Abstract
BackgroundProtein interactions are essential for most cellular functions. Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact on diversities of cellular processes such as signal transduction and immune response. Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs).ResultsIn this study, we systematically studied the evolutionary conservation of SLiMs recognized by SH2, SH3 and Ser/Thr Kinase domains in both ordered and disordered protein regions. Disordered protein regions are protein sequences that lack a fixed three-dimensional structure under putatively native conditions. We find that, in all these domains examined, SLiMs are more conserved in disordered regions. This trend is more evident in those protein functional groups that are frequently reported to interact with specific domains.ConclusionThe correlation between SLiM conservation with disorder prediction demonstrates that functional SLiMs recognized by each domain occur more often in disordered as compared to structured regions of proteins.
Highlights
Protein interactions are essential for most cellular functions
The putative Src homology 2 (SH2) binding Tyr-Short Linear Motifs (SLiMs) in Histone H3.1 is conserved among sequences from all selected species, their relative conservation was low because of the highly conserved background (Figure 1A)
The advantage of the relative conservation method is the capability to discriminate SLiMs conserved under constraints of the integral protein from those conserved to serve as functional motifs
Summary
Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact on diversities of cellular processes such as signal transduction and immune response. BMC Genomics 2008, 9(Suppl 2):S26 http://www.biomedcentral.com/1471-2164/9/S2/S26 tant roles in cellular signal transduction. These peptidelibrary methods did not depend on prior knowledge of interaction sites in vivo [1]. Motifs discovered through polypeptide library screening showed remarkable consonance with reported domain interaction sites [1,2]. Such sites later became the basis for Scansite [3,4], a bioinformatics tool developed to predict target sites recognized by specific protein domains
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