As a protein is made, the polypeptide is in an extended conformation, with every amino acid exposed to the aqueous environment. Although both polar and charged side chains can mix readily with water, this is not the case for nonpolar side chains

Question

Explain how hydrophobic interactions may play a role in the early stages of protein folding, and have an influence on the final protein conformation.

Answer 1

One reason that nonpolar groups are excluded from an aqueous environment is that a hydrophobic surface would organize water into a highly structured network of hydrogen bonds, which is energetically unfavorable. So, you would expect that nonpolar amino acids would group together early, forming "hydrophobic pockets," while the polar and charged side chains remain at the interface of the surrounding solution. In the final, folded protein, most of the nonpolar amino acids will remain buried inside the protein. This fold is more stable because nonpolar atoms are prevented from contact with water and remain in contact with each other.