PhD ceremony Ms. N.A. Oktaviani: NMR studies of folded and unfolded proteins: method developments and biological insight

PhD ceremony: Ms. N.A. Oktaviani

Dissertation: NMR studies of folded and unfolded proteins: method developments and biological insight

Promotor(s): prof. S.J. Marrink

Faculty: Mathematics and Natural Sciences

Proteins are ubiquitous in every living organism, and perform various biological functions. NMR spectroscopy is the most suitable technique to obtain comprehensive information about structure, dynamics, and electrostatics in proteins in solution, as well as protein-protein interactions. This information is essential for a comprehensive understanding of biological mechanisms at atomic detail.

In this dissertation, biological insight about a folded protein (i.e. photoactive yellow protein (PYP)) as well as soluble unfolded amyloid-beta (Abeta peptides was obtained using NMR spectroscopy. For PYP, a comprehensive sidechain pKa determination was performed to obtain an understanding of the electrostatic interactions between charged groups, particularly within the active site. Second, the conformations of soluble covalent Abeta dimers were investigated using NMR spectroscopy along with various other biophysical techniques, to obtain detailed insight into the basic building blocks of Alzheimer's Disease-related synaptotoxic species.

Two NMR methodologies were developed together with this research:

(1) A new approach to determine tyrosine sidechain pKa values in folded proteins; and

(2) A simple and tunable way to speed up the NMR measurement of intrinsically disordered proteins using co-solute paramagnetic relaxation enhancement (PRE).

The research presented in this dissertation can hopefully be beneficial not only for researchers involved in these subjects, but also to a wider NMR community.