title: Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions.
abstract: BACKGROUND
  Protein 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).
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA. rsysjtu@hotmail.com
authors.forename: Siyuan
authors.initials: S
authors.lastname: Ren
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Uversky
authors.forename: Zhengjun
authors.initials: Z
authors.lastname: Chen
authors.forename: A Keith
authors.initials: AK
authors.lastname: Dunker
authors.forename: Zoran
authors.initials: Z
authors.lastname: Obradovic
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D030562:Databases, Protein; D006801:Humans; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship; D018909:src Homology Domains
chemical_list: D011506:Proteins; D017346:Protein Serine-Threonine Kinases