Section: New Results

Protein secondary structure prediction for dynamic simulations

Participants : Marc Piuzzi, Sergei Grudinin, Stephane Redon.

There is a tight link between a protein's function and its molecular structure. Hence, global stability is essential for a protein to keep its role inside the cell. Various chemical interactions helps stabilizing the structure (covalent bonds, hydrogen bonds, etc.) but not all parts of a protein present the same stability. The most stable regions of a protein present numerous hydrogen bonds on backbone atoms composing geometrically distinguishable secondary structures (the primary structure being the amino acid sequence): helices and beta sheets.

These structures have been well studied and although important properties have been defined, there is no absolute definition of what is a helix or a beta sheet. Thus, various methods have been developed to predict the secondary structure of a protein using the amino acid sequence and/or the protein structure using different parameters and structural descriptors.

However, none of these methods have been made in the context of interactive simulation where the shape of the protein is dynamic: here the prediction has to be done at each time step on the whole protein. Moreover, the result is deterministic and returns only the type of structure without any information about the accuracy. We are developing a new approach that is appropriate in an interactive context, where secondary structure assignment has to continuously change during interaction.