Geometry and Topology of Folding Landscapes - Biological Networks - page 155

Based on a simplified harmonic potential, ENMs have been enhanced to account
for a variety of effects that influence the dynamics of biological molecules. An
advantage of ENMs is that they usually provide an accurate description of the
mechanisms of motions, although no absolute time scale and size of motions can
be predicted. Another advantage is to simplify our understanding of the complex
and diverse interactions in biological systems with the help of a simple model,
and a small number of parameters. It should be noted, however, that in a strict
sense they are applicable to the close neighborhood of the native (or equilibrium)
state. They essentially inform us on the intrinsic dynamic preferences of
biomolecular systems, which are verified in numerous applications to be
functionally relevant (Bahar et al. , 2007). ENMs also provide us with physical
insights: The overall topology of the protein plays a major role in the mechanical
behavior of the protein, implying that proteins related by evolution are expected
to show similar quantitative behavior, as seen in the case of potassium channels,
discussed above. Basic research in biology and biochemistry along with
statistical mechanical and analytical methods will thus lead to improved
transferability and predictability of such approaches.
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