Folding a protein with equal probability of being helix or hairpin

TL;DR

This study demonstrates that certain small proteins can have nearly degenerate native states, such as helix and hairpin, stabilized by subtle interaction balances, using an ab initio coarse-grained model and free energy landscape analysis.

Contribution

It reveals the existence of nearly degenerate native conformations in small proteins and analyzes the energetic factors stabilizing these states using the Wang-Landau algorithm.

Findings

Two native states with less than 2% energy difference identified.

Degenerate states stabilized by ~10 kcal/mol energy barrier.

Degeneracy occurs in proteins around 18-40 amino acids.

Abstract

We explore the possibility for the native state of a protein being inherently a multi-conformation state in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2D4X: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native states: one has a helix structure, while the other has a hairpin structure and their energy difference is less than 2% of that of local minimums. Two degenerate native states are stabilized by an energy barrier of the order 10kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that degenerate native states are stabilized by subtle balance between different interactions in proteins; furthermore, for small proteins, degeneracy only happens for proteins of sizes being around 18 amino acids or 40 amino acids. These results provide important clues to the study of native structures of proteins.