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. 2015 Feb 3;35(5):899–911. doi: 10.1128/MCB.01020-14

TABLE 3.

Prion propensity and prion maintenance propensity scores from each library

Amino acid(s)a Prion propensity score for prion formation library ofb:
 Prion maintenance propensity scorec
Sup35-27d Sup35 ND Sup35 ORD
Individual amino acids
    Phenylalanine 0.84 1.06 0.37 0.33
    Isoleucine 0.81 0.47 −0.37* −0.57*
    Valine 0.81 0.47 −0.12* −0.35*
    Tyrosine 0.78 0.49 0.34 1.03
    Methionine 0.67 −0.04 0.63 −1.80*
    Tryptophan 0.67 −0.41 0.039 1.40
    Cysteine 0.42 −0.10 0.30 0.45
    Serine 0.13 −0.14 0.084 0.18
    Asparagine 0.08 0.67 0.81 0.18
    Glutamine 0.069 −0.88 −0.067 0.11
    Glycine −0.039 −0.49 −0.047 0.047
    Leucine −0.04 −0.10 −0.039 −0.48
    Threonine −0.12 0.37 0.069 −0.059
    Histidine −0.28 0.077 0.23 −0.064
    Alanine −0.40 −0.036 0.34 0.28
    Arginine −0.41 −1.37 −0.89 −0.88
    Glutamic acid −0.61 −0.87 −0.63 0.99
    Proline −1.20 −0.73 −0.36 0.065*
    Aspartic acid −1.28 −0.51 −0.56 −0.19
    Lysine −1.58 NAe −1.17 NAe
Groups of amino acids
    Charged (D, E, K, R) −0.90 −1.04 −0.83 −0.54
    Hydrophobic (I, L, M, V) 0.68 0.34 −0.13** −0.53****
    Prion-promoting nonaromatic hydrophobic (I, M, V) 0.88 0.47 −0.15*** −0.48****
    Aromatic (F, W, Y) 0.84 0.71 0.35 0.76
    Polar (N, Q, S, T) 0.064 0.13 0.24 0.15
a

Amino acids are listed in the order of their prion propensity according to PAPA.

b

Prion formation libraries were compiled as illustrated in Fig. 1C. Prion propensity scores were calculated as the natural log of the odds ratios, according to equation 2. Statistically significant differences relative to the Sup35-27 library (13) are indicated: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

c

The prion maintenance library experiment was performed as illustrated in Fig. 1D. Prion maintenance propensity scores were calculated according to equation 4. Statistically significant differences relative to the Sup35-27 library (13) are indicated: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

d

From Toombs et al. (13).

e

NA, not applicable; lysine was not found in any of the prion-forming sequences in the ND library or in any of the white colonies in the prion propagation library.