Conservation and specialization in PAS domain dynamics

Protein Engineering, Design and Selection

Volumn 18, Issue 3, 2005, Pages 127-137

  Pandini, A ^a   Bonati, L ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

Essential motions; Molecular dynamics; Protein structures

Indexed keywords

CONFORMATIONS; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE;

FUNCTIONAL MOTIONS; HOMOLOGOUS PROTEINS; PER-ARNT-SIM (PAS) SUPERFAMILY; SIGNAL-INDUCED CONFORMATIONAL CHANGES;

PROTEINS;

BACTERIAL PROTEIN; HYPOXIA INDUCIBLE FACTOR 2ALPHA; PHOTOACTIVE YELLOW PROTEIN; POTASSIUM CHANNEL HERG; PROTEIN; PROTEIN FIXL; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY;

ADIANTUM; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CATION TRANSPORT PROTEINS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ECTOTHIORHODOSPIRA; ETHER-A-GO-GO POTASSIUM CHANNELS; HEMEPROTEINS; HUMANS; LIGANDS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; MOVEMENT; PHOTORECEPTORS; PHOTORECEPTORS, MICROBIAL; POTASSIUM CHANNELS, VOLTAGE-GATED; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN-SERINE-THREONINE KINASES; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TIME FACTORS; TRANS-ACTIVATORS;

EID: 18344395352     PISSN: 17410126     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/gzi017     Document Type: Article

References (51)

1. Amadei, A., Linssen, A.B. and Berendsen, H.J.C. (1993) Proteins, 17, 412-425.
2. Amezcua, C., Harper, S., Rutter, J. and Gardner, K. (2002) Structure (Camb.), 10, 1349-1361.
3. Anderson, S., Srajer, V., Pahl, R., Rajagopal, S., Schotte, F., Anfinrud, P., Wulff, M. and Moffat, K. (2004) Structure (Camb.), 12, 1039-1045.
4. Arcangeli, C., Bizzarri, A.R. and Cannistraro, S. (2001a) Biophys. Chem., 90, 45-56.
5. Arcangeli, C., Bizzarri, A.R. and Cannistraro, S. (2001b) Biophys. Chem., 92, 183-199.
6. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J. (1981) In Pullman, B. (ed), Intermolecular Forces. Reidel, Dordrecht, pp. 331-342.
7. Berendsen, H.J.C., van der Spoel, D. and van Drunen, R. (1995) Comput. Phys. Commun., 91, 43-56.
8. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourae, P.E. (2000) Nucleic Acids Res., 28, 235-242.
9. Borgstahl, G.E., Williams, D.R. and Getzoff, E.D. (1995) Biochemistry, 34, 6278-6287.
10. Cabral, J.H.M., Lee, A., Cohen, S.L., Chait, B.T., Li, M. and Mackinnon, R. (1998) Cell, 95, 649-655.
11. Craven, C.J., Derix, N.M., Hendriks, J., Boelens, R., Hellingwerf, K.J. and Kaptein, R. (2000) Biochemistry, 39, 14392-14399.
12. Crosson, S. and Moffat, K. (2001) Proc. Natl Acad. Sci. USA, 98, 2995-3000.
13. Crosson, S. and Moffat, K. (2002) Plant Cell, 14, 1067-1075.
14. Cusanovich, M.A. and Meyer, T.E. (2003) Biochemistry, 42, 4759-4770.
15. Darden, T., York, D. and Pedersen, L. (1993) J. Chem. Phys., 98, 10089-10092.
16. de Groot, B.L., Hayward, S., van Aalten, D.M.F., Amadei, A. and Berendsen, H.J.C. (1998) Proteins, 31, 116-127.
17. DeLano, W. (2002). The PyMOL User's Manual. DeLano Scientific, San Carlos, CA.
18. Dux, P. et al. (1998) Biochemistry, 37, 12689-12699.
19. Erbel, P.J., Card, P.B., Karakuzu, O., Bruick, R.K. and Gardner, K.H. (2003) Proc. Natl Acad. Sci. USA, 100, 15504-15509.
20. Feenstra, K.B.H. and Berendsen, H.J.C. (1999) J. Comput. Chem., 10, 255-262.
21. Getzoff, E.D., Gutwin, K.N. and Genick, U.K. (2003) Nat. Struct. Biol., 10, 663-668.
22. Gong, W., Hao, B., Mansy, S.S., Gonzalez, G., Gilles-Gonzalez, M.A. and Chan, M.K. (1998) Proc. Natl Acad. Sci. USA, 95, 15177-15182.
23. Gong, W., Hao, B. and Chan, M.K. (2000) Biochemistry, 39, 3955-3962.
24. Groenhof, G., Lensink, M.F., Berendsen, H.J., Snijders, J.G. and Mark, A.E. (2002a) Proteins, 48, 202-212.
25. Groenhof, G., Lensink, M.F., Berendsen, H.J. and Mark, A.E. (2002b) Proteins, 48, 212-219.
26. Grottesi, A. and Sansom, M.S.P. (2003) FEBS Lett., 535, 29-33.
27. Gu, Y.Z., Hogenesch, J.B. and Bradfield, C.A. (2000) Annu. Rev. Pharmacol. Toxicol., 40, 519-561.
28. Hao, B., Isaza, C., Arndt, J., Soltis, M. and Chan, M.K. (2002) Biochemistry, 41, 12952-12958.
29. Harper, S.M., Neil, L.C. and Gardner, K.H. (2003) Science, 301, 1541-1544.
30. Hellingwerf, K.J., Hendriks, J. and Gensch, T. (2003) J. Phys. Chem., 107, 1082-1094.
31. Hess, B. (2000) Phys. Rev. E, 62, 8438-8448.
32. Hess, B. (2002) Phys. Rev. E, 65, 031910/1-031910/10.
33. Hess, B., Bekker, H., Berendsen, H.J.C. and Fraaije, J.G.E.M. (1997) J. Comput. Chem., 18, 1463-1472.
34. Holm, L. and Sander, C. (1996) Science, 273, 595-603.
35. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
36. Kewley, R.J., Whitelaw, M.L. and Chapman-Smith, A. (2004) Int. J. Biochem. Cell. Biol., 36, 189-204.
37. Kurokawa, H., Lee, D.S., Watanabe, M., Sagami, I., Mikami, B., Raman, C.S. and Shimizu, T. (2004) J. Biol. Chem., 279, 20186-20193.
38. Lindahl, E., Hess, B. and van der Spoel, D. (2001) J. Mol. Mod., 7, 306-317.
39. Merlino, A., Vitagliano, L., Ceruso, M.C. and Mazzarella, L. (2003) Proteins, 52, 101-110.
40. Miyatake, H., Mukai, M., Park, S.Y., Adachi, S., Tamura, K., Nakamura, H., Nakamura, K., Tsuchiya, T., Iizuka, T. and Shiro, Y. (2000) J. Mol. Biol., 301, 415-431.
41. Razeto, A. et al. (2004) J. Mol. Biol., 336, 319-329.
42. R Development Core Team (2003). R: a Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
43. Rubinstenn, G., Vuister, G.W., Mulder, F.A., Dux, P.E., Boelens, R., Hellingwerf, K.J. and Kaptein, R. (1998) Nat. Struct. Biol., 5, 568-570.
44. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comput. Phys., 23, 327-341.
45. Taylor, B.L. and Zhulin, I.B. (1999) Microbiol. Mol. Biol. Rev., 63, 479-506.
46. van Aalten, D.M.F., Findlay, J.B.C., Amadei, A. and Berendsen, H.J.C. (1995) Protein Eng., 8, 1129-1135.
47. van Aalten, D., Bywater, R., Findlay, J., Hendlich, M., Hooft, R. and Vriend, G. (1996) J. Comput.-Aided Mol. Des., 10, 255-262.
48. van Aalten, D.M., Hoff, W.D., Findlay, J.B., Crielaard, W. and Hellingwerf, K.J. (1998a) Protein Eng., 11, 873-879.
49. van Aalten, D.M., Grotewold, E. and Joshua-Tor, L. (1998b) Methods, 14, 318-328.
50. van Aalten, D.M., Crielaard, W., Hellingwerf, K.J. and Joshua-Tor, L. (2000) Protein Sci., 9, 64-72.
51. Vreede, J., van der Horst, M.A., Hellingwerf, K.J., Crielaard, W. and van Aalten, D.M.F. (2003) J. Biol. Chem., 278, 18434-18439.