Foldability and the funnel of HP-36 protein sequence: use of hydropathy scale in protein folding

Abstract

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 interand 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.