Modeling self-assembling of proteins: Assembled structures, relaxation dynamics, and phase coexistence

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A string-of-beads model used previously to describe folding of a polypeptide into a β-barrel is transformed into four-strand model of a self-assembling system, which also produces a β-barrel. In molecular dynamics (MD) simulations, both isothermal and variable-temperature (annealing), the system behaves much like a typical small cluster, insofar as it exhibits the dynamic coexistence of several phase-like forms over ranges of temperature. A three-state analytic model, then a four-state model, supplemented by degeneracies inferred from the MD simulations, yield partition functions and phase diagrams that reproduce the simulations rather well.