Metalloenzymes catalyze the challenging chemical reactions that lie at the core of vital life processes, from carbon and nitrogen fixation to photosynthesis and respiration. Native metalloenzymes use only earth-abundant transition metals and operate under mild conditions, accessing reactivity that remains largely out of reach for synthetic systems. This is often attributed to the “complexity” of a protein scaffold. To elucidate the many components of an enzyme that are responsible for its reactivity, we have sought to recapitulate the structure, function, and mechanism of natural metalloenzymes within protein-based scaffolds. By designing an enzyme system from the “inside out”, each contribution can be clearly delineated. In this presentation, I will discuss our efforts to develop and characterize a metalloprotein model of the nickel-iron hydrogenase enzyme, which is responsible for global hydrogen gas cycling. We constructed this enzyme model within a nickel-substituted rubredoxin scaffold, which allows us to mimic the active site coordination environment. Targeted mutations in the primary sphere reveal key electronic components necessary for catalytic activity. Biological and paramagnetic NMR spectroscopy provide insight into secondary sphere dynamics and the role of local loop motion on activity, and the importance of global protein flexibility was established through studies of protein variants from diverse microbial sources. By combining functional studies of our model proteins with diverse spectroscopic techniques and computational investigations, we can obtain a comprehensive understanding of how the entire protein contributes to reactivity. These fundamental structure-function-dynamics relationships will be discussed in the context of understanding native metalloenzymes and providing design guidelines for new biological and anthropogenic catalyst development.