NMR spectroscopy of proteins - computational and experimental studies

Abstract

Nuclear magnetic resonance (NMR) spectroscopy is a powerful research technique widely used for establishing three-dimensional structures, dynamic properties and intermolecular interactions of proteins. Its non-destructiveness, high information content and applicability for a broad range of samples, both in solution and in the solid state, renders it one of the best tools in the modern structural biology. Liquid-state NMR spectroscopy, however, also has some drawbacks, such as relatively low inherent sensitivity, complexity of the resultant spectra, high time demands and poor suitability for the analysis of large biomolecular complexes and membrane proteins. Due to the variety of aspects that might be improved and optimised, it's been a target of constant development for the last few decades and still is a primary focus of modern biochemical science. The goal of my PhD projects was to understand and improve several aspects and techniques of liquid-state protein NMR spectroscopy, employing both computational and experimental analysis. In the present thesis, I describe the results of my work on a wide variety of topics. The first project is devoted to optimisations of experiments suffering from the radiation damping effect. The second project is a computational analysis aimed at investigations of the applicability of mobile lanthanide-binding tags in protein-ligand interaction studies. The third project is an investigation of the structure and functions of single-stranded DNA-binding protein (SSB) using solution NMR, targeted at the elucidation of the mechanism by which the protein plays its role in the metabolism of single-stranded DNA.