Redesigning Protein Cavities as a Strategy for Increasing Affinity in Protein-Protein Interaction: Interferon-γ Receptor 1 as a Model

Table 1

Cavities in the four molecules of the IFNγR1 receptor in crystal structures 1fg9 [19] and 1fyh [20]. The receptor molecules are labeled by chain ID (chains C and D from 1fg9 and chains B and E from 1fyh). Figure 2 shows cavities 1–8 as they project into the chain C of 1fg9.

	Surface [Å^2]^*	Number of residues lining the cavity^†	Residues selected for mutation	Cavity observed in IFNγR1 chain of
				1fg9	1fyh
1	134	7	V35, A114	C D	—
2	133	5	—	—	B E
3	470	14	D124	C D	—
4	262	9	H222	C D	B E
5	120	6	—	C D	E
6	165	7	—	C D	E
7	177	7	—	D	B E
8	138	5	—	C	B

Surface calculated with a probe radius of 0.25 Å for cavities combined from all relevant receptor chains.
^†Some residues are shared by neighboring cavities.