Foldability and funnel to HP-36 protein sequence: Use of hydropathy scale in protein folding

摘要

Brownian dynamics simulation study of the folding of a model thermostable chicken villin head piece subdomain, a 36-residue protein (HP-36), is carried out using the hydropathy scale of amino acids. The diverse interactions among the amino acid residues are categorized into three classes by introducing a simplified hydrophobic scale. The simulations incorporate all the six different inter-and intraamino acid interactions. The model protein reproduces some of the qualitative features of the complex protein folding, including the funnel-like energy landscape. Although there are several states near the minimum of the folding funnel, we could identify a stable native configuration. In addition, the study reveals a correlation between the contact order, topology, and the stability.