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

Srinivas, Goundla and Bagchi, Biman (2002) Foldability and the funnel of HP-36 protein sequence: Use of hydropathy scale in protein folding. In: Journal of Chemical Physics, 116 (19). pp. 8579-87.

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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.

Item Type:	Journal Article
Publication:	Journal of Chemical Physics
Publisher:	American Institute of Physics (AIP)
Additional Information:	The DOI is currently only displayed. Copyright for this article belongs to American Institute of Physics (AIP)
Department/Centre:	Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	08 Jun 2004
Last Modified:	19 Sep 2010 04:12
URI:	http://eprints.iisc.ac.in/id/eprint/205

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