Abstract: Purely geometric arguments are used to extract information from three-dimensional structures of oligomeric proteins, that are very common biological entities stably made of several polypeptidic chains. They are characterized by the presence of an interface between adjacent amino acid chains and can be investigated with the approach proposed here. We introduce a method, called symmetrization, that allows one to rank interface interactions on the basis of inter-atomic distances and of the local geometry. The lowest level of the ranking has been used previously with interesting results. Now, we need to complete this picture with a careful analysis of the higher ranks, that are for the first time introduced here, in a proper mathematical set up. The interface finds a very nice mathematical abstraction by the notion of weighted bipartite graph, where the inter-atomic distance provides the weight. Thus, our approach is partially inspired to graph theory decomposition methods but with an emphasis to “locality”, namely the idea that structures constructed by the symmetrization adapt to the local scales of the problem. This is an important issue as the known interfaces may present major differences in relation to their size, their composition and the local geometry. Thus, we looked for a local method, that can autonomously detect the local structure. The physical neighborhood is introduced by the concept of cluster of interactions. We discuss the biological applications of this ranking and our previous fruitful experience with the lowest symmetrized level. An example is given, using the prototypical cholera toxin.

Keywords: symmetrization, protein interfaces, oligomeric proteins, graphs, bonds ranking, interaction clusters.

ACM Classification Keywords: J.2 Physical sciences - Mathematics and statistics J.3 Life and medical sciences - Biology and genetics

Link:

SYMMETRIZATION: RANKING AND CLUSTERING IN PROTEIN INTERFACES

Giovanni Feverati, Claire Lesieur, Laurent Vuillon

http://www.foibg.com/ibs_isc/ibs-25/ibs-25-p12.pdf