Question

We discussed that the main driving force for protein folding (in an aqueous environment) is the hydrophobic effect. Using a thermodynamic analysis explain why this is the case. You analysis should take in to account the peptide bonds, polar side chains, non-polar side chains, the influence of solvent water, and the enthaplic and entropic contributions of each of these.

Answer 1

Protein structures are governed primarily by hydrophobic effects and by interactions between polar residues and other types of bonds.

The hydrophobic effect is the major determination of original protein structure. T

he aggregation of nonpolar side chains in the interior of a protein is favored by the increase in Entropy of the water molecules that would otherwise form cages around the hydrophobic groups.

Hydrophobic side chains give a good indication as to which portions of a polypeptide chain are inside, out of contact with the aqueous solvent.

Hydrogen bonding is a central feature in protein structure but only make minor contributions to protein stability.

Hydrogen bonds fine tune the tertiary structure by selecting the unique structure of a protein from among a relatively small number of hydrophobically stabilized conformations.

Disulfide bonding can form within and between polypeptide chains as proteins fold to its native conformation. Metal ions may also function to internally cross link proteins.