Optimized Folding Simulations of Protein A

TL;DR

This paper presents optimized parallel tempering simulations of protein A's B-fragment, achieving native-like structures but with limited frequency at biological temperatures, highlighting potential energy function issues.

Contribution

It introduces optimized simulation techniques for protein folding and discusses limitations in current energy models.

Findings

Native-like configurations found with ~3Å RMSD

Conformations occur at ~10% frequency at relevant temperatures

Potential shortcomings in the energy function are discussed

Abstract

We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of approximately 3A to the experimentally determined structure (Protein Data Bank identifier 1BDD) are found. However, at biologically relevant temperatures such conformations appear with only about 10% frequency in our simulations. Possible short comings in our energy function are discussed.