Figure 1.
Radius of gyration (Rg) of interacting proteins.
(a) Rg as a function of protein length for ID segments that interact with partner molecules (red squares, n = 52) and globular protein of the 3D complex dataset (black triangles, n = 762). 3D complex proteins that are disulfide-rich domains (n = 29) or coiled coils (n = 42) are enclosed in dark blue squares and green circles, respectively. The Rg/N threshold of 0.26 Å is represented by the dotted line. (b) Ribbon structure of the ID segment of p27 (red) that “wraps” around its complex partners cyclin A (grey) and Cdk2 (gold) (p27; PDB: 1JSU chain C, Rg = 21 Å, N = 69). (c) Ribbon structure of one of the 3D complexes, α-chymotrypsin (grey) and eglin c (gold) (bovine α-chymotrypsin; PDB: 1ACB chain E, Rg = 16 Å, N = 241). (d) Ribbon structure of the coiled coil EB1 (EB1; PDB: 1WU9 chain A, Rg = 20 Å, N = 59).
Table 1.
List of datasets analyzed and the number of structures in each dataset.
Figure 2.
Box plot of the fraction of disordered residues in the selected ID complex dataset (Rg/N>0.26 Å) and two controls.
Disorder content was calculated using Disopred2. The first control consists of all the structures in the non-redundant PDB dataset. The second control is the polypeptides of the non-redundant PDB dataset that have an Rg/N<0.26 Å while bound to a large protein partner. Asterisks identify distributions that are significantly different (p values<0.05; Wilcoxon test). Box plot identifies the middle 50% of the data, the median, and the extreme points. The entire set of data points is divided into quartiles and the inter-quartile range (IQR) is calculated as the difference between ×0.75 and ×0.25. The range of the 25% of the data points above (×0.75) and below (×0.25) the median (×0.50) is displayed as a filled box. The horizontal line represents the median. Data points greater or less than 1.5·IQR represent outliers and are shown as hollow circles.
Figure 3.
Residue composition of the proteins in the selected ID set relative to the 3D complex dataset.
Averaged percentage residue compositions from ID dataset are subtracted by the respective percentage from the 3D complex. Positive and negative values indicate an enrichment and depletion, respectively, of a specific residue in the ID complex set with respect to the 3D complex dataset. Amino acids are sorted according to their ranking in protein chain flexibility [41], [80]. The residue composition for the ID segments (only residues with coordinates in the PDB) and extended ID segments (30 residues on each end) are shown in red and yellow, respectively.
Figure 4.
Interface residue composition.
(a) The residue composition at the core regions of complex interfaces. (b) The residue composition at the rim regions of complex interfaces. The interface residue compositions of ID segments, ID binding partners (BPs), and 3D complex proteins are shown in red, magenta, and grey respectively.
Table 2.
Interface characteristics.
Figure 5.
Box plots of changes in free energy of binding (ΔΔGbind) in the alanine scan.
Free energy changes for hydrophobic residues, charged residues, and only charged residues that are forming salt bridge interactions are shown in (a), (b) and (c), respectively. Asterisks identify distributions that are significantly different (p values<0.05; Wilcoxon test). The results for residues in the ID segments, ID binding partners (BPs), and 3D complex proteins are shown in red, magenta and grey respectively.
Figure 6.
Box plots of electrostatic components of the binding free energy.
(a) Electrostatic contribution to the desolvation free energy of binding. (b) Coulombic interaction energy of binding. (c) Total electrostatic free energy of binding. Asterisks identify distributions that are significantly different (p values<0.05; Wilcoxon test). Electrostatic contributions to binding are shown for ID complexes and 3D complexes in red and grey, respectively. (d–f) Nup50/importin-α2 is an example of a complex that involves burial of extensive polar surfaces (PDB: 2C1M [81]). The surface of importin-α2 was generated using a probe radius of 1.5 Å. The surface is colored using the electrostatic potential map of importin-α2 that was generated by Delphi. The ID segment, Nup50, is represented by the cartoon ribbon structure with ARG, LYS, and HIS residues colored in blue and GLU and ASP residues colored in red. (d) The full view of the interacting region of the Nup50/importin-α2 complex. (e) Nup50 (37–46) contains a high concentration of positively charged residues that bind to an acidic region of importin-α2. (f) The positively charged residues of the N-terminus of Nup50 are complementary to an acidic surface on its binding partner.