Oligopeptides with a specific amino acid sequences have been observed to
aggregate in to large regular structures, forming tapes, ribbons (double
tapes) and fibrils consisting of several entwined ribbons. The molecule
comprises hydrophobic as well as charged amino acids, which should promote
aggregation with specific mutual orientation of the peptides.
Dimerisation as the first step in the macromolecular structure formation
is studied by “all atom detail” computer simulation techniques.
The dimer formation is determined by the free energy difference between two
lone peptides and the peptides forming a dimer. In case of large free energy
barriers separating the two states the probability of observing an event in a
simulation limited to nano seconds is, however, vanishingly small.
An extension to the molecular dynamics technique allows to tackle this
problem and provides at the same time a quantitative estimate of the free
energy of dimer formation. In the presentation the potential of mean force,
which reflects the effective interaction between two peptides will be
presented and the implications of its form for the dimerisation will be
discussed.
University College Dublin