Monte carlo studies on equilibrium globular protein folding. II. β‐barrel globular protein models

Abstract

In the context of dynamic Monte Carlo simulations on a model protein confined to a tetrahedral lattice, the interplay of protein size and tertiary structure, and the requirements for an all‐or‐none transition to a unique native state, are investigated. Small model proteins having a primary sequence consisting of a central bend neutral region flanked by two tails having an alternating hydrophobic/hydrophilic pattern of residues are seen to undergo a continuous transition to a β‐hairpin collapsed state. On increasing the length of the tails, the β‐hairpin structural motif is found to be in equilibrium with a four‐member β‐barrel. Further increase of the tail length results in the shift of the structural equilibrium to the four‐member β‐barrel. The random coil to β‐barrel transition is of an all‐or‐none character, but while the central turn is always the desired native bend, the location of the turns involving the two external strands is variable. That is, β‐barrels having the external stands that are two residues out of register are also observed in the transition region. Introduction into the primary sequence of two additional regions that are at the very least neutral toward turn formation produces an all‐or‐none transition to the unique, native, four‐member β‐barrel. Various factors that can augment the stability of the native conformation are explored. Overall, these folding simulations strongly indicate that the general rules of globular protein folding are rather robust—namely, one requires a general pattern of hydrophobic/hydrophilic residues that allow the protein to have a welldefined interior and exterior and the presence of regions in the amino acid sequence that at the very least are locally indifferent to turn formation. Since no site‐specific interactions between hydrophobic and hydrophilic residues are required to produce a unique four‐member β‐barrel, these simulations strongly suggest that site specificity is involved in structural fine‐tuning.