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

A string-of-beads model used previously to describe folding of a polypeptide into a beta-barrel is transformed into four-strand model of a self-assembling system, which also produces a beta-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. (C) 1999 American Institute of Physics. [S0021-9606(99)70104-2].