Quantifying oxidative folding

Proteins are involved in almost every known biological process. Their immensely diverse pool of functionalities is largely determined by their amino acid sequence, their three-dimensional structure and by additional modifications known as post translational modifications (PTMs). One of these PTMs is the disulfide bond (DSB) which can be formed between two cysteine amino acids via covalent bonding of two sulfur atoms. DSBs can be found in many important proteins such as antibodies and the processes involved in their formation have been intensely studied for decades. During this time, many - mostly qualitative - aspects of their formation and prevalence have been researched. The research described in this thesis combine parts of this immense existing knowledge and elevate our understanding of the quantitative aspects of DSB formation. The thesis introduction summarises much of this existing knowledge and current research trends are further outlined in a published review. In Chapter 1 the quantitative formation of DSBs in Escherichia coli has been modelled in order to describe and predict both host proteome and recombinant protein DSB formation. Chapter 2 expands our understanding of the DSB forming machinery in the important recombinant protein production host Komagataella phaffii (syn. Pichia pastoris). In the final Chapter, protein structure predictions by AlphaFold are used for predicting both qualitative and quantitative DSB levels in several model organisms.