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Keywords:

  • protein-complex threading;
  • protein–protein interaction;
  • polymer prediction;
  • sterile alpha motif;
  • pointed domain;
  • scaffolding proteins

Abstract

Sterile alpha motif (SAM) domains are common protein modules in eukaryotic cells. It has not been possible to assign functions to uncharacterized SAM domains because they have been found to participate in diverse functions ranging from protein–protein interactions to RNA binding. Here we computationally identify likely members of the subclass of SAM domains that form polymers. Sequences were virtually threaded onto known polymer structures and then evaluated for compatibility with the polymer. We find that known SAM polymers score better than the vast majority of known nonpolymers: 100% (7 of 7) of known polymers and only 8% of known nonpolymers (1 of 12) score above a defined threshold value. Of 2901 SAM family members, we find 694 that score above the threshold and are likely polymers, including SAM domains from the proteins Lethal Malignant Brain Tumor, Bicaudal-C, Liprin-β, Adenylate Cyclase, and Atherin. Proteins 2009. © 2008 Wiley-Liss, Inc.