Question

Proteins have segments of their polypeptide chain/chains that can be repeatedly coiled or folded into helix and pleated structures, respectively. This is due to hydrogen bonds between partially charged oxygen and hydrogen atoms in the repetitive polypeptide backbone (which excludes the amino acid side chains).

My guess is that one structure (either a helix or pleated structure) is lower in potential energy compared to the other (because one structure likely maximises the number of hydrogen bonds that can form, compared to the other), which begs the question, why do both structures form, if they are largely a result of hydrogen bonds in the polypeptide backbone, rather than only one structure forming?

Is it a result of both hydrogen bonds in the polypeptide backbone, and interactions between amino acid side chains?

My own attempt at answering the question:

Intuitively, I believe the terms 'secondary' and 'tertiary' structure are misleading. My reasoning is that, it does not make sense to say that hydrogen bonds between the atoms of different amino acids in a polypeptide backbone, bring separate amino acids closer together, before interactions between amino acid side chains (R groups) occur (especially since some of these interactions between R groups are hydrogen bonds themselves).

I assume, the previous statement can be valid stated vice versa, i.e., that interactions between amino acid side chains bring separate amino acids closer together, before hydrogen bonding can occur between the atoms of different amino acids.

Ultimately, if this is the case in reality, I would expect both H bonds and AA side chain bonds to occur, effectively, simultaneously, blurring the distinctions that have been established by humans.

Answer 1

Proteins fold into both alpha-helix and beta-pleated sheet secondary structures due to varied propensities of amino acids and interactions amongst amino acid side chains. The formation of these structures is dependent on hydrogen bonds in the peptide backbone and is also influenced by the chemical properties of the amino acids and other non-covalent interactions. These structures are integral to the unique 3D shape and function of proteins.

Step-by-step explanation:

The secondary structure of proteins involves the local folding or coiling of the polypeptide chain into alpha-helix and beta-pleated sheet structures, primarily due to hydrogen bonding between the peptide backbone constituents, excluding the side chains (R groups).

The hydrogen bonds in an alpha-helix occur every fourth amino acid, maintaining the structure's stability, while in beta-pleated sheets, they occur between segments of the polypeptide chain that can be near or far from each other, either in the same chain or between multiple chains.

While it may seem that one structure should be favored over the other, both structures form because different amino acids have a propensity for either the alpha-helix or beta-pleated sheet conformation. This propensity is influenced by the chemical properties and spatial constraints of the amino acids and their side chains.

Additionally, other non-covalent interactions, such as van der Waals forces, hydrophobic interactions, and electrostatic interactions, also play significant roles in tertiary structure formation. These interactions can occur concurrently with or as a result of the establishment of secondary structure.

Moreover, the secondary structures, alpha-helix and beta-pleated sheets, are often separated by less structured regions known as random coils, and the particular combination of these structures gives each protein its unique 3D shape, which is essential for its biological function.

The folding process is complex and dynamic, and it is facilitated by chaperone proteins to ensure that polypeptides fold into the correct bioactive conformations.