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

Figure 8

Ranked RMSF values collected at the last 50 ns of the 100 ns MD simulations of WT, N96W, and variants of IFNγR1. Solid lines labeled g-R1 denote RMSF values of the IFNγ/IFNγR1 complex; dashed lines labeled R1 denote values of IFNγR1 alone. The RMSF values are on the -axis; the rank of the values (1–50) is on the -axis. Shown are RMSF values of all atoms, main chain atoms (MC), and side chain atoms (SC) for the following residues: (a) all 40 interface residues (i.e., residue numbers 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 93, 95, 96, 97, 99, 115, 116, 118, 123, 164, 165, 166, 168, 170, 171, 186, 189, 190, 191, 192, 193, 197, 220, 221, 222, 223, 224, 225, 226, and 227); (b) residues within 6 Å of residue 96 (i.e., residue numbers 65, 66, 67, 91, 92, 93, 94, 95, 96, 97, 98, 119, 120, 121, and 224); (c) residues within 6 Å of residue 35 (i.e., residue numbers 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 100, 101, 102, 114, 115, 116, and 117); (d) the interface residues from the N-terminal domain (i.e., residues 64 to 123); (e) the interface residues from the C-terminal domain (i.e., residues 164 to 227).

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