Thermodynamics and stability of a β‐sheet complex: Molecular dynamics simulations on simplified off‐lattice protein models

We have performed discontinuous molecular dynamics simulations of the thermodynamics and stability of a tetrameric beta-sheet complex that contains four identical four-stranded antiparallel beta-sheet peptides. The potential used in the simulation is a hybrid Go-type potential characterized by the bias gap parameter g, an artificial measure of the preference of a model protein for its native state, and the intermolecular contact parameter eta, which measures the ratio of intermolecular to intramolecular native attractions. Despite the simplicity of the model, a complex set of thermodynamic transitions for the beta-sheet complex is revealed that shows there are three distinct oligomer (partially ordered, ordered, and highly ordered beta-sheet complex) states and four noninteracting monomers phases. The thermodynamic properties of the three oligomer states strongly depend on both the size of the intermolecular contact parameter eta and the temperature. The partially ordered beta-sheet complex is made up of four ordered globules and is observed at intermediate to large eta at high temperatures. The ordered beta-sheet complex contains four native beta-sheets and is located at small to intermediate eta at low temperatures in the phase diagram. The highly ordered beta-sheet complex has fully-stiff beta-sheet strands, the same as the global energy minimum structure, and is observed for all eta at low temperatures.