Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks

TL;DR

This paper investigates how proteins fold on complex, rugged energy landscapes by modeling the process as diffusion on fractal networks, revealing scaling laws and the importance of network fractal properties for reliable folding.

Contribution

It introduces a novel network-based approach to analyze protein folding on rugged landscapes, linking fractal network properties to folding dynamics.

Findings

Folding times scale with network size and connectivity.

First-passage networks exhibit power-law relationships.

Small fractal dimension enables reliable folding.

Abstract

We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to basins and transitions between them in the energy landscape. We find power-laws between the folding time and number of nodes and bonds. We show that these scalings are determined by the fractal properties of first-passage networks. Reliable folding is possible in systems with rugged energy landscapes because first passage networks have small fractal dimension.