Protein Alpha Helix: Causes and Function

In summary, alpha helices are stabilized by hydrogen bonds between amino acids in the helix, but in aqueous solution, these bonds would form with water instead, making an unfolded state more stable. In a lipid environment, however, the unfolded state is less stable, making folding into an alpha helix more likely. The rest of the protein's structure also plays a role in stabilizing the helix. Side chains will always point outside of the helix. This is exemplified by leucine zippers, where hydrophobic residues become buried in the dimerized helix.
  • #1
lha08
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Homework Statement


I'm a little confused as to how exactly a protein folds into an alpha helix...like what causes it exactly to assume that conformation...does it fold spontaneously in water (like i know hydrophobic R groups cause the protein to fold where the hydrophobic groups are faced towards the inside)? or does it like just simply fold randomly into that shape based on its function without the environment playing any role?
thanks


Homework Equations





The Attempt at a Solution

 
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  • #2
Alpha helices are stabilized because amino acids in the helix can form hydrogen bonds with their amide groups to amide groups directly above and below them in the helix. However, in aqueous solution, these amide bonds would form hydrogen bonds with water, so forming an alpha helix provides little additional stability for the folded state. Therefore, most of the time, if you take a sequence that forms an alpha helix in a protein, isolate it from the rest of the protein, and determine its structure in water, it generally will not form an alpha helix spontaneously. In a lipid environment, however, the unfolded state will not be able to form hydrogen bonds with the solvent, so folding into an alpha helix does provide significant stabilization. This is one reason why the transmembrane regions of membrane proteins are very often alpha helical.

Therefore, the rest of the protein's structure (i.e. the chemical environment around the alpha helix) plays a big role in stabilizing an alpha helix's structure.
 
  • #3
Ygggdrasil said:
Alpha helices are stabilized because amino acids in the helix can form hydrogen bonds with their amide groups to amide groups directly above and below them in the helix. However, in aqueous solution, these amide bonds would form hydrogen bonds with water, so forming an alpha helix provides little additional stability for the folded state. Therefore, most of the time, if you take a sequence that forms an alpha helix in a protein, isolate it from the rest of the protein, and determine its structure in water, it generally will not form an alpha helix spontaneously. In a lipid environment, however, the unfolded state will not be able to form hydrogen bonds with the solvent, so folding into an alpha helix does provide significant stabilization. This is one reason why the transmembrane regions of membrane proteins are very often alpha helical.

Therefore, the rest of the protein's structure (i.e. the chemical environment around the alpha helix) plays a big role in stabilizing an alpha helix's structure.

So if i understood correctly, in an aqueous environment, the protein prefers to make hydrogen bonds with water via the N--H group of the amine (and also the C double bonded O in the carboxyl?) and therefore the more stable conformation is the unfolded protein?

Like since most protein structures want to be in its most stable conformation, you said that in a lipid environment, folding is more likely, but isn't a lipid environment hydrophobic, so the hydrophobic groups of the protein will just orient themselves towards them? maybe I am just overthinking it though...but what if it folds in a lipid environment, what parts of the alpha protein will face the outside and which on the inside...?
 
  • #4
lha08 said:
So if i understood correctly, in an aqueous environment, the protein prefers to make hydrogen bonds with water via the N--H group of the amine (and also the C double bonded O in the carboxyl?) and therefore the more stable conformation is the unfolded protein?

Yes. An unfolded conformation will be more stable than a folded conformation for an isolated alpha helix.

Also, a bit of a nomenclature issue, an amine is a nitrogen attached to only sp3 carbons and hydrogens (e.g. CH3NH2). An amide is a -(C=O)-N- group, a nitrogen that is bonded to a carbonyl carbon. Both the oxygen in the C=O group and the H of the N-H of the amide participate in hydrogen bonding.

Like since most protein structures want to be in its most stable conformation, you said that in a lipid environment, folding is more likely, but isn't a lipid environment hydrophobic, so the hydrophobic groups of the protein will just orient themselves towards them? maybe I am just overthinking it though...but what if it folds in a lipid environment, what parts of the alpha protein will face the outside and which on the inside...?

Side chains will always point outside of the alpha helix since there is not enough space inside of the helix to accommodate the side chains.

A good example of how the hydrophobic effect drives protein folding and alpha helix formation in aqueous solution is a leucine zipper. A leucine zipper is an alpha helical structure that contains hydrophobic residues along one face of the helix. Here, it is unfavorable to have the hydrophobic side chains solvated in water in the unfolded state. In order to reach a state of lower free energy, the leucine zipper peptides will form alpha helices and dimerize. Here, the hydrophobic residues become buried in the space between the alpha helices.
 
  • #5


The folding of a protein into an alpha helix structure is a complex process that is influenced by several factors, including the amino acid sequence, the environment, and the function of the protein. The primary driving force for protein folding is the hydrophobic effect, where hydrophobic amino acid side chains tend to cluster together in the interior of the protein, away from the surrounding water molecules. However, other interactions such as hydrogen bonding and electrostatic interactions also play a role in stabilizing the protein's structure.

The exact mechanism by which a protein folds into an alpha helix is still not fully understood, but it is believed to involve a combination of random folding and specific interactions between the amino acid side chains. In some cases, the protein may fold spontaneously in water, while in others, the presence of chaperone proteins or specific environmental conditions may be necessary for proper folding.

The function of a protein can also play a role in its folding into an alpha helix structure. For example, proteins that are involved in cellular signaling or transport often have specific regions that are designed to interact with other molecules, and these regions may adopt an alpha helix conformation to facilitate these interactions.

In summary, the folding of a protein into an alpha helix is a complex process that is influenced by various factors such as the amino acid sequence, the environment, and the protein's function. Further research is needed to fully understand the mechanisms behind protein folding and how it relates to the protein's biological function.
 

1. What is a protein alpha helix?

A protein alpha helix is a common secondary structure found in proteins, characterized by a coiled shape formed by a polypeptide chain. It is stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid, creating a helical shape.

2. What causes a protein alpha helix to form?

The primary factor that causes a protein alpha helix to form is the hydrogen bonding between the amino acids in the polypeptide chain. This bonding is driven by the partial positive and negative charges on the carbonyl oxygen and amide hydrogen, respectively. Additionally, the hydrophobic nature of the amino acid side chains also contributes to the stability of the alpha helix.

3. What is the function of a protein alpha helix?

The function of a protein alpha helix varies depending on the specific protein it is found in. However, in general, alpha helices are involved in protein folding, stability, and specific interactions with other molecules such as DNA, RNA, and other proteins. They can also play a role in protein-protein interactions and enzymatic activity.

4. How does a protein alpha helix contribute to protein structure?

A protein alpha helix contributes to protein structure by providing stability and organization to the polypeptide chain. It also helps to form the overall 3-dimensional structure of a protein, which is crucial for its proper function. Additionally, alpha helices can act as recognition sites for other molecules, further contributing to the overall structure and function of a protein.

5. Can the formation of a protein alpha helix be influenced by external factors?

Yes, the formation of a protein alpha helix can be influenced by external factors such as changes in temperature, pH, and the presence of certain molecules. These factors can disrupt the hydrogen bonding between amino acids, leading to a change in the shape of the alpha helix or even the unfolding of the protein. This can have significant impacts on the function of the protein.

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