Energy Landscape of a Model Protein

TL;DR

This paper analyzes the energy landscape of a model protein, revealing frustration effects that hinder folding and demonstrating how a simplified 'Go-type' model exhibits a more funnel-like energy surface conducive to folding.

Contribution

It provides a detailed characterization of the energy landscape of a model protein and compares it with a simplified 'Go-type' model to understand folding behavior.

Findings

The off-lattice model protein exhibits frustration and complex energy pathways.

The 'Go-type' model shows a funnel-shaped energy landscape.

Frustration impedes efficient folding in the model protein.

Abstract

The potential energy surface of an off-lattice model protein is characterized in detail by constructing a disconnectivity graph and by examining the organisation of pathways on the surface. The results clearly reveal the frustration exhibited by this system and explain why it does not fold efficiently to the global potential energy minimum. In contrast, when the frustration is removed by constructing a `Go-type' model, the resulting graph exhibits the characteristics expected for a folding funnel.