Question

Outline how protein folding occurs and how this process is reversed to facilitate digestion with proteases such as trypsin prior to mass spectrometry analysis.

Answer 1

Proteins are formed by long chains of amino acid that are linked by polypeptide bonds. Proteins have four types of structure namely- primary, secondary, tertiary and quarternary.

A protein is said to be primary when it has only peptide bonds, that is, having linear chain.

A secondary structure is formed by spatially arranging the molecules present in the chain. They form hydrogen bonds between amino group and carboxyl group present ithe chain, but the association is present between to closely present amino acids.

Further, when this chain condenses randomly to form coil, the amino acids ineracts with other amino acids present farther to them. They can form hydrogen bonds, ionic bonds, some can form di-sulfide bonds and some weak vander wal force also operates.

The quarternay structure forms by the interaction of two different and adjacent polypeptide chains.

Now, this folding can be reversed by a process called denaturation. Denaturation is important because, the enzymes that we use to break the polypeptide chains acts on a particular site but this folding of chain hinders the activity of enzymes. Remember, denaturation process only disrupts the secondary, tertiary and quarternery structure, it does not break the peptide bonds.

The denaturation of proteins can be achieved by heating, treating them with alcohols, use of acids and bases etc.

heating disrupts the hydrogen bonds. Alcohol (70%) can disrupt hydrogen bonds and hydrophbic bonds. Acids and bases straighten the polypeptide chains by disrupting the ionic charges present on the amino acids.