Thesis defense of Rodrigo Dorantes-Gilardi

Bio-mathematical aspects of the plasticity of proteins

Abstract: Proteins are biological objects made to resist perturbations and, at the same time, to adapt to new environments. What are the structural properties of proteins allowing such plasticity? To tackle this question we first model protein structure as a network. Given the structural conformation of a mutation, a network approach allows the quantification of its structural change.

Using large sets of mutations, we concluded that structural change is independent from the type of amino acid replaced, or replacing after mutation. Looking at the composition of amino acid neighborhoods, we noticed that the location of a type of amino acid in the 3D structure is arbitrary. Leading to the observation that the neighborhood of the amino acid in the 3D structure is the single property related to structural plasticity.

Finally, we implemented three algorithms to measure the empty space around amino acids to look at the relation between void and structural plasticity. Results show a clear gap in small atomic distances, invariant across a large dataset, suggesting a cutoff to separate intra-atomic and inter-atomic void, based on the distances of covalent and non-covalent interactions.

> The subsequent toast which will the place in the same room (around 4 PM).