(b) Post-translational modificationsoccur in the cell producing the
protein. Of these, proteolytic removal of nonfunctional parts and
22 S 22 S 22 bridge formation generally are identical for all
molecules, but glycosylation, phosphorylation, and hydroxyla-
tion may induce significant variability.
(c) Changes may occur during isolation, storage, and processing.
Many modifications can occur, such as deamidation, changing
Asn into Asp and Gln into Glu; 22 S 22 S 22 bridge reshuffling;
partial proteolysis; several cross-linking reactions (especially at
high temperature); and partial or full denaturation (see Section
7.2).It should further be realized that virtually all protein preparations used
in practice are mixtures of several protein species and generally contain
many other substances.
Question
In a publication by Miller et al. (J. Mol. Biol. 196 (1987) 641) concerning a series of
one-domain globular proteins, molar mass 5–35 kDa, the surface area of the various
groups on the peptide chains was calculated and it was established which part of that
surface is in contact with water and which part buried in the interior. Of the average
surface area in contact with water 51%would be nonpolar, 24%polar noncharged,
and 19%charged; for the interior these figures were 58, 39, and 4%, respectively. This
appears to disagree with the generally accepted idea that hydrophobic residues are
predominantly in the interior and the hydrophilic ones at the outside. Can you think
of factors that may explain this discrepancy? Take the size relations of protein
molecules into account and also Eq. (7.2).
Answer
Three factors would contribute to the results obtained by Miller et al. (a) In these
fairly small molecules, the core cannot accommodate all of the apolar residues.
Taking the size relations given, M¼20 kDa would lead to a volume of
1 : 27620 ¼ 25 :4nm^3 , i.e., a radius of 1.8 nm. Assuming the outer layer to have an
average thickness of 0.5 nm (see Figure 7.3), this leads to the core comprising
ð 1 : 3 = 1 : 8 Þ^3 ¼ 0 :38 of the volume. However, the molecules are not nearly perfect
spheres and the outer surface area would not be 4p 61 : 82 ¼41 nm^2 , but about
9 : 36 M^2 =^3 ¼68 nm^2 , causing a greater proportion of the molecular surface to be
exposed. The authors found indeed that the part of the molecule that is not exposed
to the solvent was only 15–32%for the proteins studied. (b) If amino acid residues
are in the interior, so must be their peptide bonds. The so-called hydrophobicity [Eq.
(7.2)] relates to the side groups. However, all peptide bonds are clearly hydrophilic,