Master's student: Barði Benediktsson
Title: QM/MM studies of molybdenum and vanadium nitrogenase
Faculty: Faculty of Physical Sciences
Advisor: Ragnar Björnsson and Egill Skúlason, Professor at the Faculty of Physical Sciences.
Examiner: Tobias Krämer, Lecturer at Maynooth University, Ireland
Nitrogen is incorporated in a plethora of biomolecules but is inaccessible to most life in the abundant dinitrogen form present in the atmosphere. Diazotrophs are a group of organisms that contain nitrogenase enzymes and are capable of pulling nitrogen out of thin air and catalyze it to ammonia. Within these nitrogenases are exotic metal clusters that perform the catalysis in an ATP dependent process. Despite decades of studies into these enzymes, crucial details such as the substrate binding site and method of catalysis is still unknown. Theoretical studies have attempted to resolve these problems, but most of them have not accounted for the protein environment. By using the QM/MM methodology, we modeled FeMoco of molybdenum nitrogenase and FeVco of vanadium nitrogenase within their respective protein environments and characterized their resting states with respect to overall charge, protonation state and electronic structure. We also studied a recent crystal structure of vanadium nitrogenase that contains a bridging ligand postulated to be NH derived from dinitrogen. Finally, we studied CO inhibited FeMoco to shed light on its mechanism of inhibition.