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Table 2 Evaluation of global intrinsic disorder predisposition of human proteins from several datasets related to HIV-1 infection

From: Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle

Dataset (number of proteins)

PONDR® VSL2 analysis

CH-CDF analysis

Mostly ordereda

Moderately disorderedb

Mostly disorderedc

Highly disorderedd

Q1

Q2

Q3

Q4

Whole proteome (20,317)

83(0.4%)

1030(5.1%)

6841(33.7%)

4267(21.0%)

8095(39.8%)

7381(36.3%)

12,014

(59.1%)

5177

(25.5%)

2501 (12.3%)

625 (3.1%)

All human interactors (4792)

1(0.02%)

143(2.98%)

1828(38.1%)

1082(22.6%)

1738(36.3%)

1534(32.0%)

2945 (61.4%)

1149 (24.0%)

612 (12.8%)

86 (1.8%)

Capsid interactors (252)

0(0.0%)

12(4.7%)

98(38.9%)

68(27.0%)

74(29.4%)

65(25.8%)

180 (71.4%)

49 (19.5%)

21 (8.3%)

2 (0.8%)

GagPol interactors (221)

0(0.0%)

6(2.7%)

99(44.8%)

32(14.5%)

84(38.0%)

75(33.9%)

122 (55.2%)

35 (15.8%)

59 (22.7%)

5 (2.3%)

Integrase interactors (210)

0(0.0%)

8(3.8%)

95(45.2%)

50(23.8%)

57(27.2%)

54(25.7%)

143 (68.1%)

37 (17.6%)

28 (13.3%)

2 (1.0%)

Pr44Gag interactors (657)

0(0.0%)

20(3.0%)

264(40.2%)

126(19.2%)

247(37.6%)

226(34.4%)

374 (56.9%)

140 (21.3%)

130 (19.8%)

13 (2.0%)

RT Interactors (106)

0(0.0%)

2(1.9%)

58(54.7%)

21(19.8%)

25(23.6%)

21(19.8%)

78 (73.6%)

19 (17.9%)

9 (8.5%)

0 (0.0%)

Tat Interactors (1667)

0(0.0%)

42(2.5%)

617(37.0%)

420(25.2%)

588(35.3%)

508(30.5%)

1034 (62.0%)

380 (22.8%)

234 (14.0%)

19 (1.2%)

Vpr interactors (657)

0(0.0%)

19(2.9%)

272(41.4%)

166(25.3%)

200(30.4%)

173(26.3%)

432 (65.8%)

140 (21.3%)

73 (11.1%)

12 (1.8%)

  1. aMostly ordered proteins are those found in the dark blue and light blue areas of the mean disorder score (MDS) vs. percent of predicted intrinsically disordered residues (PPIDR) plots; i.e., areas containing proteins with PPIDR < 10% and MDS < 0.15, where dark blue correspond to area where these two parameters agree (upper values in the corresponding cells), whereas light blue color show areas in which only one of these criteria applies (bottom values in the corresponding cells)
  2. bModerately disordered proteins are those found in the dark pink and light pink areas of the mean disorder score (MDS) vs. percent of predicted intrinsically disordered residues (PPIDR) plots; i.e., areas containing proteins with 10% ≤ PPIDR < 30% and 0.15 ≤ MDS < 0.1, where dark pink correspond to the area where these two parameters agree (upper values in the corresponding cells), whereas light pink color show areas, in which only one of these criteria applies (bottom values in the corresponding cells)
  3. cMostly disordered proteins are those found in the red area of the mean disorder score (MDS) vs. percent of predicted intrinsically disordered residues (PPIDR) plots; i.e., area containing proteins with PPIDR ≥ 30% and MDS ≥ 0.5
  4. dHighly disordered proteins are a subset of mostly disordered proteins that are characterized by PPIDR ≥ 50% and MDS ≥ 0.5