Unravelling structural motifs of intrinsically disordered proteins employing Raman optical activity: Understanding the basis of neurodegenerative diseases
23 November 2018
Campus Middelheim, G.010 - Middelheimlaan 1 - 2020 Antwerpen (route: UAntwerpen, Campus Middelheim
Organization / co-organization:
Department of Chemistry
Christian Johannessen & Patrick Bultinck
PhD defence Carl Mensch - Faculty of Science, Department of Chemistry
In the aging population of the Western World, age-related neurodegenerative diseases, such as Alzheimer's and Parkinson's, are becoming an ever-increasing issue. Common to these diseases are build-up of protein matter in the brain, leading to degeneration of brain tissue. The proteins responsible for this degeneration belong to a group of proteins usually found on the periphery of structural biology; the intrinsically disordered proteins (IDPs). Lacking the structural elements traditionally associated with function, IDPs were historically ignored by structural biologists as "non-functioning". In the modern age of proteomics, this group of proteins has indeed proven to be functional, but in connection with disease, it is the sudden malfunction of IDPs that is in focus. As this group of proteins lack classically defined structural elements and are highly dynamic, the usual structural characterisation tools fall short in the analysis of IDPs, and even our fundamental understanding of "structure" fails. It is therefore imperative to develop new tools, and to generate a new understanding of protein structure itself when analysing IDPs.
In this dissertation, different IDPs were therefore studied in detail using the advanced spectroscopic technique Raman optical activity (ROA) combined with cutting-edge computational chemistry. IDPs have characteristic ROA patterns that differ distinctly from the patterns of proteins with a well-defined three-dimensional structure. It was furthermore shown that different IDPs show small spectral differences among each other. These observations were demonstrated by studying different forms of α-synuclein; the protein that plays a central role in the pathogenesis of Parkinson’s disease. By using systematic computational approaches, the contributions of the different structural properties of proteins to the ROA patterns were scrutinized. Not only the contributions of the structural components such as the secondary structure, β-turns and side-chains where examined in detail, but furthermore the inherent flexibility and the aqueous environment were studied. General relations between the solution structure of a protein and its spectral components could be deduced, which showed that a few common spectral assignments in scientific literature were inaccurate and needed revision. Based on these new insights it was concluded that the ROA patterns of proteins arise from extensive averaging of specific structural components. The methodologies and databases that were developed will be of great relevance in the future development and application of ROA in (un)structural biology.