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Two-state cooperativity is an important characteristic in protein folding. Itis defined by a depletion of states lying energetically between folded andunfolded conformations. While there are different ways to test for two-statecooperativity, most of them probe indirect proxies of this depletion. Yet,generalized-ensemble computer simulations allow to unambiguously identify thistransition by a microcanonical analysis on the basis of the density of states.Here we perform a detailed characterization of several helical peptides usingcoarse-grained simulations. The level of resolution of the coarse-grained modelallows to study realistic structures ranging from small alpha-helices to a denovo three-helix bundle - without biasing the force field toward the nativestate of the protein. Linking thermodynamic and structural features shows thatwhile short alpha-helices exhibit two-state cooperativity, the type oftransition changes for longer chain lengths because the chain forms multiplehelix nucleation sites, stabilizing a significant population of intermediatestates. The helix bundle exhibits the signs of two-state cooperativity owing tofavorable helix-helix interactions, as predicted from theoretical models. Thedetailed analysis of secondary and tertiary structure formation fits well intothe framework of several folding mechanisms and confirms features observed sofar only in lattice models.

Structural Basis of Folding Cooperativity in Model Proteins: Insights from a Microcanonical Perspective