General Index


Secondary Structure of Proteins




Torsion angles

First we show a tripeptide in which side chains are represented as green atoms:

The atoms of both peptide bonds are on the same plane (peptide bond doesn't allow rotation). However, rotation (torsion) is possible around bonds N-Ca and C-Ca, that are known as torsion angles or conformation angles. Angle Y (Psi) is the torsion around the a-carbon and the carbon of the -C=O group; angle F (Phi) is the torsion between nitrogen (N) and the next a-carbon.

The tripeptide appears in the screen with values F=60º and Y=180º.

Angle F is the torsion between the N of the peptide bond and the previous a-carbon:

Angle Y is the torsion between the C of the peptide bond and the next a-carbon:

Not all possible values are allowed. For example, values of F=0º and Y=0º, F=180º and Y=0º or F=0º y Y=180º are never seen in proteins. They show Steric Hindrance, that is, atoms ovelap. On the contrary, some values are very frequent, for example:

  • Values of F = -57º, Y= -47º. They are the torsion values of the Right-handed a-helix:
  • Values of F = -119º, Y= 113º. These values correspond to the Parallel b sheet:
  • Values of F = -139º, Y= 135º. These values correspond to the Antiparallel b sheet:

The spatial conformation of a protein is such that some torsion angles are preferred (see The Ramachandran Plot in the text). These values represent not only a minimum of steric hindrance, but also the conformations that maximize the formation of hydrogen bonds between the peptide groups -C=O and -N-H. The resulting structures are what we call Secondary Structures. Secondary structure can be of three main types: Helices, Sheets and Turns.




Helices

a-Helix

For torsion values of F=-57º and Y=-47º, Hydrogen bond formation is maximized, giving a right-handed helix. For a hexadecapeptide (16),

The polypeptide chain folds as la regular right-handed helix with the side chains (represented here as green atoms) directed towards the exterior of the helix. The main features are:

  • Helix pitch, 0.54 nm
  • Mean translation per residue, 0.15 nm, meaured along the main axis of the helix.
  • Residues per turn, 3.6

This structure allows the formation of hydrogen bonds in such a way that the group -C=O of the n residue is hydrogen-bonded to the -N-H of the n+4 residue:

The a-helix was so named thanks to the studies of Pauling and Corey, that proposed this structure for the a-keratins, fibrous proteins that are the main constituent of hair, nails and other skin annexes. a-helices are rendered by Jmol as red-colored ribbons. A cytoskeletal protein analogous lo a-keratins is Vimentine:

Other fbrous proteins whose structure is mainly a-helix are Fibrinogen of blood plasma and Myosin of the muscle:


However, the a-helix is by no means restricted to fibrous proteins. This structure is indeed the most frequent secondary structure in all proteins, erither fibrous or globular. As an example, let's see the structure of Myoglobin, an oxygen storage protein in muscle having a simlar estructure to any of the hemoglobin subunits:

With a heme B prothetic group:

Also the peptide hormone Glucagon, a single a-helix:

The tendency to form a-helices is largely determined by the nature of the side chains. Some are stabilizers while other are destabilizers (see text, Ch. 9).

An interesting case is that of the aminoacid Proline. Being a secondary amine, lacks a donor -NH group for hydrogen bonding. In addition, proline often forms cis peptide bonds instead of the normal trans. Then, proline very often interrupts a-helices creating and inflexion point in the general direction of the helix:

In this image we see how proline interrupts the a-helix. The protein backbone appears in green, proline in cpk colours and hydrogen bonds in white.


Other helicoidal structures

Much less frequently than a-helix appears in proteins the so-called 3.10 Helix:

With values of F= -49 and Y=-26, giving a longer and narrower structure, with three aminoacids per turn. Hydrogen bonding takes place between the -CO of the residue in position n and the -NH of position n+3:

Other helicoidal structure (theoretical, not seen in practice) is the p-Helix:

wider anf shorter than the a-helix, having values of F=-57 and Y=-70. Hydrogen bonding is established between residues n and n+5:

Far more importance have the helices based on the aminoacid Proline. The structure of the synthetic peptide Polyproline shows a left-handed helix, wider than the a-helix:

A structure similar to polyproline can be found in Collagen. The Collagen Monomer or Tropocollagen is formed by three left-handed helices similar to polyproline;

This structure is the basis of the collagen fibers, widely distributed in all mesodermic animal tissues:



Laminar structures

The studies of Astbury in the thirties on the crystal structure of fibrous proteins showed that the stretching of a-keratins in conditions of high humidity gave a different structure, called b-keratin.

Futhter studies by Pauling and Corey showed that b-structures are not fully extended, having torsion values F between -115 y -140 and Y between 110 and 140. Studies on many other proteins demonstrated that this structure not only appears in fibrous proteins, but also in the globular ones.

b structures correspond to two general types. For F=-119º and Y=113º, we get the Parallel b chain:

And for F=-139º and Y=135º the Antiparallel b chain:

The names "parallel" and "antiparallel" define the pattern of hydrogen bonding between chains, as explained below. In both cases, the polypeptide chain appears extended along the N-C axis.

In the a-helix, hydrogen bonds are established within the structure. In b structures, hydrogen bonds form with other chains, either in the same of in a different polypeptide. The hydrogen bonds are directed perpendicular to the main axis of the peptide chain. This interaction can take place in two ways:

In one case, the chain interacts with another being both in the same N-C direction (parallel). When the interaction takes place between several chains, it appears the structure called Parallel b Pleated Sheet:

In this figure appear four polypeptide chains (side chains are not represented) extended in the same sense N-C. Hydrogen bonds are formed:

The general structure is that of a pleated sheet or a stair in which the a-carbons are located at the vertices of the dihedral angles and the peptide planes on the planes, horizontal or vertical, of the stair.

By convention, b structures are represented as yellow arrows pointing the direction N - C:

When the b chains interact in such a way that the polarity is opposite in adjoining chains, the resulting structure is an Antiparallel b Pleated Sheet:

In this figure appear four polypeptide chain forming an antiparallel pleated sheet. Hydrogen bonding pattern is:

In this case, arrows appear in opposite senses:

b Structures appear both in fibrous and globular protein. Among the first we have silk Fibroin:

It consists in several stacked antiparallel b-sheets. It is represented as:



An example of b parallel structure in globular proteins is the so-called b-barrel:

It is represented as:

An example of globular protein with predominant b structure is any of the subunits of Concanavallin A:

We can see that b structure is predominant:



Turns

Very often the peptide chain shows 180 degree turns. These inflexions present a special secondary structure, stabilized by hydrogen bonds. It is usually seen associated with sucessive tracts in antiparallel b structure. It is then called b-Turn:

Hydrogen atoms are not represented. The stabilizing hydrogen bond is:

This is a class I b-turn, in the sequence NVDN. There is a hydrogen bond between the first and the fourth aminoacids.

In the peptide FHGR we can see another b-turn:

With its stabilizing hydrogen bond:

The third position is occupied by Glycine, a normal occurrence in b-turns due to its small volume.

b-Turns appear generally intercalated between peptide tracts in b structure. an example is the following:

b-Turns are represented in color blue:



Overview

As an overview of all the secondary structures, we'll look at the molecule of Cytochrome P450 CAM:

The different secondary structures are:

  • a-Helices:
  • b-Structures:
  • b-Turns:

And in grey (or in white) portions not having secondary structure.


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