  Previous studies of the flexibilities of ancestral proteins suggests that
proteins evolve their function by altering their native state ensemble. Here we
propose a more direct method of visualizing this by measuring the changes in
the vibrational density of states (VDOS) of proteins as they evolve. Through
analysis of VDOS profiles of ancestral and extant proteins we observe that
$\beta$-lactamase and thioredoxins evolve by altering their density of states
in the terahertz region. Particularly, the shift in VDOS profiles between
ancestral and extant proteins suggests that nature utilize dynamic allostery
for functional evolution. Moreover, we also show that VDOS profile of
individual position can be used to describe the flexibility changes,
particularly those without any amino acid substitution.
