Identifying polymer-forming SAM domains - PubMed (original) (raw)

Identifying polymer-forming SAM domains

Alejandro D Meruelo et al. Proteins. 2009 Jan.

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-beta, Adenylate Cyclase, and Atherin.

(c) 2008 Wiley-Liss, Inc.

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Figures

Figure 1

Figure 1. SAM polymer architecture

The structure shown is the SAM domain from TEL. Every other SAM domain is shaded dark or light.

Figure 2

Figure 2. Outline of the polymer compatibility test algorithm

See text.

Figure 3

Figure 3. Histogram of the Z-final score distribution

The scores for the known polymers are indicated by the positions of the shaded arrows and the scores for the known non-polymers are indicated by the positions of the white arrows. The dotted line indicates the Z-final cutoff used to separate polymers from non-polymers.

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