As described before, we can distinguish in proteins four different organizational levels:
The secondary structure or secondary level of organization has been defined as the conformation present in a local region of the polypeptide or protein, stabilized through hydrogen bonds between the elements of the peptide bond.
The organized secondary structures are maintained by Hydrogen bonding between different peptide groups, it means, between the N-H group of one peptide bond and a C=O group of another peptide bond.
Pauling and Corey, when studying the possible secondary structures of proteins, described that the main structures forming part of this level of organization should have the following characteristics (Pauling and Corey postulates):
• All amino acids belong to the steric L series
• The peptide group is planar and in trans configuration
• Every carbonyl oxygen and amide nitrogen are involved in hydrogen bond formation
• Rotation of the molecule only around the alpha-carbon atoms
• The hydrogen-bonded hydrogens lie close to a line joining the oxygen and nitrogen atoms involved in formation of the bond
• The R side chain of amino acids are not involved in the structure
The structures that are considered in this secondary level of organization include:
Beta -turns (aka Beta-bends aka hairpin bends)
Nonrepetitive secondary structure
It’s the secondary level of protein organization in which the polypeptide backbone is tightly wound around an imaginary axis as a spiral structure. (Helicoidal arrangement of the peptide chain)
In this clip, Linus Pauling describes how he discovered the alpha-helix:
Structural features of the Alpha-Helix:
- There are 3.6 amino acids per turn of the helix.
- Each peptide bond is trans and planar
- N-H groups of all peptide bonds point in the same direction, which is roughly parallel to the axis of the helix
- C=O groups of all peptide bonds point in the opposite direction, and also parallel to the axis of the helix
- The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it
- All R- groups point outward from the helix
Alpha-helix stability is affected by different factors, which include:
1. – electrostatic interaction between successive amino acids with R charged groups.
2. – the bulkiness of adjacent R groups
3. – Interactions between R groups spaced 3 or 4 residues apart.
About 1/4th of all amino acid residues in polypeptides are found in alpha-helices, the exact fraction varying greatly from one protein to the next
Observe in this example the alpha helix structures in calmoludin:
Beta pleated sheet
This secondary structure has been defined as the secondary level of protein organization in which the backbone of the peptide chain (Beta-strands) is extended into a zigzag arrangement resembling a series of pleats, with the peptide bonds organized in planes of alternating slopes (alternating ascending and descending direction). The Beta pleated sheet can be formed between two peptide chains or between different segments of the same peptide chain.
Characteristics of the Beta-pleated sheet include;
1. – Each peptide bond is planar and has the trans conformation
2.- The C=O and N-H groups of peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them
3.- All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.
There are two kinds of Beta pleated sheets:
Antiparallel: when the adjacent polypeptide chains run in opposite direction
Parallel: Adjacent polypeptide chains running in the same direction
Usually the segment of polypeptides that shows a Beta conformation are called individually beta-strands, and they are represented by an arrow pointing in the direction in which the strand runs (from the amino to the carboxyl group)
Both models are found in proteins, but the antiparallel structure is more stable than the parallel beta-sheet.
Betas conformation content in proteins is very variable: myoglobin, for example, does not show this kind of secondary structure, while 45 percent of the amino acids in chymotrypsin are part of a beta conformation.
It is important to note that not all the polypeptide chain is part of an alpha-helix or a beta conformation. There are also bends, segments irregularly coiled or forming extended stretches: Carboxypeptidase, for example, shows 38 % of the amino acids forming alpha-helix and 27 % forming beta structures, consequently around 35 % of the residues are not included in these secondary structures.
It’s the secondary level of protein organization which permits the change of direction of the peptide chain to get a folded structure.
They are known as well as reverse turns, hairpin bends or Omega-loops; they occur often in 5 amino acid residues or less and they lie on the protein surface because they are hydrophilic. Beta-turn loops allow for protein compaction, since the hydrophobic amino acids tend to be in the interior of the protein, while the hydrophilic residues interact with the aqueous environment.
Observe in the following figure how alpha-helix structures and Beta- conformations (beta strands represented by arrows) are linked through bents and beta turns that make this protein compact
Different amino acids favor different kind of secondary structures: while alanine, glutamate, and leucine have a propensity for being in α helices, valine and isoleucine apparently favor β strands, and glycine, asparagine, and proline tend to be present in beta-turns.
If you are interested in obtaining more information about secondary structure, this would be a very interesting article for beginning:
The discovery of the α-helix and β-sheet, the principal structural features of proteins
H. Jakubowski: Biochemistry On line. Protein Structure
Very good animations: