Often, the subunits are composed of two domains connected by a flexible linker, and flexure of the subunit is used to adopt different conformations. Biomolecular Flexibility and Dynamics Engineers in our macroscopic world typically build rigid structures that stoically resist the forces of nature. Nature, however, has taken a different approach, developing machines that flex over the course of their action. In fact, biological molecules take advantage of flexibility for many aspects of their function. Many of these functions would be severely compromised, or not even possible, given a rigid molecule.
Subtle motions can have surprisingly large effects on reaction rates or assembly.
Biological molecules are perfectly placed to take advantage of these subtle motions. This process is easy for evolution but far more difficult for biotechnological design. We design our machines in one step, instead of through many small random optimization steps, and we expect to get it right with a minimum of tweaking and redesign. Thus, to anticipate all of the subtle effects of motion, our design techniques must be accurate enough to predict conformation and flexibility of molecules at scales far smaller than the radius of an atom. All biological molecules are flexible to some extent and are battered into different conformations by the constant pressure of surrounding water and the kinetic energy of their own atoms.