Optimized Folding Simulations of Protein A

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.