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

TL;DR

This study uses microcanonical analysis of coarse-grained simulations to investigate folding cooperativity in model proteins, revealing how chain length influences the transition type and confirming theoretical folding mechanisms.

Contribution

It provides a detailed microcanonical perspective on protein folding, demonstrating how chain length affects cooperativity and intermediate states in realistic peptide models.

Findings

Short alpha-helices show two-state cooperativity.

Longer chains form multiple nucleation sites, reducing cooperativity.

Helix bundles exhibit two-state behavior due to helix-helix interactions.

Abstract

Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state cooperativity, most of them probe indirect proxies of this depletion. Yet, generalized-ensemble computer simulations allow to unambiguously identify this transition by a microcanonical analysis on the basis of the density of states. Here we perform a detailed characterization of several helical peptides using coarse-grained simulations. The level of resolution of the coarse-grained model allows to study realistic structures ranging from small alpha-helices to a de novo three-helix bundle - without biasing the force field toward the native state of the protein. Linking thermodynamic and structural features shows that while short alpha-helices exhibit two-state cooperativity, the type of transition changes for longer chain lengths because the chain forms multiple helix nucleation sites, stabilizing a significant population of intermediate states. The helix bundle exhibits the signs of two-state cooperativity owing to favorable helix-helix interactions, as predicted from theoretical models. The detailed analysis of secondary and tertiary structure formation fits well into the framework of several folding mechanisms and confirms features observed so far only in lattice models.