Protein Structure Alignment through a Contact Topology Profile using SABERTOOTH

Abstract

The contact vector (CV) of a protein structure is one of the simplest and most condensed descriptions of protein structure available. It lists the number of con- tacts each amino acid has with the surrounding structure and has frequently been used e.g. to derive approximative folding energies in protein folding analysis. The CV, however, is a lossy structure representation, as it does not contain sufficient information to allow for the reconstruction of the full protein structure it was derived from. The loss of information leads to a degeneracy in the sense that a single contact vector is compatible with many different contact matrices, but it has been shown that this degeneracy is nearly fully compensated by the physical constraints protein structure is subject to. We recently developed the alignment framework ‘SABERTOOTH’ that is able to generically align connectivity related vectorial structure profiles to compute protein alignments. Here we show that also the CV allows for state-of-the-art alignment quality, just like the elaborated ‘Effective Connectivity’ profile (EC) that SABERTOOTH currently uses. This simplification leeds to a very simple and elegant approach to structure alignment, which accelerates and generalizes the algorithm we previously proposed. Furthermore, we conclude from our work that the CV in itself is a useful structure description if its collective properties are called for.