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

Using redox proteomics studies, the cellular redox state has thus far been revealed to either directly or indirectly affect a wide range of physiological processes in the cell. However, proteomics studies provide no information about the underlying mechanisms of thiol modifications, nor to what degree the detected thiol modifications correspond to redox-regulated conditional disorder. In order to explore this aspect of redox regulation, we took advantage of a recently introduced new feature of the IUPred method (IUPred2A) that enables the sequence based prediction of regions that are likely to undergo disorder-to-order transitions upon redox changes [21] . IUPred is a robust sequence-based prediction method for protein disorder that uses an energy estimation method [22] . The strength of the method originates from its ability to capture the basic biophysical properties of disordered segments: their inability to form enough stabilizing interactions to adopt a well-defined globular structure. The core of the method is a statistical potential that assigns more favorable scores to amino acid pairs that are observed more frequently in the proximity of each other within the structure of globular proteins, as compared to a background model. In this regard, cysteine residues clearly stand out, as they often form covalent contacts with other cysteines, thus providing large stabilizing contributions either by forming disulfide bridges or coordinating Zn 2+ and other metal ions. Consequently, the cysteine residues have a strong order promoting character in IUPred. However, thiol modifications of either paired or single cysteine residues may lead to a reversible order-todisorder transformation, exposing unfolded regions crucial for protein function [6, 7] . This regulatory effect of redox conditions on protein structure not only follows the presence of oxidation sensitive cysteine residues, but is also influenced by the presence of disorderpromoting residues in the surrounding sequence. In such cases, cysteine residues may simply be considered small, polar residues akin to serine, located within a sequence region exhibiting distinct features. The prediction of redox-sensitive disordered regions is based on capturing this dual characteristics of cysteines. This novel method opens new doors to explore redox-sensitive conditionally disordered segments in various proteomes.