Principal eigenvector of contact matrices and hydrophobicity profiles in proteins

With the aim of studying the relationship between protein sequences and their native structures, we adopted vectorial representations for both sequence and structure. The structural representation was based on the principal eigenvector of the fold's contact matrix (PE). As has been recently shown, the latter encodes sufficient information for reconstructing the whole contact matrix. The sequence was represented through a hydrophobicity profile (HP), using a generalized hydrophobicity scale that we obtained from the principal eigenvector of a residue-residue interaction matrix, and denoted as interactivity scale. Using this novel scale, we defined the optimal HP of a protein fold, and, by means of stability arguments, predicted to be strongly correlated with the PE of the fold's contact matrix. This prediction was confirmed through an evolutionary analysis, which showed that the PE correlates with the HP of each individual sequence adopting the same fold and, even more strongly, with the average HP of this set of sequences. Thus, protein sequences evolve in such a way that their average HP is close to the optimal one, implying that neutral evolution can be viewed as a kind of motion in sequence space around the optimal HP. Our results indicate that the correlation coefficient between N-dimensional vectors constitutes a natural metric in the vectorial space in which we represent both protein sequences and protein structures, which we call vectorial protein space. In this way, we define a unified framework for sequence-to-sequence, sequence-to-structure and structure-to-structure alignments. We show that the interactivity scale is nearly optimal both for the comparison of sequences to sequences and sequences to structures. (C) 2004 Wiley-Liss, Inc.