PolyAlanine Peptides shown below spontaneously fold into alp

Poly-Alanine Peptides (shown below), spontaneously fold into alpha-helices. Why is it unfavorable for beta-peptides to fold into helical structures? Explain in terms of the Second Law of Thermodynamics. You can induce beta-peptide folding if you introduce positively and negatively charged side chains that can form salt bridges. Explain why introducing salt bridges makes beta-peptide folding spontaneous.

Solution

17a. ANS: Beta-peptide:

Beta peptides are composed with beta-amino acids. These are rare in nature; the only naturally occurring beta- amino acid is Beta-alanine. All biological peptide bods are present in an alfa form.

Beta peptides are sometimes artificially made from beta-amino acids, which are using in making of antibiotics.

In Alfa amino acids both the amino and carboxylic groups are present on same carbon center.

In beta amino acids the amino group is bonded to beta carbon rather than an Alfa carbon. The amino and carboxyl groups are a way from each other. So the helix formation of beta peptides is not possible.

Second law of thermodynamics:

It states “The heat cannot flow itself from colder body to a hotter body”. The entropy defines ideal thermodynamic processes.

The peptide bond formation is also considered as a chemical reaction, in which the water molecule is eliminated from each peptide bond formation. So it faces both thermodynamic and kinetic constraints.

Second law of thermodynamics states the peptide bond formation does not occur spontaneously. In this the energy is added into the system by some means and amino acids must be \"activated.\" The energy is produced by ATP hydrolysis.

17b. ANS:

Salt bridges in protein:

Natural proteins are only found with alpha peptide bonds. In proteinoids , beta, gamma and epsilon peptide bonds largely predominate.

Salt bridges help Beta peptides to fold into helix structure, due to its non-covalent interactions between the positive and negatively charged ions. It alters the chemical structure of peptide and favors to fold into helix structure.

Salt bridges effect on peptide ions:

The salt bridge mostly arisen from the anionic carboxylate (RCOO) and cationic ammonium (RNH₃⁺).

It neutralizes the amino and carboxyl (Acidic and basic) groups, which are present on side chains.

It promotes ionic interaction between positive and negatively charged ions (Amino group contain positive charge and carboxyl group contains negative group).

Any combination of the various amine and carboxyl groups of amino acid side chains will have this effect.