Alpha helix is a secondary structure of protein. The main chains or the backbone twists in a helical fashion while the side chains hang outwards and away from it.
Alpha helix structures of protein are composed of similar residues with same configuration such that the hydrogen bonds are formed at proper spaces. Hydrogen bonds are responsible for the stability of the alpha helix protein.
Alpha Helix Structure Of Protein
Alpha helix structure of protein has a helical structure as the name suggests. Let us look at the details of alpha helical structure of a protein.
- Alpha helix is a secondary structure of proteins or polymers of peptides that have a rigid, rod like structure.
- These polypeptide chains can be both left and right-handed but the right-handed ones are more commonly found secondary structure of protein.
- Side chains of the polypeptides are faced out and away from the helix.
- Polar side chains improve the stability of the structure.
- To further increase the stability of the alpha helix, several such coiled alpha proteins come together to form a functional motif.
- The alpha helix proteins have 3.6 amino acid residues in every helical turn and a pitch of 0.54 nm (or 5.4 Å).
- They have length of 10-15 amino acid residues and are around 12 Å wide.
- Intramolecular hydrogen bonds that form between the -NH group of the amino acids and the -COOH group of the amino acids, are placed four residues apart, keep the alpha helix structure of protein stable.
Alpha Helix Amino Acid Sequence
Some amino acids are capable of forming an alpha helical structure while others disrupt it. Let us learn in detail why this happens.
- Alpha helix structure of proteins consist of the same residues that can be either D- or L- amino acid residues in a single polymeric chain.
- Amino acids such as Alanine, Glutamine, Leucine, Methionine and Arginine have higher tendency of forming an alpha helix protein and are often found in it.
- Amino acids such as Proline, Glycine, Tyrosine and Serine are not found in alpha helix structure protein as often because the hydrophobic surface of their side chains does not contribute towards the hydrogen bonding.
- Amino acids having -R groups that are too long or too short are not capable of forming a stable main chain.
- Glycine residues distort the structure of the helix due it’s extremely small size which allows it to attain several alternate main chain conformations.
- Unavailability of the -NH group in the proline residues for the formation of the hydrogen bond and their rigid ring structure, makes it unfavorable for alpha helix formation as it disrupts the hydrogen bond formation. As a result, proline residues, if present in the alpha helix structure of protein are usually found in the beginning or the end of the main chain.
Helix Turn Helix
A helix-turn-helix motif of 20 amino acids that acts as the DNA binding motif, contains a dimer of alpha helix structure of protein. Let us learn more about helix-turn-helix.
- They fit perfectly into the major groove of the DNA which is also 12 Å wide and 6-8 base pairs deep (based on the B- DNA which is the most common form of DNA) as they have structurally evolved to be able to fit into it.
- Helix turn helix, DNA binding motifs are composed of two alpha helix protein structures, that are joined together at the turn by a short amino acids chain. Helix turn helix motif contains a total of twenty amino acids, of which the first alpha helix protein is composed of eight amino acids while the second alpha helix is composed of nine amino acids.
- The short amino acid chain connecting these two alpha helices protein structures are only three amino acid long.
- These DNA binding motifs have a total of three highly conserved amino acids, such that every component of the helix turn helix has one conserved region.
- In the first alpha helix protein structure, alanine at the fifth position is highly conserved followed by glycine which is the 1st amino acid out of the three present in the turn chain and is found at the ninth position in the helix turn helix motif. The third conserved amino acid is usually found at the fifteenth position within the second alpha helix and is either valine or isoleucine.
- These conserved amino acids are mainly responsible for maintaining the structure of helix–turn–helix so that they can fit into the major groove of the DNA.
Globular proteins are composed of both alpha helical structures and beta sheets. Let us see in detail how these two different secondary structures of protein are arranged.
- In the globular proteins, the beta sheet is completely covered up with alpha helices on one side such that one side has polar side chains and other has non polar side chains.
- The alpha helix protein structure in a globular protein, usually has 11 amino acid residues with a 17 Å length.
- They have a hydrophobic or non polar part that is buried inside the core while the hydrophilic part is present exposed outer surface. This configuration allows a globular protein to become water soluble.
Transmembrane proteins are present in the plasma membrane of a cell, such that they pass through it. Let us discuss the composition of transmembrane protein in detail.
- Alpha helical proteins form a major part of the transmembrane proteins.
- Alpha helix structure of protein present in the lipid bilayer of the cell, as a transmembrane protein, usually possesses both hydrophobic and hydrophilic side chains.
- The hydrophobic side chains interact with the lipid that is present in the membrane while the hydrophilic side chains remain exposed on the outer surface.
Alpha solenoids are supercoiled structures composed of helix turn helix motifs arranged in anti-parallel fashion. Let us have a look at alpha solenoid structures.
- They can be composed of Armadillo or HEAT repeat proteins as well.
- They are structurally efficient for protein- protein interactions as their conformation can be easily changed by the use of mechanical forces.
Functions Of Alpha Helix Of Protein
Although specific function of the alpha helical proteins depend on their tertiary structure, they are involved in several diverse metabolic processes inside a cell.
The functional groups of the side chains of the amino acids in the cylindrical helix or the main chain of the alpha helix structure of protein, that protrude out are responsible for interacting with other protein structural motifs or with hydrogen bonding sites in the major or minor grooves of the DNA.
Let us look into the detailed structures of some functional motifs of alpha helical structures of proteins.
DNA binding motifs
DNA binding motifs are proteinaceous structures that bind to the major groove of the DNA and take part in gene regulation.
Helix Turn Helix
- An alpha helix protein of 20 amino acids that acts as a DNA binding motif, also called helix- turn- helix domain, is responsible for maintaining the structural integrity of the DNA by binding at its major groove while beta- sheet protein binds to the minor groove of the DNA. It also allows the transcription factors to bind to the target sequence in the DNA.
- Helix- turn- helix can fit into the major groove of the DNA with different orientation, that is, parallel or anti- parallel.
- In the major groove, –NH2 terminus of the first alpha helix interacts with the negative charge of the phosphate backbone because the -NH2 terminus possesses a slight positive charge. The helix turn helix motif interacts with very specific phosphate groups of around 5-6 base pairs present in the backbone of the DNA to form hydrogen bonds.
Helix Loop Helix
- These helix- loop- helix motifs are the DNA binding proteins that play the role of transcription factors and have a conserved sequence of 40-50 amino acids.
- Their specificity for DNA binding depends on 15 amino acid residues called the basic helix- loop- helix proteins (bHLH).
- Absence of basic helix- loop- helix leads to hetero- dimerization of these motifs which renders them incapable of binding to the DNA.
- Helix loop helix proteins having this bHLH segment, act as transcription factors while those that lack the bHLH segment act as their negative regulators.
Globular proteins are the most abundant form of proteins and are called so due to their shape, where, the hydrophobic face is hidden inside the globule while the hydrophilic surface remains exposed.
- They are capable of performing a diverse range of functions such as binding protein (example: histone that bind to the DNA), bio-catalysis (all enzymes are globular proteins), regulation, transport, blood clotting (example: fibrin), cellular and extra cellular structures (example: actin in microfilament formation and cell membrane proteins), immunity (example: immunoglobulins), membrane proteins (example: transmembrane proteins) and cellular signaling.
Alpha helix structure of protein are usually composes the transmembrane proteins and travel the bilipid layer many time.
- Functions of these transmembrane helical proteins depend upon their location within the lipid bilayer.
- They can function as the transportation bridge for polar or hydrophilic solutes, signal recognition, receptors and as the ion pumps.
Coiled Coils Domains
- These domains are ubiquitous in proteins found in most of the organisms.
- As the alternate third or fourth hydrophobic residues are conserved in the coiled coils domains, they assemble into a unique manner such that their hydrophobic sides are towards each other. They can coil around each other in parallel or anti parallel fashion.
- Coiled coil domains play important roles in membrane vesicle transport system, where they facilitate conformational changes in centrioles, Golgi apparatus and transport vesicles.
- They are present in the kinetochores as well, where allow attachment of spindle fibers to the chromatids.
- They are often used as molecular spacers for oligomerization. They mediate vesicle tethering by acting as a spacer molecule that bridges the gap of 0.5um between the Golgi and the transport vesicles.
Alpha solenoids are composed of repeated pairs of alpha helix structure of proteins that ensemble in an anti- parallel manner.
- They can be present on the outer surface of the protein where they can facilitate interaction between proteins or can be buried inside the protein as well where they take part in shaping the protein.
- They are involved in protein biosynthesis, vesicle transport, DNA repair and act as transcription factors as well.
- Alpha solenoids are found in nuclear pore complexes as well.
It can be said that the alpha helix structure of protein is not only ubiquitous in its presence but is also ubiquitous in its functions. There functions are varied based on not only their structure and co-polymers but also their topology.