A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilities and limitations.
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 alpha-helices for peptide B.
Piñeiro
Angel
A
Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands.
Villa
Alessandra
A
Vagt
Toni
T
Koksch
Beate
B
Mark
Alan E
AE
D001665:Binding Sites; D003198:Computer Simulation; D019281:Dimerization; D004355:Drug Stability; D004745:Enkephalins / Q000032:analysis / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000032:analysis / Q000737:chemistry / Q000648:ultrastructure; D011485:Protein Binding; D011487:Protein Conformation; D011498:Protein Precursors / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure; D017433:Protein Structure, Secondary
D004745:Enkephalins; D046912:Multiprotein Complexes; D011498:Protein Precursors; C056943:peptide B; C039933:peptide E (adrenal medulla)