Computational investigation of thiol-based redox modifications in proteins: redox-active disulfides, Zn2+ sites and their associations

Thiol based redox signalling is an emerging area of research in protein science. Reversible disulfide bonding and Zn2+ expulsion are two important but less explored oxidative thiol modifications associated with redox signalling. They have numerous implications in health and disease. Three computational methods have previously been developed to predict redox-active disulfides in proteins: redox pair protein (RP) method, forbidden disulfides (FD) method and torsional energy (TE) method. These methods and other tools of bioinformatics are used in my study to investigate redox-active disulfides, Zn2+ sites and the association between FDs and Zn fingers in protein structures. The first objective of my study was to apply the RP method to predict novel proteins containing likely redox-active disulfides. Over 300 novel RP proteins were found during this study. Significant conformational changes associated with disulfide redox activity in RP protein structures were also identified. I accomplished another objective, to predict proteins with likely redox-active disulfides and thiols in M. tuberculosis and C. glutamicum by matching protein disulfide templates derived by the FD, RP and TE methods to the genomes of these organisms. Expulsion of Zn2+ from proteins following oxidation of ligating cysteine residues is an emerging area in oxidative stress response. Trends in the ligating residue combination patterns at redox-active and inert protein Zn2+ sites were successfully identified, to achieve the second objective of my study. The third objective was to identify specific types of FDs associated with Zn fingers. A novel type of FD motif called the anti-parallel hairpin-diagonal disulfide (aHDD) was discovered during the study. The presence of this motif and its variants in the structure is characteristic of different types of Zn fingers, suggesting a functional relationship. An aHDD motif based extension to a Zn finger classification system was also proposed in this study. I have also estimated around 81% of human Zn finger proteins to be associated with the aHDD motif, suggesting its likely importance in Zn2+ signalling. Finally, the above investigations are discussed and future directives are proposed to further enhance our knowledge of redox-active disulfides, Zn2+ sites and their associations in protein structures.