The Secondary structure of protein was first recognized by Corey and Pauling in 1951. They both observed that secondary structure of protein must accommodate the hydrogen bonding potential of the peptide bond by utilizing the dihedral angles (Φ and Ψ) found in the peptides (free rotation is possible at Φ and Ψ bond). Secondary structure of protein plays key role in formation of tertiary and quaternary protein. In this section we will have a complete description of all secondary structure of protein.

Table of Contents

• Alpha helix (secondary structure of protein)
  • Other regular helical secondary structure of protein
    • 310 Helix
    • Pi Helix (π)
• Beta-Pleated Sheet
  • Antiparallel pleated sheet (βa)
  • Parallel pleated sheet (βp)
• β Turns
• Loops

If a polypeptide is immersed in water, a chain of polypeptide will not stay in an extended form, but fold up according to the polarity of the side chains it contains and the rotation of peptide backbone bond angels largely determined by Van der Waals radii of side chains. When a series of aminoacyl residues are arranged in an ordered fashion, they tend to adopt similar phi and psi angles leading to the formation of a secondary structure. Also, extended segments of polypeptide (e.g., loops/turns) can possess a variety of such angles.

General Properties of Secondary Structure of Protein

• Secondary structure of a protein is a regular, repetitive structure.
• All the φ and ψ angles in the polypeptide are the same.
• The φ and ψ angles define the two most common types of secondary structure which are
  • The alpha (α) helix, fall within the lower left-hand quadrants of a Ramachandran plot.
  • The beta (β) sheet, fall within the upper left-hand quadrants of a Ramachandran plot.
• Very few secondary structures are energetically possible.
• Secondary structure of protein is stabilized by
  • Sequence-dependent side-chain interactions and
  • Sequence-independent backbone interactions (particularly hydrogen bonding-which are 1/10 the strength of covalent bonds).

Alpha helix (secondary structure of protein)

At the California Institute, 1951, Linus Pauling, Robert Corey, and their colleagues proposed a new model for a helical structure in proteins, from atomic-resolution X-ray crystallography which they termed as the α helix. The common properties of α helix are

• This secondary structure is also sometimes called as classic Pauling-Corey-Branson alpha helix
• A common motif in the secondary structure of proteins, the alpha helix (α-helix) is a right-handed coiled or spiral conformation.
• The backbone hydrogen bonds are arranged such that the peptide C=O bond of the n^th residue points along the helix axis toward the peptide N-H group of the (n + 4^th) residue.
• H-bonds are approximately parallel to the helix axis.
• The R groups of each amino acyl residue in α helix face outward.
• The polypeptide backbone of an α helix is twisted by an equal amount about each α -carbon with a phi angle of approximately -57° and a psi angle of approximately -47°.
• One turn of the helix represents n=3.6 amino acid residues (A single turn of the α -helix involves 13 atoms from the O to the H of the H bond for this reason, the α -helix is sometimes referred to as the 3.6₁₃ helix) with a helical rise of 1.5 Å (0.15 nm) per residue which gives a helical pitch of 5.4 Å (p=0.54 nm).
• Among all types of local structure found in proteins, the α-helix is the most regular and the most predictable from sequence, as well as the most prevalent.
• An α helix can be either right-handed or left-handed, as presented in the figure 2.2.17. However, right-handed helices are energetically more favorable because there is less steric clash between the side chains and the backbone.  Essentially all α helices found in proteins are right handed.  Helices can be formed from either D- or L-amino acids, but a given helix must be composed entirely of amino acids of one configuration.
• The Ramachandran plot reveals that both the right-handed and the left-handed helices are among allowed conformations.
• α -Helices cannot be formed from a mixed copolymer of D- and L-amino acids. An α -helix composed of D-amino acids is left-handed. Keratin is one of the most abundant fibrous proteins and is almost entirely α-helical in nature. Proline disrupts the conformation of the helix, producing a bend. Glycine also often induces bends in α helices because of its small size.

Dipole moment in alpha helix

A peptide unit has a dipole moment arising from the different polarity of NH and C=O groups, these dipole moments are also aligned along the helical axis. The overall effect is a significant net dipole for the α helix that gives a partial positive charge at the amino end and a partial negative charge at the carboxy end of the α helix. This can lead to destabilization of the helix through entropic effects. As a result, α helices are often capped at the N-terminal end by a negatively charged amino acid, such as glutamic acid, in order to neutralize this helix dipole. Less common (and less effective) is C-terminal capping with a positively charged amino acid, such as lysine. The N-terminal positive charge is commonly used to bind negatively charged ligands such as phosphate groups, which is especially effective because the backbone amides can serve as hydrogen bond donors (Figure below).

Other regular helical secondary structure of protein

3₁₀ Helix

A 3₁₀ helix is a type of secondary structure rarely found in proteins. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier; this repeated n+3 → n hydrogen bonding defines a 3₁₀-helix. The amino acids in a 3₁₀-helix are arranged in a right-handed helical structure. Each amino acid specifically corresponds to a 120° turn in the helix which means helix has three residues per turn, and a translation of 2.0 Å (= 0.2 nm) along the helical axis, and has  almost 10 atoms in the ring that are formed by making the hydrogen bond. Residues in 3₁₀-helices typically adopt (Φ, Ψ) dihedral angles near (−49°, −26°).

Pi Helix (π)

A pi helix / π-helix is a type of secondary structure found in proteins. Although π-helices are rare and actually found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an alpha helix. The amino acids  in a standard π-helix are arranged in a right-handed helical structure. Each amino acid corresponds to a 87° turn in the helix (i.e., the helix has 4.1 residues per turn), and a translation of 1.15 Å (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier; this repeated n+5→n hydrogen bonding defines a π-helix. The majority of π-helices are only 7 residues in length and do not adopt regularly repeating (Φ, Ψ) dihedral angles throughout the entire structure. 

Beta-Pleated Sheet

The second most commonly occurring and identifiable secondary structure of protein is the β-strand.  β -strands are elongated peptide segments with atomic distances from side chain n to side chain n+2 of 0.7nm (7Å). Single β -strands are not stable structures but occur in association with neighboring strands. Thus they can be found as either parallel or anti-parallel with respect to the N- to C-terminal direction of the adjacent peptide strands.

Again, H bonds can only form between neighboring chains (“strands”) in pleated sheets and the following two conformation exists:

• When the two strands run in opposite directions the structure is referred to as an antiparallel pleated sheet (βa).
• When the two strands run in the same direction it is a parallel pleated sheet (βp). The side chains point outwards which is alternate up or down from the folds of the pleats and are roughly perpendicularly to the plane of the sheet.

Antiparallel pleated sheet (βa)

In an antiparallel arrangement, the successive β strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next. This arrangement produces the strongest inter-strand stability because it allows the inter-strand hydrogen bonds between carbonyls and amines to be planar & linear, which is their preferred orientation and therefore more stable. The peptide backbone dihedral angles are about Φ =–140°, Ψ= 135° in antiparallel sheets.

Parallel pleated sheet (βp)

In a parallel arrangement, all of the N-termini of successive strands are oriented in the same direction; this orientation may be slightly less stable because it introduces non planarity in the inter-strand hydrogen bonding pattern. The dihedral angles (Φ, Ψ) are about (–120°, 115°) in parallel sheets. This has been figure out that it is rare to find less than five interacting parallel strands in a motif. This is so because that a smaller number of strands may be unstable. If the β -strand contains alternating polar and non-polar residues it forms an amphipathic β -sheet. This distribution of hydrophilic and hydrophobic residues has been observed in the membrane protein porin that forms a β -barrel structure, where the non-polar residues stick into the hydrophobic part of the lipid membrane and the hydrophilic residues form part of the channel interior responsible for the passage of small molecules across the membrane. 

The higher-level association of β sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidosis  such as Alzheimer’s disease.

β Turns

β Turns are often found at sites where the peptide chain changes direction. These are sections in which four amino acid residues are arranged in such a way that the course of the chain reverses by about 180° into the opposite direction. To combine helices and sheets in their various combinations, protein structures must contain turns that allow the peptide backbone to fold back. Two turn structures are presented here in figure below using their Ramachandran plot coordinates.

These turns can be found almost always on the surface of proteins and often contain Proline and/or Glycine. Proline gives the backbone a special rigidity (fixed Phi torsion angle at -60°) and glycine has a high flexibility because of its hydrogen substituent. These secondary structure of protein are also stabilized through H-bond formation.

Loops

α helices and β strands are connected by loop regions of various lengths, irregular shape (Figure below),  and these regions are present at the surface of the molecule. The main-chain C=O and NH groups of these loop regions, in general do not form hydrogen bonds to each other, but are exposed to the solvent and can form hydrogen bonds to water molecules. Loop regions exposed to solvent are rich in charged and polar hydrophilic residues. As the combination of secondary structure elements forms the stable hydrophobic core of the molecule. During evolution, cores are much more stable than loops. The specific arrangement of secondary structure elements in the core is rather insensitive to the lengths of the loop regions. Loop regions are inherently flexible and usually participate in formation of binding sites and active sites of enzymes (e.g. antigen-binding sites in antibodies). Loop regions that connect two adjacent antiparallel β strands are called hairpin loops. Short hairpin loops are usually called reverse turns or simply turns.