Abstract
As protein crystals generally possess a high water content, it is assumed that the behaviour of a protein in solution and in crystal environment is very similar. This assumption can be investigated by molecular dynamics (MD) simulation of proteins in the different environments. Two 2ns simulations of hen egg white lysozyme (HEWL) in crystal and solution environment are compared to one another and to experimental data derived from both X-ray and NMR experiments, such as crystallographic B-factors, NOE atom–atom distance bounds, 3JH Nα-coupling constants, and 1H-15N bond vector order parameters. Both MD simulations give very similar results. The crystal simulation reproduces X-ray and NMR data slightly better than the solution simulation.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Artymiuk, P.J., Blake, C.C.F., Rice, D.W. and Wilson, K.S. (1982) Acta Crystallogr., B38, 778–783.
Baldwin, E.T., Weber, I.T., Charles, R.S., Xuan, J.-C., Appella, E., Yamada, M., Matsushima, K., Edwards, B.F.P., Clore, G.M., Gronenborn, A.M. and Wlodawer, A. (1991) Proc. Natl. Acad. Sci. USA, 88, 502–506.
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R. (1984) J. Chem. Phys., 81, 3684–3690.
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J. (1981) In Intermolecular Forces (Ed., Pullman, B.), Reidel, Dordrecht, pp. 331–342.
Berndt, K.D., Güntert, P., Orbons, L.P.M. and Wüthrich, K. (1992) J. Mol. Biol., 227, 757–775.
Bernstein, F.C., Koetzle, T.F., Williams G.J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535–542.
Billeter, M., Kline, A.D., Braun, W., Huber, R. and Wüthrich, K. (1989) J. Mol. Biol., 206, 677–687.
Billeter, M., Vendrell, J., Wider, G., Avilès, F.X., Coll, M., Gausch, A., Huber, R., and Wüthrich, K. (1992) J. Biomol. NMR, 2, 1–10.
Braun, W., Vašák, M., Robbins, A.H., Stout, C.D., Wagner, G., Kägi, J.H.R., and Wüthrich, K. (1992) Proc. Natl. Acad. Sci. USA, 89, 10124–10128.
Buck, M., Boyd, J., Redfield, C., MacKenzie, D.A., Jeenes, D.J., Archer, D.B. and Dobson, C.M. (1995) Biochemistry, 34, 4041–4055.
Carter, D., He, J., Ruble, J.R. and Wright, B. (1997) Protein Data Bank, entry 1AKI.
Dornberger, U., Flemming, J. and Fritzsche, H. (1998) J. Mol. Biol.,284, 1453–1463.
Evenäs, J. Forsén, S. and Akke, M. (1999) J. Mol. Biol., 289, 603-617.
Fede, A., Billeter, M., Leupin, W. and Wüthrich, K. (1993) Structure, 1, 177–186.
Hünenberger, P.H., Mark, A.E. and van Gunsteren, W.F. (1995) J. Mol. Biol.,252, 492–503.
Kallen, J., Spitzfaden, C., Zurini, M.G.M., Wider, G., Widmer, H., Wüthrich, K. and Walkinshaw, M.D. (1991) Nature, 353, 276-279.
Lu, J., Lin, C.-L., Tang, C., Ponder, J.W., Kao, J.L.F., Cistola, D.P.,and Li, E. (1999) J. Mol. Biol., 286, 1179–1195.
Moore, J.M., Lepre, C.A., Gibbert, G.P., Chazin, W.J., Case, D.A. and Wright, P.E. (1991) J. Mol. Biol., 221, 533–555.
Neri, D., Billeter, M. and Wüthrich, K. (1992) J. Mol. Biol., 223,743–767.
Ryckaert, J.-P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comput. Phys., 23, 327–341.
Scott, W.R.P., Hünenberger, P.H., Tironi, I.G., Mark, A.E., Billeter, S.R., Fennen, J., Torda, A.E., Huber, T., Krüger, P. and van Gunsteren, W.F. (1999) J. Phys. Chem., A103, 3596–607.
Smith, L.J., Dobson, C.M. and van Gunsteren, W.F. (1999) Proteins, 36, 77–86.
Smith, L.J., Mark, A.E., Dobson, C.M. and van Gunsteren W.F. (1995) Biochemistry, 34, 10918–10931.
Smith, L.J., Sutcliffe, M.J., Redfield, C. and Dobson, C.M. (1991) Biochemistry, 30, 986–996.
Smith, L.J., Sutcliffe, M.J., Redfield, C. and Dobson, C.M. (1993) J. Mol. Biol., 229, 930–944.
Smith, P.E. and van Gunsteren, W.F. (1994) J. Chem. Phys., 100, 3169–3174.
Tironi, I.G., Sperb, R., Smith, P.E. and van Gunsteren, W.F. (1995) J. Chem, Phys., 102, 5451–5459.
van Gunsteren, W.F. and Berendsen, H.J.C. (1984) J. Mol. Biol., 176, 559–564.
van Gunsteren, W.F. and Berendsen, H.J.C. (1990) Angew. Chem. Int. Ed. Engl., 29, 992–1023.
van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P. and Tironi, I.G. (1996) Vdf Hochschulverlag, Zürich, Switzerland.
Yang, F., Bewley, C.A., Louis, J.M., Gustafson, K.R., Boyd, M.R., Gronenborn, A.M., Clore, G.M. and Wlodawer, A. (1999) J. Mol. Biol., 288, 403–412.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Stocker, U., Spiegel, K. & van Gunsteren, W. On the similarity of properties in solution or in the crystalline state: A molecular dynamics study of hen lysozyme. J Biomol NMR 18, 1–12 (2000). https://doi.org/10.1023/A:1008379605403
Issue Date:
DOI: https://doi.org/10.1023/A:1008379605403