The Earliest Stages of a Protein's Life Influence Its Long-term Solubility and Structural Accuracy
Author | : Matthew Dalphin |
Publisher | : |
Total Pages | : 426 |
Release | : 2020 |
Genre | : |
ISBN | : |
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Despite its fundamental importance for life, many details regarding how the cell promotes the solubility and structural accuracy of proteins remains poorly understood. This lack of knowledge poses serious challenges in basic science, biotechnology and medicine as the inability to prevent inclusion body formation limits the efficient overproduction of recombinant proteins and protein-based therapeutics. In this thesis, experimental and computational approaches were combined to explore factors that help discriminate folding and aggregation pathways at various stages of a protein's life in the cell. If folded properly, the native states of many proteins, including apomyoglobin and the soluble E. coli proteome, were shown to be kinetically-trapped from stable aggregate states under physiologically-relevant conditions. However, kinetic simulations suggest that this kinetic trapping can be circumvented at high protein concentrations and, importantly, in the presence of small pre-nucleated aggregate seeds capable of further elongation. In order to further explore how the intracellular environment further influences protein folding and aggregation, we developed a novel bacterial Hsp70 inhibitor which targets and inhibits DnaK. This inhibitor is functional in dilute buffer and cell-free systems. Importantly, it does not also inhibit nascent protein biosynthesis. Our novel inhibitor was then used to probe how the ribosome and DnaK coordinate co- and post-translational events which ultimately support proper protein folding. The ribosome was observed to act as a powerful facilitator of protein solubility during the earliest stages of translation and upon ribosome release. However, it requires additional help from molecular chaperones (e.g. DnaK) to ensure the soluble proteins produced are structurally accurate. Kinetic simulations further highlight that this chaperone requirement for proper folding increases for proteins which are slow to fold at the end of translation. This highlights the synergistic, yet distinct, roles of the ribosome and DnaK required to produce soluble, properly folded proteins which would otherwise be aggregation-prone on their own. Taken together, the work highlighted in this thesis sheds light on the unique mechanism by which the cell shapes, and ultimately traps, proteins into their native state during the earliest stages of protein life.