Protein S, a cytoplasmic protein, is folded into its tertiary structure, surroun

Question

Protein S, a cytoplasmic protein, is folded into its tertiary structure, surrounded by water molecules (red and white). The environment has a pH of 7.4.

What would happen to the noncovalent interactions if the cell transported protein S from the cytoplasm to the lysosome, which has a pH ~4.5?

The amino acids shown are: (A) asparagine, (B) leucine, (C) alanine, (D) serine, (E) aspartate, and (F) arginine. Sometimes, a mutation occurs that substitutes alanine (yellow circle) with isoleucine (above right).

hint: utililize an online source to determine pka values

Explanation / Answer

pka values for the amino acids given

pka1. pka2. pka3. pl

Aspargine. 2.02. 8.80. ---- 5.97

Leucine. 2.36. 9.60. ---- 5.98

Alanine. 2.34. 9.60. ---- 5.97

Serine. 2.21. 9.15. ---- 5.68

Aspartate. 1.88. 9.60. ---- 2.77

Arginine. 2.17. 9.04. ---- 10.76

High concentration of hydrogen ions (low pH) (ph=4.5) will result in more groups being protonated. Carboxyl groups (aspartic acid, glutamic acid, the carboxy terminus) and phenolic groups are uncharged when protonated. The nitrogen groups (amines on lysine, guanidino of arginine, and imidazole in histidine, etc.) are charged when protonated.

Charged groups will tend to move towards the surface of the protein. Uncharged groups tend to move inwards. There may be a region that has an excess of like charges on adjacent chains which repel each other when there were mixed charges at physiological pH.

There is can be an increased ionic strength to the medium that impacts the electrostatic interactions of atoms, but the same can be achieved with neutral salts. This is the principle behind "salting in"/"salting out".

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