Abstract
The large concerted motions in the apo/holo bovine serum retinol- binding protein were studied using molecular dynamics simulation and 'essential dynamics' analysis. Initially, concerted motions were calculated from conformational differences between various crystal structures. The dynamic behaviour of the protein in the configurational space directions, described by these concerted motions, is analysed. This reveals that the large backbone dynamics of the protein is not influenced by the presence of retinol. Study of free retinol dynamics and retinol in the retinol binding site reveals that the protein binds retinol in a favourable conformation, as opposed to what has been previously described for the bovine cellular retinol-binding protein.
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Abrahamson, E.W. and Ostroy, S.E., (1981) Molecular Processes in Vision, Stroudsburg, Dowden, Hutchinson and Ross, Philadelphia, PA.
Berry, C. Virchows Archiv, 430 (1997) 267.
Goodman, D.S., New Engl. J. Med., 310 (1984) 1023.
Sivaprasadarao, A. and Findlay, J.B.C., Biochem. J., 300 (1994) 437.
Cowan, C.W., Newcomer, M.E. and Jones, T.A., J. Mol. Biol., 230 (1993) 442.
van Aalten, D.M.F., Findlay, J.B.C., Amadei, A. and Berendsen, H.J.C., Protein Eng., 8 (1996) 1129.
van Aalten, D.M.F., de Groot, B.L., Berendsen, H.J.C. and Findlay, J.B.C., Biochem. J., 319 (1996) 543.
Zanotti, G., Berni, R. and Monaco, H.L., J. Biol. Chem., 268 (1993) 10728.
Noy, N. and Xu, Z.J., Biochemistry, 29 (1990) 3888.
Åqvist, J., Sandblom, P., Jones, T.A., Newcomer, M.E., van Gunsteren, W.F. and Tapia, O., J. Mol. Biol., 192 (1986) 593.
Cowan, S.W., Newcomer, M.E. and Jones, T.A., Proteins Struct. Funct. Genet., 8 (1990) 44.
van Aalten, D.M.F., Conn, D.A., de Groot, B.L., Findlay, J.B.C., Berendsen, H.J.C. and Amadei, A., Biophys. J., 73 (1997) 2891.
Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C., Proteins Struct. Funct. Genet., 17 (1993) 412.
van Aalten, D.M.F., Amadei, A., Vriend, G., Linssen, A.B.M., Venema, G., Berendsen, H.J.C. and Eijsink, V.G.H., Proteins Struct. Funct. Genet., 22 (1995) 45.
de Groot, B.L., van Aalten, D.M.F., Scheek, R.M., Amadei, A., Vriend, G. and Berendsen, H.J.C., Proteins Struct. Funct. Genet., 29 (1997) 240.
Monaco, H.L., Rizzi, M. and Coda, A., Science, 268 (1995) 1039.
Zanotti, G., Ottonello, S., Berni, R. and Monaco, H.L., J. Mol. Biol., 230 (1993) 613.
Zanotti, G., Malpeli, G. and Berni, R., J. Biol. Chem., 268 (1993) 24873.
Zanotti, G., Marcello, M., Malpeli, G., Folli, C., Sartori, G. and Berni, R., J. Biol. Chem., 269 (1994) 29613.
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J. (1981) In Pulmann, B. (Ed.), Intermolecular Forces, Reidel, Dordrecht, p. 331.
Berendsen, H.J.C., Postma, J.P.M., DiNola, A. and Haak, J.R., J. Chem. Phys., 81 (1984) 3684.
Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C., J. Comp. Phys., 23 (1997) 327.
Vriend, G., J. Mol. Graphics, 8 (1990) 52.
Fischer, E., Ber. Deutschen Chem. Ges., 27 (1894) 2985.
Koshland, D.E., Proc. Natl. Acad. Sci. USA, 44 (1958) 98.
Gschwend, D.A., Good, A.C. and Kuntz, I.D., J. Mol. Recog., 9 (1996) 175.
Miller, D.W. and Dill, K.A., Protein Sci., 6 (1997) 2166.
Peters, G.H., Olsen, O.H., Svendsen, A. and Wade, R.C., Biophys. J., 71 (1996) 119.
Goodford, P.J., J. Med. Chem., 28 (1985) 849.
Gillett, V.J., Johnson, A.P., Mata, P. and Sike, S., Tetrahedron Comp. Methodol., 3 (1990) 681.
Moon, J.B. and Howe, W.J., Proteins Struct. Funct. Genet., 11 (1991) 314.
Lawrence, M.C. and Davis, P.C., Proteins Struct. Funct. Genet., 12 (1992) 31.
Harris, M.H., Kihlen, M. and Bywater, R.P., J. Mol. Recogn., 6 (1993) 111.
Böhm, H.J., J. Comput.-Aided Mol. Design, 6 (1992) 61.
Leach, A.R. and Kuntz, I.D., J. Comp. Chem., 13 (1992) 730.
Goodsell, D.S., Morris, G.M. and Olson, A.J., J. Mol. Recogn., 9 (1996) 1.
Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. and Kraut, J., J. Biol. Chem., 257 (1982) 3650.
Kern, P., Brunne, R.M. and Folkers, G., J. Comput.-Aided Mol. Design, 8 (1994) 367.
Rognan, D., Scapozza, L., Folkers, G. and Daser, A., Biochemistry, 33 (1994) 11476.
Grubmüller, H., Heymann, B. and Tavan, P., Science, 271 (1996) 997.
Lüdemann, S.K., Carugo, O. and Wade, R.C., J. Mol. Modelling, 3 (1997) 369.
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Chau, PL., van Aalten, D., Bywater, R. et al. Functional concerted motions in the bovine serum retinol-binding protein. J Comput Aided Mol Des 13, 11–20 (1999). https://doi.org/10.1023/A:1008099903676
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DOI: https://doi.org/10.1023/A:1008099903676