of the Guanine Nucleotide Exchange Factor FARP2
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1 Structure, Volume 21 Supplemental Information Structural Basis for Autoinhibition of the Guanine Nucleotide Exchange Factor FARP2 Xiaojing He, Yi-Chun Kuo, Tyler J. Rosche, and Xuewu Zhang Inventory of Supplemental Information Figure S1. Comparison of the 9 protomers in the asymmetric unit of the crystal of the FARP2 DH domain, Related to Figure 1. Figure S2. Structural comparison of the DH-PH-PH domains of human FARP1 and mouse FARP2, Related to Figure 2. Figure S3. Potential PtdInsP(s) binding site in PH1 of FARP2, Related to Figure 3. Figure S4. Structural comparison of PH2 with PH1 and the PH domain in DAPPI/PHISH, Related to Figure 5. Figure S5. In vitro fluorescence-based GEF activity assays for FARP2, Related to Figure 6.
2 Figure S1. Comparison of the 9 protomers in the asymmetric unit of the crystal of the FARP2 DH domain, Related to Figure 1.
3 Figure S2. Structural comparison of the DH-PH-PH domains of human FARP1 and mouse FARP2, Related to Figure 2. (A) The experimental electron density map (green) with the final model of the FARP1 DH-PH-PH domains superimposed. Cyan: the DH domain; yellow: Helix 6 C ; light brown: PH1; blue: the PH1-PH2 linker; magenta: PH2. (B) Superimposition of the DH-PH-PH structures of FARP1 and FARP2. The color scheme for FARP1 is the same as in (A). FARP2 is colored in gray. The r.m.s.d. for the 396 pairs aligned C atoms from the two structures is ~1.1 Å. The actual structural difference is likely bigger, since many loop regions, which usually deviate more between homologous proteins, are not built in the FARP1 structure due to lack of density. Nevertheless, it is evident from this comparison that FARP1 and FARP2 use the same structural mechanism for auto-inhibition. (C) Conserved surface patches in the DH-PH-
4 PH domains. The molecular surface of the FARP2 DH-PH-PH domains is shown, with residues conserved between FARP1 and FARP2 colored in blue. The structure in the left panel is rotated horizontally by ~90 relative to (A) and (B) as indicated by the axis on the top of the panel. A large conserved surface patch is present on the side of the two PH domains that is distal to the DH domain. In contrast, the exposed surface in the DH domain (the right panel) is largely non-conserved.
5 Figure S3. Potential PtdInsP(s) binding site in PH1 of FARP2, Related to Figure 3. (A) Superimposition of PH1 of FARP2 (light brown) with the structure of the PH domain of DAPPI/PHISH (gray) bound to inositol 1,3,4,5-tetrakisphosphate (PDB ID: 1FAO). (B) Electron density at the potential binding site in PH1 of FARP2. The four potential binding sites, each from the two PH domains in the asymmetric unit (light brown and gray) and their respective symmetry mates (cyan and yellow), pack together in the crystal and appear to be involved in crystal contacts. The density map (red) contoured at 3 with coefficients (2 F o F c )e iαc was calculated prior to including water molecules at the site.
6 Figure S4. Structural comparison of PH2 with PH1 and the PH domain in DAPPI/PHISH, Related to Figure 5. (A) Superimposition of PH2 (magenta) and the PH domain in DAPPI/PHISH (gray) bound to inositol 1,3,4,5-tetrakisphosphate (PDB ID: 1FAO). The three positively charged residues in the potential PtdInsP(s) binding site of PH2 are highlighted. (B) Superimposition of PH2 (magenta) and PH1 (light brown).
7
8 Figure S5. In vitro fluorescence-based GEF activity assays for FARP2, Related to Figure 6. (A-D) Rac1, Cdc42, RhoA and RhoC were preloaded with mant-gdp, and decrease of the fluorescence signal upon mant-gdp dissociation was monitored. RhoC appeared to have a relatively high intrinsic exchange rate. Adding the FARP2 DH- PH L730R/L733Q slowed down the decrease of the fluorescence signal, which was caused by precipitation of the proteins. (E-K) Mant-GDP was present in the reaction buffer and its binding to the RhoGTPases was measured by monitoring the increase of the fluorescence signal. None of the tested FARP2 proteins displayed significant GEF activity to any of the tested RhoGTPases, while the positive control SopE showed robust activity to both Rac1 and Cdc42.
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