We present simulation results for peptide dimers, trimers, and tetramers using the multicanonical simulation algorithms Replica Exchange Statistical Temperature Molecular Dynamics and Generalized Replica Exchange. These algorithms use biased dynamics to overcome sampling problems related to broken ergodicity at low temperatures. Changes in the Potential Energy Surface of the system as it grows from a single molecule to a small oligomer are discussed. We show for dimers that, at low temperatures, both peptides are helical; at high temperatures, both peptides are random coils; and at intermediate temperatures, one peptide is folded while the other adopts an extended configuration that minimizes the solvent exposed surface area. Dimerization causes one peptide to become more stable and fold at a higher temperature than an isolated monomer while the other peptide becomes less stable and folds at a lower temperature than an isolated monomer. A similar stability effect is discussed for larger aggregates.

Multicanonical molecular dynamics simulations of low-molecular weight peptide oligomers

244th National Meeting (2012)

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