3 Facts On Alpha Helix Structure Of Protein And Functions

• 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 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.