Cysteine redox proteoforms by the numbers

Introduction

Online resource for the manuscript “Defining the vast theoretical cysteine redox proteoform space: A quantitative bioinformatic analysis of the human proteome”.

Data used in this document were retrieved from UniProt database for Humans and filtering for Reviewed entries only. Then, the protein accession entries and number of cysteine residues for each protein were derived programmatically using a custom Python script. More information on the database can be found on the associated manuscript.

First, load the data from github.

Load the custom helper functions from github to query the database and find the cysteine number for a given protein.

Please, enter the UniProtKB accession entry. Make sure to provide the correct number. An error could either mean that the protein number is not correct or that the protein doesn’t exist in the database.

Find the number of cysteine residues for the given protein.

Estimate the theoretical i space using Equation 1, where n is the redox space phase in binary form (oxidised and reduced) and R is the number of cysteine residues.

\[ i = n^R \]

References

Cobley, J. N. and Chatzinikolaou, P. N. Defining the vast theoretical cysteine redox proteoform space: A quantitative bioinformatic analysis of the human proteome. Under preparation, (2024).

Cobley, J. N. Oxiforms: Unique cysteine residue‐ and chemotype‐specified chemical combinations can produce functionally‐distinct proteoforms. Bioessays. 45, (2023).

Cobley, J. N. 50 shades of oxidative stress: A state-specific cysteine redox pattern hypothesis. Redox Biol. 67, 102936 (2023).