Large-scale analysis of redox-sensitive conditionally disordered protein regions reveal their widespread nature and key roles in high-level eukaryotic processes

Gábor Erdos; Bálint Mészáros; Dana Reichmann; Zsuzsanna Dosztányi

For the prediction of redox-regulated conditionally disordered segments a slightly modified version of the IUPred2a method was used. The basic principle is the same as published [21] . We generate two prediction profiles with the default settings of the IUPred method, one for the native sequence corresponding to the state achieved through cysteine stabilization (redox-plus) and one calculated for a modified sequence with cysteines residues mutated to serine, corresponding to the state without cysteine stabilization (redox-minus). To initiate a redoxsensitive conditionally disordered region, the difference between the two profiles has to be larger than 0.3, while the minus profile is below 0.5 and the plus profile is above this threshold at a given position. This region is then extended until the difference between the two profiles becomes lower than 0.15, or the redox plus profile falls below 0.35. Two adjacent regions are combined if they are closer than 10 amino acids. Two minor modifications were introduced compared to the original web server implementation, aimed at decreasing potential overprediction of such regions. First, a predicted redox-sensitive conditionally disordered region must have at least 3 residues that meets the opening criterion. Second, the minimal length of the predicted region must be at least 15 residues. The current version of the program is available at: http://gerdos.web.elte.hu/data/iupred_redox_2.0.tar.gz