Most of the interactions holding a protein together are conserved covalent bonds remain connected, hydrogen bonds and salt bridges link portions of the chain but entire elements of secondary structure flex, bending slightly or separating momentarily from the globule. Breathing is essential in the function of myoglobin, a deep red protein that stores oxygen in muscle cells. Oxygen is bound to myoglobin in a pocket that is completely buried within the protein. Looking at the static structures provided by x-ray crystallography, there are no channels leading into or out of the pocket. For the oxygen to enter and exit, the molecule must breathe, transiently forming channels that allow passage.
Many proteins use a carefully designed change of shape to regulate their action.
In the simplest model of their action, each subunit may adopt two conformations, one functionally active, the other less active. Regulation is performed by propagation of the shape change from one subunit to its neighbors. For instance, phosphofructokinase, a key enzyme in sugar metabolism, uses allosteric regulation to modify its action. When ATP binds to this second site, it forces the entire enzyme complex into a different shape, which is less active than the original form. In the cell, this regulation is used as a negative-feedback loop.