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A Molecular Dynamics Study of the Formation, Stability, and Oligomerization State of Two Designed Coiled Coils: Possibilities and Limitations

Ángel Piñeiro ^*, Alessandra Villa ^*, Toni Vagt , Beate Koksch  and Alan E. Mark ^*

^* Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands; and Free University Berlin, Institute of Chemistry-Organic Chemistry, 14195 Berlin, Germany

Correspondence: Address reprint requests to Prof. Alan E. Mark, Dept. of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. Tel.: 31-50-3634457; Fax: 31-50-3634800; E-mail: a.e.mark{at}rug.nl.

The formation, relative stability, and possible stoichiometries of two (self-)complementary peptide sequences (B and E) designed to form either a parallel homodimeric (B + B) or an antiparallel heterodimeric (B + E) coiled coil have been investigated. Peptide B shows a characteristic coiled coil pattern in circular dichroism spectra at pH 7.4, whereas peptide E is apparently random coiled under these conditions. The peptides are complementary to each other, with peptide E forming a coiled coil when mixed with peptide B. Molecular dynamics simulations show that combinations of B + B and B + E readily form a dimeric coiled coil, whereas E + E does not fall in line with the experimental data. However, the simulations strongly suggest the preferred orientation of the helices in the homodimeric coiled coil is antiparallel, with interactions at the interface quite different to that of the idealized model. In addition, molecular dynamics simulations suggest equilibrium between dimers, trimers, and tetramers of -helices for peptide B.

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