Question

Looking at the TP53 primary structure, what percentage of this sequence is hydrophobic at pH 7? Note: hydrophobic is not synonymous with non-polar; spectroscopic studies suggest at least 3 disulfide bonds

Answer 1

The hydrophobicity index is a measure of the relative hydrophobicity, or how soluble an amino acid is in water. In a protein, hydrophobic amino acids are likely to be found in the interior, whereas hydrophilic amino acids are likely to be in contact with the aqueous environment.

The values in the table below are normalized so that the most hydrophobic residue is given a value of 100 relative to glycine, which is considered neutral (0 value).

Amini acids at Ph 7 highly hydrophobic

Phe

Ile

Trp

Leu

Val

Met

Physio-chemical properties of p53

Number of amino acids: 393

No Of Hydrophobic amino acids in sequence = %Ile+%Leu+%Met+ %phe+%Trp+%val = 2+8.1+3.1+2.8+1+4.8 = 21.8%

We can also calculate it by formula = (No of hydrophobic amino acids/total no. of amino acids ) * 100 =   [(8+32+12+11+4+19)/393 ] *100 = 21.88%

So, 21.88% of sequence is hydrophobic

Molecular weight: 43754.3

Theoretical pI: 6.48

Amino acid composition:

Ala (A) 24 6.1%

Arg (R) 27 6.9%

Asn (N) 14 3.6%

Asp (D) 20 5.1%

Cys (C) 10 2.5%

Gln (Q) 15 3.8%

Glu (E) 30 7.6%

Gly (G) 22 5.6%

His (H) 12 3.1%

Ile (I) 8 2.0%

Leu (L) 32 8.1%

Lys (K) 20 5.1%

Met (M) 12 3.1%

Phe (F) 11 2.8%

Pro (P) 44 11.2%

Ser (S) 38 9.7%

Thr (T) 22 5.6%

Trp (W) 4 1.0%

Tyr (Y) 9 2.3%

Val (V) 19 4.8%

Pyl (O) 0 0.0%

Sec (U) 0 0.0%