The research in Thomas J.D. Jørgensen’s group is focussed on protein structural dynamics determined by mass spectrometry and amide hydrogen (1H/2H) exchange. Protein function is intimately linked to the dynamic nature of protein structure. A well-known example is enzymatic activity and its allosteric regulation which involve an ensemble of interconverting conformations. Protein dysfunction is, however, also linked to protein dynamics. Several diseases are now recognized as protein conformational diseases, where mutations or environmental factors cause the affected protein to adopt unfolded or misfolded conformations that often lead to protein aggregation and disease (e.g., Parkinson’s disease). To achieve a fundamental understanding of the function and dysfunction of proteins at the molecular level, it is thus crucial to obtain a detailed knowledge about their dynamic and structural properties. The kinetics of backbone amide hydrogen exchange is intimately linked to the structural dynamics of the protein and we utilize mass spectrometry in combination with isotopic exchange to monitor the exchange kinetics of these hydrogens. The basis of this methodology is that amide hydrogens that participate in stable hydrogen bonds are protected against isotopic exchange with the solvent (i.e., D2O). Thus, backbone amide hydrogens in a natively folded protein exchange slowly, if they are part of a stable hydrogen-bonded structure, whereas those located within unstructured or very flexible regions exchange fast having subsecond half lives. The amide hydrogens located within the interface of a protein complex are also protected against isotopic exchange. We exploit this phenomenon to study binding epitopes and the dynamics of protein-protein interactions.
Business PhD Daniel Weltz Pedersen