Proteins are known to demonstrate fractal like properties of their surface and volume. Consequently the protein interior is not tightly packed but contains multiple cavities of varying sizes. Several computational methods, such as elastic network models or contact map analysis, demonstrated that fractal-like interior of proteins is closely related to their function. It has been also demonstrated that protein fractal structures are volatile and can change dramatically upon small molecule binding. This opens the door to an explanation of long distance allosteric signaling that is based solely on protein dynamics and does not involve any structural changes. Our work on protein kinases show that major fractal related features of protein kinase interior correspond to the well known functional elements of the kinase core. Furthermore, residues with high centrality that serve as major connectors within the protein kinase interior highly conserved and known to be critical for protein kinase  function. These findings support the idea that fractal nature of protein kinases is a conserved feature in the whole protein kinase family. This makes studies of protein fractal structure an important analytical tool that can shed light on the most critical regulatory mechanisms in molecular biology.

Fractal nature of protein interior and its implications for allostery

253rd National Meeting (2017)

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