Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.Author summary: Enzymatic function is often the result of a sequence of events, which include precisely synchronized electron, proton and substrate delivery, that goes beyond the mere chemistry at the active site. To achieve this level of sophistication, enzymes must exploit a network of long-range communication through which chemical events, such as the binding of an effector to an allosteric site, hydrolysis of ATP, or electrochemical activity at a given location, affect on the function of a remote site. The nitrogenase complex vividly exemplifies the hierarchical complexity of enzymes. Nitrogenase catalyzes the reduction of atmospheric dinitrogen to ammonia, whose activity is regulated by long-range mechanical coupling between distant parts of the complex. After decades since the first structure of the nitrogenase complex was solved, this coupling network is still unclear. We used a computationally inexpensive, yet accurate approach, which is based on graph theory, to elucidate how distant regions of the protein complex communicate with each other. In particular, our study provides valuable insights on how the two halves of nitrogenase communicate and what the most important regions for this communication are, laying out a strategy for future mechanistic studies.