Concerted motions in the photoactive yellow protein

Protein Engineering

Volumn 11, Issue 10, 1998, Pages 873-879

  Van Aalten, D M F ^a,c   Hoff, W D ^b   Findlay, J B C ^a   Crielaard, W ^b   Hellingwerf, K J ^b  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

Chromophore; Essential dynamics; Molecular dynamics; p coumaric acid; Photo active yellow protein; Photocycle

Indexed keywords

GLYCINE; PHOTOPROTEIN;

ARTICLE; CHROMATOPHORE; ISOMERISM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MODIFICATION; SIGNAL TRANSDUCTION; SIMULATION;

EID: 0031788430     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/11.10.873     Document Type: Article

References (39)

1. Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Proteins, 17, 412-425.
2. Baca, M., Borgstahl, G.E.O., Boissinot, M., Burke, P.M., Williams, D.R., Slater, K.A. and Getzoff, E.D. (1994) Biochemistry, 33, 14369-14377.
3. Baltuska, A., van Stokkum, I.H.M., Kroon, A., Monshouwer, R., Hellingwerf, K.J. and van Grondelle, R. (1997) Chem. Phys. Lett., 270, 263-266.
4. Berendsen, H.J.C., Postma, J.P.M., DiNola, A. and Haak, J.R. (1984) J. Chem. Phys., 81, 3684-3690.
5. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J. (1981) In Pullmann, B. (ed.), Intermolecular Forces. Reidel, Dordrecht, p. 331.
6. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, J. and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
7. Borgstahl, G.E.O., Williams, D.R. and Getzoff, E.D. (1995) Biochemistry, 34, 6278-6287.
8. Changenet, P., Zhang, H., van der Meer, M., Hellingwerf, K.J. and Glasbeek, M. (1998) Phys. Chem. Lett., in press.
9. Crosthwaite, S.K., Dunlap, J.C. and Loros, J.J. (1997) Science, 276, 763-769.
10. Genick, U.K., Borgstahl, G.E.O., Kingman, N., Ren, Z., Pradervand, C., Burke, P., Srajer, V., Teng, T., Schildkamp, W., McRee, D.E., Moffat, K. and Getzoff, E.D. (1997) Science, 275, 1471-1475.
11. Hoff, W.D., Kwa, S.L.S., van Grondelle, R. and Hellingwerf, K.J. (1992) Photochem. Photobiol., 56, 529-539.
12. Hoff, W.D., Düx, P., Devreese, B., Nugteren-Roodzant, I.M., Crielaard, W., Boelens, R., Kaptein, R., van Beeumen, J. and Hellingwerf, K.J. (1994a) Biochemistry, 33, 13959-13962.
13. Hoff, W.D., van Stokkum, I.H.M., van Ramesdonk, H.J., van Brederode, M.E., Brouwer, A.M., Fitch, J.C., Meyer, T.E., van Grondelle, R. and Hellingwerf, K.J. (1994b) Biophys. J., 67, 1691-1705.
14. Hoff, W.D., Matthijs, H.C.P., Schubert, H., Crielaard, W. and Hellingwerf, K.J. (1995) Biophys. Chem., 56, 193-199.
15. Hoff, W.D., Devreese, B., Fokkens, R., Nugteren-Roodzant, I.M., van Beeumen, J.F., Nibbering, N. and Hellingwerf, K.J. (1996) Biochemistry, 35, 1274-1281.
16. Imhoff, J.F., Hashwa, F. and Trüper, H.G. (1978) Arch. Hydrobiol., 84, 381-388.
17. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
18. Kim, M., Mathies, R.A., Hoff, W.D. and Hellingwerf, K.J. (1995) Biochemistry, 34, 12669-12672.
19. Kort, R., Hoff, W.D., van West, M., Kroon, A.R., Hoffer, S.M., Vlieg, K.H., Crielaard, W., van Beeumen, J.J. and Hellingwerf, K.J. (1996a) EMBO J., 15, 3209-3218.
20. Kort, R., Vonk, H., Xu, X., Hoff, W.D., Crielaard, W. and Hellingwerf, K.J. (1996b) FEBS Lett., 32, 73-78.
21. McRee, D.E., Meyer, T.E., Cusanovich, M., Parge, H.E. and Getzoff, E.D. (1986) J. Biol. Chem., 261, 13850-13851.
22. McRee, D.E., Tainer, J.A., Meyer, T.E., van Beeumen, J., Cusanovich, M.A. and Getzoff, E.D. (1989) Proc. Natl Acad. Sci. USA, 86, 6533-6537.
23. Meyer, T.E. (1985) Biochim. Biophys. Acta, 806, 175-183.
24. Meyer, T.E., Yakali, E., Cusanovich, M.A. and Tollin, G. (1987) Biochemistry, 26, 418-423.
25. Meyer, T.E., Tollin, G., Hazzard, J.H. and Cusanovich, M.A. (1989) Biophys. J., 56, 559-564.
26. Meyer, T.E., Tollin, G., Causgrove, T.P., Cheng, P. and Blankenship, R.E. (1991) Biophys. J., 59, 988-991.
27. Meyer, T.E., Cusanovich, M.A. and Tollin, G. (1993) Arch. Biochem. Biophys., 306, 515-517.
28. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comp. Phys., 23, 327-341.
29. Salamon, Z., Meyer, T.E. and Tollin, G. (1995) Biophys. J., 68, 648-654.
30. Sprenger, W.W., Hoff, W.D., Armitage, J.P. and Hellingwerf, K.J. (1993) J. Bacteriol., 175, 3096-3104.
31. van Aalten, D.M.F., Amadei, A., Linssen, A.B.M., Eijsink, V.G.H., Vriend, G. and Berendsen, H.J.C. (1995a) Proteins, 22, 45-54.
32. van Aalten, D.M.F., Findlay, J.B.C., Amadei, A. and Berendsen, H.J.C. (1995b) Prot. Engng, 8, 1129-1135.
33. van Aalten, D.M.F., Amadei, A., Bywater, R., Findlay, J.B.C., Berendsen, H.J.C., Sander, C. and Stouten, P.F.W. (1996a) Biophys. J., 70, 684-692.
34. van Aalten, D.M.F., Bywater, R., Findlay, J.B.C., Hendlich, M., Hooft, R.W.W. and Vriend, G. (1996b) JCAMD, 10, 255-262.
35. van Aalten, D.M.F., de Groot, B.L., Findlay, J.B.C., Berendsen, H.J.C. and Amadei, A. (1997) J. Comp. Chem., 18, 169-181.
36. van Brederode, M.E., Gensch, T., Hoff, W.D., Hellingwerf, K.J. and Braslavsky, S.E. (1995) Biophys.J., 68, 1101-1109.
37. van Brederode, M.E., Hoff, W.D., van Stokkum, I.H.M., Groot, M.L. and Hellingwerf, K.J. (1996) Biophys. J., 71, 365-380.
38. van Gunsteren, W.F. and Berendsen, H.J.C. (1987) Gromos Manual. BIOMOS. Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen, The Netherlands.
39. Vriend, G. (1990) J. Mol. Graph., 8, 52-56.