Substrate and reaction specificity are critical pressures upon the evolution of enzymes. While there are numerous extant strategies for achieving specificity, perhaps the most striking is the emergence of substrate tunnels: voids within the core of the protein that allow for specific molecules to traverse from site to site, without exposure to solvent. As these tunnels can extend up to tens of angstroms in length away from critical catalytic residues, there is often reduced conservation of tunnel-lining positions. This allows for enzyme-level adaptation to an organism’s environment through the evolution of a substrate tunnel’s composition. Here, we survey the relationships between the structure and dynamics of the CO2 access tunnel of various formylmethanofuran dehydrogenase (FMDH) genes from methanogenic archaea and their environments, particularly the availability of dissolved CO2.

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