzeska, H., and Korn, E. D. (1992) J. Cell Biol. 119, 1193-1203
9. Doberstein, S. K., Baines, I. C., Wiegand, G., Korn, E. D., and Pollard, T. D. (1993) Nature 365, 841-843
10. Ostap, E. M., Maupin, P., Doberstein, S. K., Baines, I. C., Korn, E. D., and Pollard, T. D. (2003) Cell Motil. Cytoskeleton 54, 29-40
11. Heo, W. D., Inoue, T., Park, W. S., Kim, M. L., Park, B. O., Wandless, T. J., and Meyer, T. (2006) Science 314, 1458-1461
12. Wimley, W. C., and White, S. H. (1996) Nat. Struct. Biol. 3, 842-848
13. Liu, X., Brzeska, H., and Korn, E. D. (2000) J. Biol. Chem. 275, 24886-24892
14. Fujiwara, I., Remmert, K., and Hammer, J. A., 3rd (November 19, 2009) J. Biol. Chem. 10.1074/jbc.M109.031203
15. Kyte, J., and Doolittle, R. F. (1982) J. Mol. Biol. 157, 105-132
16. Morita, Y. S., Jung, G., Hammer, J. A., 3rd, and Fukui, Y. (1996) Eur. J. Cell Biol. 71, 371-379
17. Senda, S., Lee, S. F., Côté, G. P., and Titus, M. A. (2001) J. Biol. Chem. 276, 2898-2904
18. Jung, G., Fukui, Y., Martin, B., and Hammer, J. A., 3rd (1993) J. Biol. Chem. 268, 14981-14990
19. Sweet, R. M., and Eisenberg, D. (1983) J. Mol. Biol. 171, 479-488
20. Wang, Z. Y., Sakai, J., Matsudaira, P. T., Baines, I. C., Sellers, J. R., Hammer, J. A., 3rd, and Korn, E. D. (1997) J. Muscle Res. Cell Motil. 18, 395-398
21. Ishikawa, T., Cheng, N., Liu, X., Korn, E. D., and Steven, A. C. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 12189-12194
22. Van Troys, M., Dewitte, D., Verschelde, J. L., Goethals, M., Vandekerckhove, J., and Ampe, C. (2000) Biochemistry 39, 12181-12189
23. Kim, K., McCully, M. E., Bhattacharya, N., Butler, B., Sept, D., and Cooper, J. A. (2007) J. Biol. Chem. 282, 5871-5879
24. Stock, A., Steinmetz, M. O., Janmey, P. A., Aebi, U., Gerisch, G., Kammerer, R. A., Weber, I., and Faix, J. (1999) EMBO J. 18, 5274-5284
25. Sengupta, P., Bosis, E., Nachliel, E., Gutman, M., Smith, S. O., Mihályné, G., Zaitseva, I., and McLaughlin, S. (2009) Biophys. J. 96, 4887-4895
26. Wang, J., Gambhir, A., Hangyás-Mihályné, G., Murray, D., Golebiewska, U., and McLaughlin, S. (2002) J. Biol. Chem. 277, 34401-34412
27. Yu, F. X., Sun H. Q., Janmey, P. A., and Yin, H. L. (1992) J. Biol. Chem. 267, 14616-14621
28. Janmey, P. A., Lamb, J., Allen, P. G., and Matsudaira, P. T. (1992) J. Biol. Chem. 267, 11818-11823
29. Feng, L., Mejillano, M., Yin, H. L., Chen, J., and Prestwich, G. D. (2001) Biochemistry 40, 904-913
30. Takahashi, S., and Pryciak, P. M. (2007) Mol. Biol. Cell 18, 4945-4956
31. Arbuzova, A., Wang, L., Wang, J., Hangyás-Mihályné, G., Murray, D., Honig, B., and McLaughlin, S. (2000) Biochemistry 39, 10330-10339
32. Wang, J., Arbuzova, A., Hangyás-Mihályné, G., and McLaughlin, S. (2001) J. Biol. Chem. 276, 5012-5019
33. Spudich, G., Chibalina, M. V., Au, J. S., Arden, S. D., Buss, F., and Kendrick- Jones, J. (2007) Nature Cell Biol. 9, 176-183
34. Rohatgi, R., Ho, H. Y., and Kirschner, M. W. (2000) J. Cell Biol. 150, 1299-1310
35. Nomikos, M., Mulgrew-Nesbitt, A., Pallavi, P., Mihalyne, G., Zaitseva, I., Swann, K., Lai, F. A., Murray, D., and McLaughlin, S. (2007) J. Biol. Chem. 282, 16644-16653
36. Winters, M. J., Lamson, R. E., Nakanishi, H., Neiman, A. M., and Pryciak, P. M. (2005) Mol. Cell 20, 21-32
37. McLaughlin, S., and Murray, D. (2005) Nature 438, 605-611
38. Hokanson, D. E., Laakso, J. M., Lin, T., Sept, D., and Ostap, E. M. (2006) Mol. Biol. Cell 17, 4856-4865
39. Brzeska, H., Lynch, T. J., and Korn, E. D. (1990) J. Biol. Chem. 265, 3591-3594
40. Lee, S. F., Mahasneh, A., de la Roche, M., and Côté, G. P. (1998) J. Biol. Chem. 273, 27911-27917
41. Brzeska, H., Young, R., Knaus, U., and Korn, E. D. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 394-399
42. Brzeska, H., Kulesza-Lipka, D., and Korn, E. D. (1992) J. Biol. Chem. 267, 23870-23875
43. Bokoch, G. M., Reilly, A. M., Daniels, R. H., King, C. C., Olivera, A., Spiegel, S., and Knaus, U. G. (1998) J. Biol. Chem. 273, 8137-8144
44. Brzeska, H., Lynch, T. J., Martin, B., Corigliano-Murphy, A., and Korn, E. D. (1990) J. Biol. Chem. 265, 16138-16144
45. Kulesza-Lipka, D., Baines, I. C., Brzeska, H., and Korn, E. D. (1991) J. Cell Biol. 115, 109-119
46. Wild, A. C., Yu, J. W., Lemmon, M. A., and Blumer, K. J. (2004) J. Biol. Chem. 279, 17101-17110
47. Jung, G., Remmert, K., Wu, X., Volosky, J. M., and Hammer, J. A., 3rd (2001) J. Cell Biol. 153, 1479-1497
48. Uruno, T., Remmert, K., and Hammer, J. A., 3rd (2006) J. Biol. Chem. 281, 10635-10650
49. Yang, Y., Gourinath, S., Kovács, M., Nyitray, L., Reutzel, R., Himmel, D. M., O'Neall-Hennessey, E., Reshetnikova, L., Szent-Györgyi, A. G., Brown, J. H., and Cohen, C. (2007) Structure 15, 553-564
50. Swanljung-Collins, H., and Collins J. H. (1992) J. Biol. Chem. 267, 3445-3454
51. Scott, D. L., Diez, G., and Goldmann, W. H. (2006) Theor. Biol. Med. Model 3, 17
52. Swanljung-Collins, H., and Collins, J. H. (1994) Adv. Exp. Med. Biol. 358, 205-213
53. Hirono, M., Denis, C. S., Richardson, G. P., and Gillespie, P. G. (2004) Neuron 44, 309-320
54. McKenna, J. M., and Ostap, E. M. (2009) J. Biol. Chem. 284, 28650-28659
55. Tang, N., Lin, T., and Ostap, E. M. (2002) J. Biol. Chem. 277, 42763-42768
56. Hokanson, D. E., and Ostap, E. M. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 3118-3123