Skip to main content

Advertisement

Table 2 Physical property terms in the GGT1 scoring function

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 Å 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