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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 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