The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.

ABSTRACT:

Background

Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains.

Results

Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/p

SUBMITTER: Ren S 

PROVIDER: S-EPMC2576256 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature