Internal motions in proteins take place on a broad range
of time-
and space-scales. The potential roles of these dynamics in the biochemical
functions of proteins have intrigued biophysicists for many years,
and multiple mechanisms to couple motions to function have been proposed.
Some of these mechanisms have relied on equilibrium concepts. For
example, the modulation of dynamics was proposed to change the entropy
of a protein, hence affecting processes such as binding. This so-called
dynamic allostery scenario has been demonstrated in several recent
experiments. Perhaps even more intriguing may be models that involve
out-of-equilibrium operation, which by necessity require the input
of energy. We discuss several recent experimental studies that expose
such potential mechanisms for coupling dynamics and function. In Brownian
ratchets, for example, directional motion is promoted by switching
a protein between two free energy surfaces. An additional example
involves the effect of microsecond domain-closure dynamics of an enzyme
on its much slower chemical cycle. These observations lead us to propose
a novel two-time-scale paradigm for the activity of protein machines:
fast equilibrium fluctuations take place on the microsecond-millisecond
time scale, while on a slower time scale, free energy is invested
in order to push the system out of equilibrium and drive functional
transitions. Motions on the two time scales affect each other and
are essential for the overall function of these machines.