Table 1 Physical property terms in the FT scoring function
From: Refinement and prediction of protein prenylation motifs
Property | Position | Rationale | Explanation |
|---|---|---|---|
ARGP820103 [62] | +3 | Corr = 0.7(nrLS) | Membrane-buried preference, lipid contact when entering binding pocket |
logPREN_CKQX_FT [15] | +3 | Corr = -0.72(nrLS) | Kinetic measurement, relative unprocessed FPP amounts with tetrapeptide CKQX |
CHOC760101 [63] | +1 to +3 | Fisher = 1.3 | Side chain volume |
ZVEL_CHARG [64] | +1 to +3 | LS composition | General charge penalty |
ZVEL_CHNEG [64] | +1 to +3 | LS composition | Special negative charge penalty |
WERD780102 [65] | +1 and +3 | Fisher = 1.51 | Hydrophobicity compensation for inside preference |
ZVEL_ALI_1 [64] | +1 and +2 | +2: Corr = 0.85(prof) +1: continuing deviation from Uniref50 average | Amino-acid property: aliphatic |
LIFS790102 [66] | +1 and +2 | +2: Correlation = 0.76(prof) +1: continuing deviation from Uniref50 average | Preference for extended conformations |
ZVEL_TINY_ [64] | -1 | Corr = 0.68(prof) | Size, bulkiness |
MOBILITY_2 [21] | -1 | Corr = 0.61(nrLS) | Side chain mobility |
VINM940101 [67] | -11 to -1 | -2: Corr = 0.72(prof) -3: Corr = 0.75(prof) -4: Corr = 0.78(nrLS) -5: Corr = 0.82(nrLS) -6: Corr = 0.84(nrLS) -7: Corr = 0.79(nrLS) -8: Corr = 0.74(prof) -9: Corr = 0.82(nrLS) -10: Corr = 0.84(nrLS) -11: Corr = 0.79(nrLS) Rest: continuing deviation from Uniref50 average | Normalized flexibility average |
KRIW790102 [68] | -11 to -1 | -2: Corr = 0.76(prof) -6: Corr = 0.83(nrLS) -7: Corr = 0.83(nrLS) -8: Corr = 0.76(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 C-terminus |