3D Structure Prediction Bioinformatics Protein Structure

Alpha-Helices

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The α-helix is a common element of protein secondary structure, formed when amino acids “wind up” to form a right-handed helix where the side-chains point out from the central coil. 

Properties

  • An α-helix has 3.6 residues per turn, meaning amino acid side chains that are three or four residues apart are bought together in space and so α-helices are stabilized by hydrogen bond 
  • An α-helix secondary structure is stabilized by hydrogen bonds between carbonyl oxygen and the amino group of every third residue in the helical turn with each helical turn consisting of 3.6 amino acid residues
  • The side chain of amino acids is projected outward from the outer helical surface
  • Some amino acid residues in a peptide sequence promote α-helical assembly
  • α-helix is not so stable secondary structure and therefore more stable coiled-coil-like helices are generated through association with other α-helices
  • The α-helix motif is adapted by comparatively simple homopeptides such as poly(Z-l-lysine) or poly(Bz-l-glutamate), which are traditionally prepared by ring-opening polymerization of AA NCAs 

Although the rigid-rod character is preserved, the helices resulting from sequence-defined peptides can be longitudinal polarized, laterally amphiphilic, or can have hydrophobic patches or sticky ends. This allows programming of the interaction capabilities of α-helices and leads to a more complex self-assembly behavior.

The “screw sense” of an alpha helix can be right-handed (clockwise) or left-handed (counter-clockwise). Despite the fact that, based on the Ramachandran plot, both right-handed and left-handed alpha helices are among the permitted conformations, the right-handed alpha helix is energetically more favorable because of fewer steric clashes between the side chains and the main chain. 

The first two protein structure to be determined, myoglobin and hemoglobin, consists mainly of alpha helices. When an alpha helix runs along the surface of the protein, one side of it will show polar side chains (solvent accessible) while the other side will show non-polar side chains (part of the hydrophobic core). The alpha helix fits nicely into the major groove of DNA. Many common DNA-binding motifs, such as the helix-turn-helix or the zinc finger motif, feature a short alpha helix that binds to the major groove of DNA.

A common fold found in transmembrane proteins is alpha-helical bundles running from one side to the other side of the membrane. 

Alpha helices are named after alpha keratin, a fibrous protein consisting of two alpha helices twisted around each other in a coiled-coil. In leucine zipper proteins (such as Gcn4), the ends of the two alpha helices bind to two opposite major grooves of DNA. The name leucine zipper comes from the regularly spaced leucine side chains from both helices that form the hydrophobic core of these structures. 

There are multiple spectroscopic techniques that allow the detection of alpha helices in proteins without determining their three-dimensional structures

  • CD spectroscopy 
  • NMR chemical shifts 

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