Table 2. The effect phosphorylation/dephosphorylation on complex formation of Smad proteins.

Change in binding energy upon phosphorylation/dephosphorylation is calculated in terms of ΔΔG (negative and positive values correspond to stabilizing and destabilizing effects correspondingly). Phosphorylated/dephosphorylated positions in SSXS motif are shown as bold and underlined characters in “Site” column. Since FoldX can only handle dimeric complexes, Smad trimers were decomposed into three dimers: “AB”, “BC” and “AC”. “Average ΔΔG” is the average of all three pair of chains.

Protein	Site	pSite	AB	BC	AC	Average ΔΔG
Smad2 (1khx)	SSXS	S->pS	0.59	0.59	0.59	0.59
	SSXS	pS->S	0.88	0.88	0.88	0.88
	SSXS	pS->S	1.53	1.53	2.86	1.97
Smad1 (1khu)	SSXS	S->pS	−2.11	1.58	−0.22	−0.25
	SSXS	S->pS	−0.9	1.49	−1.74	−0.38
	SSXS	S->pS	−1.45	−1.87	−1.08	−1.47