Deciphering the Molecular and Functional Basis of RHOGAP Family Proteins

Abstract

Background: Rho and Dbl family proteins are largely uncharacterized that makes analysis of specific upstream pathways difficult. Results: Not all Rho proteins, including RhoD and Rif, need Dbl GEFs. Dbl family proteins can be divided in mono-, isoform-, and oligo-specific groups. Conclusion: Catalytic efficiency of Dbl proteins is proportional to their association reaction. Significance: Dbl family classification into distinct subfamilies opens doors to further systems biology-oriented and cell-based research. The diffuse B-cell lymphoma (Dbl) family of the guanine nucleotide exchange factors is a direct activator of the Rho fam-ily proteins. The Rho family proteins are involved in almost every cellular process that ranges from fundamental (e.g. the establishment of cell polarity) to highly specialized processes (e.g. the contraction of vascular smooth muscle cells). Abnormal activation of the Rho proteins is known to play a crucial role in cancer, infectious and cognitive disorders, and cardiovascular diseases. However, the existence of 74 Dbl proteins and 25 Rho-related proteins in humans, which are largely uncharacterized, has led to increasing complexity in identifying specific upstream pathways. Thus, we comprehensively investigated sequence-structure-function-property relationships of 21 representatives of the Dbl protein family regarding their specificities and activ-ities toward 12 Rho family proteins. The meta-analysis approach provides an unprecedented opportunity to broadly profile func-tional properties of Dbl family proteins, including catalytic efficiency, substrate selectivity, and signaling specificity. Our analysis has provided novel insights into the following: (i) understanding of the relative differences of various Rho protein members in nucleotide exchange; (ii) comparing and defining individual and overall guanine nucleotide exchange factor activ-ities of a large representative set of the Dbl proteins toward 12 Rho proteins; (iii) grouping the Dbl family into functionally dis-tinct categories based on both their catalytic efficiencies and their sequence-structural relationships; (iv) identifying con-served amino acids as fingerprints of the Dbl and Rho protein interaction; and (v) defining amino acid sequences conserved within, but not between, Dbl subfamilies. Therefore, the charac-teristics of such specificity-determining residues identified the regions or clusters conserved within the Dbl subfamilies.