Investigating the Many Roles of Internal Water in Cytochrome c Oxidase
In a recent publication (Farahvash and Stuchebrukhov, The Journal of Physical Chemistry: B, 2018) the Stuchebrukhov Lab use Dowser++ (a protein hydration program designed by the group) to illustrate that the mitochondrial enzyme cytochrome c oxidase (CcO) permits a significantly higher hydration state than is seen in x-ray crystal structures. Analyzing the dynamic nature of these waters with MD simulations leads to several interesting results. First, the new waters are characteristically more dynamic, supporting why they are hard to resolve in x-ray crystal structure. Second, while they do form water chains, such chains are transient, meaning additional hydration may still occur as a result of nonequilibrium shifts around catalytic center of the enzyme. Finally, the water molecules tend to form tightly packed clusters, which can significantly impact the dielectric properties of the enzyme. These results shed a great deal of light on the many mysteries surrounding water in CcO.
More information at https://pubs.acs.org/doi/10.1021/acs.jpcb.7b11920