Welcome to RedoxDB!
Introduction to RedoxDB
Protein oxidative modification is common in both prokaryotic and eukaryotic organisms. Cysteine thiol groups of proteins are particularly susceptible to oxidation by ROS/RNS and other electrophilic molecules, and their reversible oxidation is of critical roles for redox regulation of proteins. They can be oxidized to several different products, including disulfide (S-S), sulfenic acid (S-OH), sulfinic acid (SO2H), sulfonic acid (SO3H), S-nitrosothiols (S-NO), or S-glutathione (S-SG). Protein oxidative modification has caught increasing attention in recent years. With the tremendous progress in the field of redox proteomics in the last decade, our knowledge about protein oxidative modification began to accumulate at the speed that has never been reached before.
RedoxDB is a manually curated database of experimentally verified protein oxidative modification. RedoxDB mainly consists of two types of data: dataset (A) includes redox proteins for which the modified Cys have been experimentally verified, and dataset (B) includes redox proteins that the modified Cys have not been determined yet. When searching or blasting RedoxDB, user can decide to included dataset(B) or not.
Text based literature search strategy is the major method to obtain a comprehensive list of experimentally verified protein oxidative modification data. The used keywords for collecting dataset (A) are listed in the table below. When collecting dataset (B), we removed "cysteine" from the keyword list, and mainly focus on proteomic data. Initially, we got about 6000 papers from PubMed. The abstract (and full text paper if necessary) for each literature is manually checked. If cysteine oxidative modification was reported, the protein sequence and cysteine residues undergo oxidative modification was manually curated and included in RedoxDB. Moreover, additional methods besides keyword searching are also used to obtain data about protein cysteine oxidative modification. For example, we also searched UniprotKB for protein oxidative modification, and the data are also included if experimental evidence is available.
|Modification||Keywords for dataset (A)|
|Reversible disulfide||(reversib* OR sensitiv* OR susceptib* OR ROS OR redox* OR oxidati* OR reduct*) AND cysteine* AND disulfide*|
|Sulfenic acid||sulfenic AND cysteine*|
|Sulfinic acid||sulfinic AND cysteine*|
|S-glutathionylation||glutathionylat* AND cysteine*|
|S-nitrosylation||nitrosylat* AND cysteine*|
- 1277 proteins with 2205 redox-sensitive Cys from 93 organisms .
Dataset B: (modified Cys not determined)
- 880 redox-sensitive proteins from 49 organisms.
Last updated: Oct 20, 2015
Ming-an Sun et al. RedoxDB - a curated database of experimentally verified protein redox modification. Bioinformatics, 28(19):2551-2552.