Summary
The structure of the ColE1 repressor of primer (rop) protein in solution was determined from the proton nuclear magnetic resonance data by a combined use of distance geometry and restrained molecular dynamics calculations. A set of structures was determined with low internal energy and virtually no violations of the experimental distance restraints. Rop forms homodimers: Two helical hairpins are arranged as an antiparallel four helix bundle with a left-handed rope-like twist of the helix axes and with left-handed bundle topology. The very compact packing of the side chains in the helix interfaces of the rop coiled-coil structure may well account for its high stability. Overall, the solution structure is highly similar to the recently determined X-ray structure (Banner, D.W., Kokkinidis, M. and Tsernoglou, D. (1987)J. Mol. Biol.,196, 657–675), although there are minor differences in regions where packing forces appear to influence the crystal structure.
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Abbreviations
- rop:
-
repressor of primer
- NMR:
-
nuclear magnetic resonance
- NOE:
-
nuclear Overhauser enhancement
- NOESY:
-
NOE spectroscopy
- RAN Set:
-
Structures generated from random choice of the dihedrai angles
- HEL Set:
-
Structures generated from random choice of the dihedral angles restricted to ranges allowed for helices
- MD:
-
molecular dynamics
- EM:
-
energy minimization
- RMSD:
-
root-mean-square deviation of atomic positions
References
Banner, D.W., Cesareni, G. and Tsernoglou, D. (1983)J. Mol. Biol.,170, 1059–1060.
Banner, D.W., Kokkinidis, M. and Tsernoglou, D. (1987)J. Mol. Biol.,196, 657–675.
Braun, W. and Go, N. (1985)J. Mol. Biol.,186, 611–626.
Brünger, A.T. (1987) In ‘Methods and Applications in Crystallographic Computing’ (Ed, Isaacs, N.), Oxford Press, Oxford.
Castagnoli, L., Scarpa, M., Kokkinidis, M., Banner, D.W., Tsernoglou, D. and Cesareni, G. (1989)EMBO J.,8, 621–629.
Cesareni, G. and Banner, D.W. (1985)Trends Biochem. Sci.,10, 303–306.
Chotia, C. and Lesk, A. (1986)EMBO J.,5, 823–826.
Cohen, C. and Parry, D.A.D. (1986)TIBS,11, 245–248.
Eberle, W., Klaus, W., Cesareni, G., Sander, C. and Rösch, P. (1990)Biochemistry,29, 7402–7407.
Emery, S.C., Blöcker, H., Cesareni, G., Kingswell, A. and Sander, C. (1990)Protein Eng., in press.
Eijsink, V.G.H., Vriend, G., van den Burg, B., Venema, G. and Stulp, B.K. (1990)Protein Eng., in press.
Ho, S.P. and DeGrado, W.F. (1987)J. Am. Chem. Soc.,109, 6751–6758.
Kabsch, W. (1976)Acta Cryst.,A32, 922.
Kabsch, W. and Sander, C. (1983)Biopolymers,22, 2577–2637.
Lesk, A.M. and Chothia, C. (1980)J. Mol. Biol. 136, 225–270.
Markley, J.L., Croll, D.H., Krishnamoorthi, R., Ortiz-Polo, G., Westler, W.M., Bogard, W.C., Jr. and Laskowski, M., Jr. (1986)J. Cell Biochem.,30, 291–309.
Nilges, M., Gronenborn, A.M., Brünger, A.G. and Clore, M.G. (1988)Protein Eng.,2, 27–38.
Petsko, G. and Ringe, D. (1984)Ann. Rev. Bioeng.,13, 331–371.
Presnell, S.R. and Cohen, F.E. (1989)Proc. Natl. Acad. Sci. USA,86, 6592–6596.
Sander, C. (Ed) (1987)EMBL BIOcomputing Technical Document 1.
Schlichting, I., John, J., Frech, M., Chardin, P., Wittinghofer, P., Zimmermann, H. and Roesch, P. (1990)Biochemistry,29, 504–511.
Twigg, A.J. and Sherratt, D.J. (1980)Nature,283, 216–218.
Wagner, G., Braun, W., Havel, T.F., Schaumann, T., Go, N. and Wüthrich, K. (1987)J. Mol. Biol.,196, 611–639.
Weber, P.C. and Salemme, F.R. (1980)Nature,287, 82–84.
Wüthrich, K., Billeter, M. and Braun, W. (1983)J. Mol. Biol.,169, 946–961.
Wüthrich, K. (1986)NMR of Proteins and Nucleic Acids, Wiley, New York, NY.
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Eberle, W., Pastore, A., Sander, C. et al. The structure of ColE1 rop in solution. J Biomol NMR 1, 71–82 (1991). https://doi.org/10.1007/BF01874570
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DOI: https://doi.org/10.1007/BF01874570