Question

Proteins, like DNA, often adopt a coiled-like structure, known as an a-helix. This helical structure is stabilized by the formation of intramolecular hydrogen bonds between the backbone amino group of one amino acid and the \(\mathrm{C}=\mathrm{O}\) group of another amino acid a bit further down the chain. The amino acid proline is often referred to as a "helix breaker" because when it is part of a protein molecule, the \(\alpha\) -helix begins to unravel at its position. What is so different about this particular amino acid that would cause this disruption of the helix structure and earn it that name?

Short answer

Proline's unique ring-like side chain, which forms a bond between its amino nitrogen and side chain carbon, confers rigidity and prevents it from adopting the conformations required to form hydrogen bonds in the α-helix. As a result, proline is unable to form stable hydrogen bonds with other amino acids, disrupting the α-helix structure and earning it the name "helix breaker."

Step-by-step solution

1. Brief overview on α-helix structure and hydrogen bonds in proteins

The α-helix structure in proteins is a coiled-like structure stabilized by intramolecular hydrogen bonds. These hydrogen bonds form between the amino group (-NH) of one amino acid and the carbonyl group (C=O) of another amino acid further down the chain.

2. Introducing proline amino acid

Proline is an amino acid that is different from other amino acids in a protein. It disrupts the α-helix structure when it is part of a protein molecule, hence earning the name "helix breaker."

3. Unique structure of proline

Proline has a unique structure compared to other amino acids as it has a ring-like side chain, forming a bond between the amino nitrogen and its side chain. This bond between the nitrogen atom and side chain carbon atom confers rigidity, preventing proline from adopting the conformations necessary to form hydrogen bonds in the α-helix.

4. Inability to form stable hydrogen bonds

Because of proline's unique structure, it is unable to form stable hydrogen bonds with other amino acids in the α-helix. When proline is present in a protein molecule, the intramolecular hydrogen bonding that helps to stabilize the α-helix structure is disrupted, causing the helix to unravel at that position.

5. Conclusion

Proline, an amino acid with a distinct ring-like structure, disrupts the intramolecular hydrogen bonds in α-helix of proteins because it cannot form stable hydrogen bonds necessary for maintaining the helix structure. Its unique structure and effect on the protein's α-helix earn it the name "helix breaker."

Key concepts

Protein Structure

Proteins are the workhorses of the cell, performing a vast array of functions critical for life. They are made up of chains of amino acids, and the sequence of these amino acids determines each protein's unique 3-dimensional structure. The α-helix is a common structural motif in proteins, resembling a coiled spring, which contributes to the flexibility and stability of the overall protein architecture. Proteins can also display other structural features like β-sheets and random coils, which, together with helices, fold into a functional 3D conformation.

• The primary structure of a protein is its amino acid sequence.
• The secondary structure includes α-helices and β-sheets, formed by hydrogen bonds.
• Tertiary structure is the overall 3D shape of a single protein molecule.
• Quaternary structure involves the arrangement and interaction of multiple protein subunits.

Intramolecular Hydrogen Bonding

Within the elegant twist of an α-helix, intramolecular hydrogen bonds are the invisible hands holding the structure together. These bonds are formed when a hydrogen atom, covalently attached to a more electronegative atom like nitrogen or oxygen, exhibits an attraction towards another electronegative atom with a lone pair of electrons, often in close proximity on the protein backbone.

The Role of Hydrogen Bonds in Protein Structures

Hydrogen bonds bestow proteins with both structural integrity and flexibility, allowing for the dynamic nature required for biological function. For instance, enzymes can adapt their shape to match the molecules they act upon due to these bonds, exemplifying their role beyond mere structural elements.

Proline Amino Acid

Among the cast of twenty standard amino acids, proline is the maverick. With its distinct ring structure that links the nitrogen atom to the side chain, proline is more rigid than its peers. This rigidity affects how proline fits into protein structures; although it can disrupt helices, it also provides kinks and turns necessary for the full range of protein shapes that dictate their functions.

Proline's Structural Implications

In the cinema of protein folding, proline acts like a plot twist, often redirecting the protein's storyline and introducing bends necessary for complex tertiary structures. Because of its structural uniqueness, proline is a vital player in the shaping of biological molecules.

Helix Breaker

The term 'helix breaker' isn't a nickname given lightly in the world of proteins. It signifies the profound impact proline has on the α-helix structure. As an intruder in the helical realm, proline's inability to participate in the network of hydrogen bonds makes it a disruptor of peace, causing the helix to lose its stable, coiled form. In the context of protein folding, this disruption is not necessarily a negative attribute but can be essential for achieving the final protein structure.

Proline's Role in Function and Flexibility

While 'breaker' may evoke thoughts of destruction, proline's impact on helices is a nuanced one. It introduces flexibility and function into protein structures, facilitating the tight turns and complex folding required for proteins to carry out their diverse roles within the cell.