1 research outputs found
Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices
Position-specific scoring matrices (PSSMs) are useful for detecting weak
homology in protein sequence analysis, and they are thought to contain some
essential signatures of the protein families. In order to elucidate what kind
of ingredients constitute such family-specific signatures, we apply singular
value decomposition to a set of PSSMs and examine the properties of dominant
right and left singular vectors. The first right singular vectors were
correlated with various amino acid indices including relative mutability, amino
acid composition in protein interior, hydropathy, or turn propensity, depending
on proteins. A significant correlation between the first left singular vector
and a measure of site conservation was observed. It is shown that the
contribution of the first singular component to the PSSMs act to disfavor
potentially but falsely functionally important residues at conserved sites. The
second right singular vectors were highly correlated with hydrophobicity
scales, and the corresponding left singular vectors with contact numbers of
protein structures. It is suggested that sequence alignment with a PSSM is
essentially equivalent to threading supplemented with functional information.
The presented method may be used to separate functionally important sites from
structurally important ones, and thus it may be a useful tool for predicting
protein functions.Comment: 22 pages, 7 figures, 4 table