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Open Access Methodology article

Graph-representation of oxidative folding pathways

Vilmos Ágoston1, Masa Cemazar23, László Kaján2 and Sándor Pongor2*

Author Affiliations

1 Bioinformatics Group, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary

2 Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy

3 Institute for Molecular Bioscience, University of Queensland, St. Lucia 4072, QLD, Australia

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BMC Bioinformatics 2005, 6:19  doi:10.1186/1471-2105-6-19

Published: 27 January 2005

Abstract

Background

The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS) which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations) that the given DIS can adopt in three dimensions.

Results

The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor), the observed intermediates appear as part of contiguous oxidative folding pathways.

Conclusions

Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ webcite can be obtained from V.A.