An effective all-atom potential for proteins

TL;DR

This paper introduces a new all-atom potential for protein simulations that accurately models folding and aggregation, enabling efficient exploration of complex free-energy landscapes with modest computational resources.

Contribution

It presents a novel implicit solvent all-atom potential validated across diverse peptides and proteins, demonstrating high accuracy and computational efficiency.

Findings

Accurately models structural and thermodynamic properties of peptides.

Successfully applied to various protein systems with good results.

Enables detailed free-energy landscape studies with modest resources.

Abstract

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49--67-residue systems with high statistical accuracy, using only modest computational resources by today's standards.