Delineation of the Native Basin in Continuum Models of Proteins

TL;DR

This paper introduces two novel methods for identifying native basins in off-lattice protein models, providing a new way to analyze folding landscapes and estimate folding temperatures.

Contribution

It presents two approaches for delineating native basins in protein models, one based on saddle point exploration and the other on shape distortions, with consistent results.

Findings

Both methods produce similar native basin delineations.

A simple technique for estimating folding temperature is introduced.

The approaches enhance understanding of protein folding landscapes.

Abstract

We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories emerging from the native state. In the second approach, the basin size can be determined by monitoring random distortions in the shape of the protein around the native state. Both techniques yield the similar results. As a byproduct, a simple method to determine the folding temperature is obtained.