Abstract
The geometry and energy of parallel and antiparallel peptidic β-sheets have been calculated using AM1. β-Sheets composed of two peptide chains of up to 11 amino acid residues (Ala and Gly) and the dimers of cyclooctapeptides are used as model systems. The enthalpic difference between the parallel and the antiparallel arrangement is calculated to be very small, as it is found experimentally for the cyclic systems. The coordinates of the calculated structure of the cyclooctapeptide dimer 1 (cyclo-D,L-(Ala)8) have an rms deviation of only 0.223 Å to the coordinates of the corresponding cyclopeptide obtained by X-ray analysis.
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Creighton, T.E., Proteins – Structures and Molecular Principles, Freeman, New York, NY, U.S.A., 1984, p. 191.
Prusiner, S.B., Science, 216 (1982) 136. b. Prusiner, S.B., Science, 252 (1991) 1515. c. Prusiner, S.B., Collinge, J., Powell, J. and Anderton, B. (Eds.) Prion Diseases of Humans and Animals, Ellis Horwood, Chichester, U.K., 1992.
Vásquez, M., Némethy, G. and Sheraga, H.A., Chem. Rev., 94 (1994) 2183. b. Chou, K.-C., Némethy, G. and Sheraga, H.A., J. Mol. Biol., 168 (1983) 389. c. Chou, K.-C., Némethy, G. and Sheraga, H.A., Biochemistry, 22 (1983) 6213. d. Chou, K.-C., Némethy, G. and Sheraga, H.A., Acc. Chem. Res., 23 (1990) 134. e. Salemme, F.R. and Weatherford, D.W., J. Mol. Biol., 146 (1981) 101. f. Salemme, F.R. and Weatherford, D.W., J. Mol. Biol., 146 (1981) 119. g. Salemme, F.R., J. Mol. Biol., 146 (1981) 143. h. Salemme, F.R., Prog. Biophys. Mol. Biol., 42 (1983) 95.
Clark, T., Rauhut, G. and Chandrashekhar, J., VAMP 5.0, Erlangen, Germany.
Parameterization in accordance with Dewar, M.J.S., Zoebisch, E.G., Healy, E.F. and Stewart, J.J.P, J. Am. Chem. Soc., 107 (1985) 3902.
Ghadiri, M.R., Kobayashi, K., Granja, J.R., Chadha, R.K. and McRee, D.E., Angew. Chem., Int. Ed. Engl., 34 (1995) 93. b. Kobayashi, K., Granja, J.R. and Ghadiri, M.R., Angew. Chem., Int. Ed. Engl., 34 (1995) 95.
Sun, X. and Lorenzi, G.P., Helv. Chim. Acta, 77 (1994) 1520.
Hartgerink, J.D., Granja, J.R., Milligan, R.A. and Ghadiri, M.R., J. Am. Chem. Soc., 118 (1996) 43.
Stewart, J.J.P., MOPAC 6.0, QCPE Program No. 455, Indiana University, Bloomington, IN, U.S.A.
Sauer, W.B., Ph.D. Thesis, University of Erlangen, Erlangen, Germany, 1995.
Mohamadi, F., Richards, N.G.J., Guida, W.C., Liskamp, R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T. and Still, W.C., J. Comput. Chem., 11 (1990) 440.
Ghadiri, M.R., Granja, J.R. and Buehler, L., Nature, 369 (1994) 301. b. Granja, J.R. and Ghadiri, M.R., J. Am. Chem. Soc., 116 (1994) 10785.
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Gailer, C., Feigel, M. Is the parallel or antiparallel β-sheet more stable? A semiempirical study. J Comput Aided Mol Des 11, 273–277 (1997). https://doi.org/10.1023/A:1007908728919
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DOI: https://doi.org/10.1023/A:1007908728919