Table 1.

Grafting of Protein-Protein Interaction Sites

scaffold protein	rms deviationa (Å)	overlap volb (Å3)	candidate positions	distance violationc (Å)	calcd ΔGbind (kcal·mol−1)	buried surfaced(Å2)
Transferring of Barstar Three Hot-Spot Residues Tyr29, Asp35, and Asp39
barstar NMR structure	0.42	31	29, 35, 39	0.17	−16.9	1533
NS1 RNA binding domain	1.49	69	60, 51, 53	0.23	−13.4	1679
IF-3 C terminal domain	1.25	72	93, 125, 126	0.33	−9.3	1298
allergen PHL P2	1.37	68	14, 87, 85	0.43	−11.4	1367
Transferring of Barstar Two Hot-Spot Residues Asp35 and Asp39
barstar NMR structure	0.44	27	35, 39	0.16	−16.8	1531
scorpion toxin II	0.63	48	28, 24	0.11	−10.7	1538
OMPR DNA binding domain	0.31	30	183, 187	0.19	−11.1	1347
phosphotransferase	0.83	55	17, 15	0.17	−9.8	1798
Transferring of BPTI Two Hot-Spot Residues Lys15 and Ile18
BPTI unbound structure	0.32	34	15, 18	0.27	−18.4	1383
tenascin	1.02	57	854, 857	0.68	−9.0	1976
CheY	0.45	64	12, 17	0.25	−14.5	2130
allergen PHL P2	0.91	51	10, 90	0.43	−11.8	1596
Transferring of Antibody D1.3 Three Hot-Spot Residues H100Asp, H101Tyr, and L92Trp
D1.3 unbound structure	1.30	29	H100, H101, L92	0.32	−7.4	1075
scorpion toxin BJXTR-IT	1.29	37	15, 14, 34	0.53	−9.9	1402
MBP1 DNA binding domain	1.28	52	80, 33, 30	0.31	−10.1	1472
α-amylase inhibitor	1.08	50	55, 54, 49	0.28	−10.0	1172

^aThe rms difference between the “key interaction atoms” of native ligand protein in complex structure and those of the superposed scaffold protein.

^bThe overlap volume between the rigid atoms of scaffold protein and receptor.

^cMean violations from target distances for strongly interacted atom–atom pairs across the interface. The violations were measured after energy minimization and the target distance was derived from the observed complex structure.

^dThe buried surface at the interface of designed scaffold protein and receptor (probe = 1.4 Å).