Graph-representation of oxidative folding pathways

Agoston, Vilmos, Cemazar, Masa, Kajan, Laszlo and Pongor, Sandor (2005) Graph-representation of oxidative folding pathways. Bmc Bioinformatics, 6 19.1-19.7. doi:10.1186/1471-2105-6-19


Author Agoston, Vilmos
Cemazar, Masa
Kajan, Laszlo
Pongor, Sandor
Title Graph-representation of oxidative folding pathways
Journal name Bmc Bioinformatics   Check publisher's open access policy
ISSN 1471-2105
Publication date 2005
Sub-type Article (original research)
DOI 10.1186/1471-2105-6-19
Open Access Status DOI
Volume 6
Start page 19.1
End page 19.7
Total pages 7
Place of publication London, United Kingdom
Publisher Biomed Central
Language eng
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/ can be obtained from V. A.
Keyword Biochemical Research Methods
Biotechnology & Applied Microbiology
Growth-factor-i
Colony-stimulating Factor
Transition-state
Secondary Structure
Complex Networks
Proteins
Bpti
Residues
Q-Index Code C1
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Institute for Molecular Bioscience - Publications
 
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Created: Fri, 25 Jan 2008, 16:28:17 EST