| Protein folding is a physico-chemical process by which polypeptide chains attain their native 3D structures. Understanding of the mechanisms of protein folding informs the search for a cure to protein misfolding diseases, e.g., Alzheimer's and Parkinson's. The need for these cures is unquestionable: Alzheimer's, for instance, is predicted to affect 1 out of 85 people by 2050 and is considered the most costly disease, accounting for ca. ;For many decades protein folding was studied in the test tube on isolated protein samples where many physiologically relevant components and conditions were ignored, for simplicity. This dissertation attempts to understand how one of such components, the ribosome, modifies the protein folding process. The ribosome is a protein-synthesizing machinery, a mega-dalton macromolecular complex consisting of proteins and large RNAs. The process of protein synthesis is known as translation and is highly directional, i.e., each protein is synthesized from the N- to C-termini. The folding of a growing protein chain starts on the ribosome and is a ubiquitous process in all organisms.;In order to understand the details of protein folding on the ribosome, this dissertation tackles two main questions: 1) how the interactions between N- and C-termini affect the secondary structure of the N-terminus, and 2) how to study protein folding in the presence of the ribosome.;I found that specific long-range interactions between N- and C-termini induce some secondary structure in unfolded apomyoglobin. This finding informs studies of protein folding on the ribosome where the C-terminus is buried inside the ribosome and the N-terminus is solvent-exposed. Additionally, I found that the electrostatic surface of ribosomes from ten different organisms across all domains of life is highly negatively charged due to both solvent-exposed ribosomal RNA and negatively charged sides of ribosomal proteins. I discovered the ubiquitous property of ribosomal proteins - charge segregation exhibited on their surfaces. Taken together, two above-mentioned discoveries of this dissertation advance the studies of protein folding on the ribosome and, specifically, aid in the choice of suitable ribosome-bound nascent chains for further future studies. |
