Question

For each of the following side chain interactions in a protein, give an example of two amono acids that interact that way and draw a structure that illustrates the interaction.

a. Hydrophobic interaction, b. Metal ion coordination, c. Covalent bond (in the side chain), d. Hydrogen bonding, e. Salt bridge

Answer 1

Hydrogen Bonding:

Examples of amino acid side chains that may hydrogen bond to each other:

Two alcohols: ser, thr, and tyr.
Alcohol and an acid: asp and tyr
Two acids: asp and glu
Alcohol and amine: ser and lys
Alcohol and amide: ser and asn

           

Salt Bridges:

The example is the prion protein with the salt bridge of glutamic acid 200 and lysine 204. In this case a very small loop is made because there are only three other amino acids between them. This salt bridge has the effect of straightening an alpha helix.

Hydrophobic Interactions:

Val,ile,leu,phe,ale

Disulfide bonds(covalent)

are formed by oxidation of the sulfhydryl groups on cysteine. Different protein chains or loops within a single chain are held together by the strong covalent disulfide bonds.