From: Refinement and prediction of protein prenylation motifs
Property | Position | Rationale | Explanation |
---|---|---|---|
ARGP820103 [62] | +3 | Corr = 0.8(prof) | Membrane-buried preference, lipid contact when entering binding pocket |
LEVM760105 [69] | +1 to +3 | Fisher = 1.36 | Size limitation (radius of gyration of side-chain) |
YUTK870101 [70] | +1 to +3 | Fisher = 1.38 | Hydrophobicity compensation (Unfolding Gibbs energy in water, pH7.0) |
ZVEL_CHARG [64] | +1 to +3 | LS composition | General charge penalty |
ZVEL_CHNEG [64] | +1 to +3 | LS composition | Special negative charge penalty |
ZVEL_ALI_1 [64] | +1 and +2 | +2: Corr = 0.87(prof) +1: continuing deviation from Uniref50 average | Amino-acid property: aliphatic |
LIFS790102 [66] | +1 and +2 | +2: Corr = 0.77(prof) +1: continuing deviation from Uniref50 average | Preference for extended conformations |
FAUJ880101 [71] | -1 and +2 | Fisher = 1.52 | Size, bulkiness (residues although 10 Ã… apart, face to same side of base pair) |
FINA910103 [72] | -1 | Corr = 0.75(prof) | Helix termination (for example, K, S favored, D,E,L,I,V disfavored) |
KARP850103 [73] | -7 to-1 | -1: Corr = 0.69(prof) -2: Corr = 0.70(prof) -3: Corr = 0.71(prof) -4: Corr = 0.74(nrLS) -5: Corr = 0.75(prof) -6: Corr = 0.70(nrLS) -7: Corr = 0.78(nrLS) | Flexibility (GGT1 lysine preference) |
VINM940101 [67] | -11 to -1 | -4: Corr = 0.72(prof) -5: Corr = 0.82(prof) -6: Corr = 0.84(nrLS) -7: Corr = 0.75(nrLS) -8: Corr = 0.77(nrLS) -9: Corr = 0.68(prof) -10: Corr = 0.86(prof) Rest: continuing deviation from Uniref50 average | Normalized flexibility average |
KRIW790102 [68] | -11 to -1 | -3: Corr = 0.70(prof) -4: Corr = 0.73(prof) -5: Corr = 0.84(prof) -6: Corr = 0.81(prof) -7: Corr = 0.83(nrLS) -8: Corr = 0.85(nrLS) -9: Corr = 0.76(prof) -10: Corr = 0.86(prof) Rest: continuing deviation from Uniref50 average | Fraction of site occupied with water |
Buried helix (see Materials and methods) | -20 to -1 | Remove false positives | Helix with strongly hydrophobic sides folds back to protein core and reduces flexibility and accessibility of carboxy terminus |