Graph-representation of oxidative folding pathways.
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.
Agoston
Vilmos
V
Bioinformatics Group, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary. vilagos@brc.hu
Cemazar
Masa
M
Kaján
László
L
Pongor
Sándor
S
D000818:Animals; D007611:Aprotinin / Q000737:chemistry; D002417:Cattle; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003461:Crystallography; D004220:Disulfides / Q000737:chemistry; D004815:Epidermal Growth Factor / Q000737:chemistry; D020407:Internet; D008958:Models, Molecular; D015233:Models, Statistical; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013002:Somatomedins / Q000737:chemistry; D013438:Sulfhydryl Compounds; D014361:Trypsin Inhibitors / Q000737:chemistry
D004220:Disulfides; D010455:Peptides; D011506:Proteins; D013002:Somatomedins; D013438:Sulfhydryl Compounds; D014361:Trypsin Inhibitors; D004815:Epidermal Growth Factor; D007611:Aprotinin; D010100:Oxygen