Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 11

Progress in Prediction of Oxidation States of Cysteines via Computational Approaches

AIGUO DU, HUI LIU, HAI DENG and YI PAN

11.1 Introduction

Cysteine is one of the few amino acids that contain sulfur. The free thiol group allows it to bond with another cysteiene residue to form disulfide bond and help maintain the structure of proteins. The thiol group on cysteine residues is nucleophilic and easily oxidized. Because of this reactivity, cysteine residues serve numerous biological functions such as activation of certain biological activities [1], DNA binding [2], and reproductive systems [3] as well as the aging process of proteins [4]. As was shown in Figure 11.1, cysteine residues can be found in two chemical states in proteins: oxidized state and reduced state. The two states are interchangeable when proper conditions are met. When in reduced form, cysteine undergoes chemical reactions such as alkylation [5, 6], oxidation [7], or forming complex compounds with metal ions [8]. These chemical reactions play critical biological roles such as activation, deactivation of the active sites of enzymes, and altering the local environment of the proteins. In their oxidized form, two cysteine residues form disulfide bond and enable more complicated protein structures [9, 10] and functions [11, 12].

Figure 11.1 Reduced form (a) and oxidized form (b) of cysteine residues (twoStates.png).

The disulfide bond is the covalent bond formed between two cysteine residues on protein ...