Eukaryotic Protein Domains as Functional Units of Cellular Evolution

Jing Jin,* Xueying Xie, Chen Chen, Jin Gyoon Park, Chris Stark, D. Andrew James, Marina Olhovsky, Rune Linding, Yongyi Mao,* Tony Pawson*

*To whom correspondence should be addressed. E-mail: pawson{at}lunenfeld.ca (T.P.); yymao{at}site.uottawa.ca (Y.M.); jjin{at}lunenfeld.ca (J.J.)

This PDF file includes:

• Section S-I. Characterization of the functional relationships between RhoGEF/RhoGAP pairs Tuba/Rich1, and DEPDC1/P-Rex1.
• Section S-II. Correlation between protein kinase regulatory and catalytic domains.
• Section S-III. Web site for domain clubs across seven genomes.
• Section S-IV. Supplementary methods.
• Section S-V. Supplementary references.
• Table S1. Domains found in common versus domains that are unique to SH2 domain proteins or SH3 domain proteins.
• Fig. S1. Functional characterization of RhoGEF and RhoGAP protein pairs.
• Fig. S2. Domain profiling of human protein kinases (PTK) and protein tyrosine phosphatases (PTP).
• Fig. S3. Domain profiling of the human kinome.
• Fig. S4. Domain profiling across six eukaryotic kinomes.
• Fig. S5. Domain club cut-off selection.
• Fig. S6. Test of the robustness of the domain profiling method for applications in large data sets.
• Fig. S7. A Web site for domain club analysis—example of Dicer1 and its DSRM domain.
• Fig. S8. General procedure for spreading-on-graph (SOG) clustering in the analysis of the molecular environments of domain families.
• Fig. S9. The interactomes of the 70 domain families employed in the analysis of domain-based functional compartments.
• Fig. S10. An overview of the Royal Family of domains.
• Fig. S11. Sequence characteristics of the mouse Piwi clade of the Argonaute proteins.
• Fig. S12. An MS/MS spectrum of a tryptic peptide containing dimethylated (2me) Arg53 of endogenous Miwi protein from testis.

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© 2009 American Association for the Advancement of Science