Abstract
In contrast to soluble proteins, membrane proteins offer the possibility, to predict their secondary structure with some reliability. Based on such predictions a set of initial conformation can be constructed on which molecular dynamics simulations are performed in order to find the most stable state. The important point is that all those degrees of freedom which change slowly in time must be varied artificially in the set of initial conformations. This procedure is demonstrated for the membrane protein bacteriorhodopsin.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Jähnig, F.: Prediction of protein structure and the principles of protein conformation. Fasman, G.D. (ed.), pp. 707–717. New York: Plenum Press 1989
Henderson, R., Unwin, P.N.T.: Nature257, 28–32 (1975)
Henderson, R., Baldwin, J.M., Downing, K.H., Lepault, J., Zemlin, F.: Ultramicroscopy19, 147–178 (1986)
Tsygannik, I.N., Baldwin, J.M.: Eur. Biophys. J.14, 263–272 (1987)
Engelman, D.M., Henderson, R., McLachlan, A.D., Wallace, B.A.: Proc. Natl. Acad. Sci. USA77, 2023–2027 (1980)
Trewhella, J., Popot, J.L., Zaccai, G., Engelman, D.M.: EMBO J.5, 3045–3049 (1986)
Heyn, M.P., Westerhausen, J., Wallat, I., Seiff, F.: Proc. Natl. Acad. Sci. USA85, 2146–2150 (1988)
Fauchere, J.L., Pliska, V.: Eur. J. Med. Chem. Chim. Ther.18, 369–375 (1986)
Wallace, B.A., Henderson, R.: Biophys. J.39, 233–239 (1982)
Harbison, G.S., Smith, S.O., Pardoen, J.A., Courtin, J.M.L., Lutgenberg, J., Herzfeld, J., Mathies, R.A., Griffin, R.G.: Biochemistry24, 6955–6962 (1985)
Edholm, O., Jähnig, F.: Biophys. Chem.30, 279–292 (1988)
Parsegian, V.A., Fuller, N., Rand, R.P.: Proc. Natl. Acad. Sci. USA76, 2750–2754 (1979)
Jähnig, F., Edholm, O.: (submitted for publication)
van Gunsteren, W.F., Karplus, M.: Macromolecules15, 1528–1544 (1982)
Ryckaert, J.P., Cicotti, G., Berendsen, H.J.C.: Comp. Phys.23, 327–341 (1977)
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., Dinola, A., Haak, J.R.: J. Chem. Phys.81, 3684–3690 (1984)
Vogel, H., Gärtner, W.: J. Biol. Chem.262, 11464–11469 (1987)
Earnest, T.N., Roepe, P., Braiman, M.S., Gillespie, J., Rothschild, K.J.: Biochemistry25, 7793–7798 (1986)
Siebert, F.: (to be published)
Fimmel, S., Choli, T., Dencher, N.A., Büldt, G., Wittmann-Liebold, B.: Biochim. Biophys. Acta978, 231–240 (1989)
Polland, H.J., Franz, M.A., Zinth, W., Kaiser, W., Oesterhelt, D.: Biochim. Biophys. Acta851, 407–415 (1986)
Khorana, H.G.: J. Biol. Chem.263, 7439–7442 (1988)
Soppa, J., Oesterhelt, D.: J. Biol. Chem.264, 13043–13048 (1989)
Author information
Authors and Affiliations
Additional information
Dedicated to Professor W. Brenig on the occasion of his 60th birthday
Rights and permissions
About this article
Cite this article
Jähnig, F., Edholm, O. Can the structure of proteins be calculated?. Z. Physik B - Condensed Matter 78, 137–143 (1990). https://doi.org/10.1007/BF01317366
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF01317366