Protein Secondary Structure

– In the last topic in Biochemistry section , we discussed The Protein Primary Structure but now we will talk about Protein Secondary Structure.

Secondary structure of protein

– The polypeptide backbone does not assume a random three-dimensional structure, but instead generally forms regular arrangements of amino acids that are located near to each other in the linear sequence.

– These arrangements are termed the secondary structure of the polypeptide.

– The α-helix, β-sheet, and β-bend (β-turn) are examples of secondary structures frequently encountered in proteins.

– [Note: The collagen α-chain helix, another example of Protein secondary structure]

A. α-Helix

– Several different polypeptide helices are found in nature, but the α-helix is the most common.

– It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outward from the central axis to avoid interfering sterically with each other (Figure 1).

Protein Secondary Structure

– A very diverse group of proteins contains α-helices.

– For example, the keratins are a family of closely related, fibrous proteins whose structure is nearly entirely α-helical.

– They are a major component of tissues such as hair and skin, and their rigidity is determined by the number of disulfide bonds between the constituent polypeptide chains.

– In contrast to keratin, myoglobin, whose structure is also highly α-helical, is a globular, flexible molecule.

(1) Hydrogen bonds

– An α-helix is stabilized by extensive hydrogen bonding between the peptide-bond carbonyl oxygens and amide hydrogens that are part of the polypeptide backbone (see Figure 1).

– The hydrogen bonds extend up and are parallel to the spiral from the carbonyl oxygen of one peptide bond to the – NH – group of a peptide linkage four residues ahead in the polypeptide.

– This ensures that all but the first and last peptide bond components are linked to each other through intrachain hydrogen bonds.

– Hydrogen bonds are individually weak, but they collectively serve to stabilize the helix.

(2) Amino acids per turn

– Each turn of an α-helix contains 3.6 amino acids.

– Thus, amino acid residues spaced three or four residues apart in the primary sequence are spatially close together when folded in the α-helix.

(3) Amino acids that disrupt an α-helix

– Proline disrupts an α-helix because its secondary amino group is not geometrically compatible with the right handed spiral of the α-helix.

– Instead, it inserts a kink in the chain, which interferes with the smooth, helical structure.

– Large numbers of charged amino acids (for example, gluta- mate, aspartate, histidine, lysine, or arginine) also disrupt the helix by forming ionic bonds, or by electrostatically repelling each other.

– Finally, amino acids with bulky side chains, such as tryptophan, or amino acids, such as valine or isoleucine, that branch at the β-carbon (the first carbon in the R-group, next to the α-carbon) can interfere with formation of the α-helix if they are present in large numbers.

B. β-Sheet

– The β-sheet is another form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding (Figure 2).

Protein Secondary Structure

– The surfaces of β-sheets appear “pleated,” and these structures are, therefore, often called “β pleated sheets.

– When illustrations are made of protein structure, β-strands are often visualized as broad arrows (Figure 2B).

(1) Comparison of a β-sheet and an α-helix

– Unlike the α-helix, β-sheets are composed of two or more peptide chains (β-strands), or segments of polypeptide chains, which are almost fully extended.

– Note also that in β-sheets the hydrogen bonds are perpendicular to the polypeptide backbone (see Figure 2A).

(2) Parallel and antiparallel sheets

– A β-sheet can be formed from two or more separate polypeptide chains or segments of polypeptide chains that are arranged either antiparallel to each other (with the N-terminal and C-terminal ends of the β-strands alternating as shown in Figure 2B), or parallel to each other (with all the N-termini of the β-strands together as shown in Figure 2C).

– When the hydrogen bonds are formed between the polypeptide backbones of separate polypeptide chains, they are termed interchain bonds.

– A β-sheet can also be formed by a single polypeptide chain folding back on itself (see Figure 2C). In this case, the hydrogen bonds are intrachain bonds.

– In globular proteins, β-sheets always have a right-handed curl, or twist, when viewed along the polypeptide backbone.

– [Note: Twisted β- sheets often form the core of globular proteins.]

C. β-Bends (reverse turns, β-turns)

– β-Bends reverse the direction of a polypeptide chain, helping it form a compact, globular shape.

– They are usually found on the surface of protein molecules, and often include charged residues.

– [Note: β-Bends were given this name because they often connect successive strands of antiparallel β-sheets.]

– β-Bends are generally composed of four amino acids, one of which may be proline—the amino acid that causes a “kink” in the polypeptide chain.

– Glycine, the amino acid with the smallest R-group, is also frequently found in β-bends.

– β-Bends are stabilized by the formation of hydrogen and ionic bonds.

D. Nonrepetitive secondary structure

– Approximately one half of an average globular protein is organized into repetitive structures, such as the α-helix and/or β-sheet.

– The remainder of the polypeptide chain is described as having a loop or coil conformation.

– These nonrepetitive secondary structures are not “random,” but rather simply have a less regular structure than those described above.

[Note: The term “random coil” refers to the disordered structure obtained when proteins are denatured.]

E. Supersecondary structures (motifs)

Globular proteins are constructed by combining secondary structural elements (α-helices, β sheets, nonrepetitive sequences).

– These form primarily the core region—that is, the interior of the molecule.

– They are connected by loop regions (for example, β-bends) at the surface of the protein.

– Supersecondary structures are usually produced by packing side chains from adjacent secondary structural elements close to each other.

– Thus, for example, α-helices and β-sheets that are adjacent in the amino acid sequence are also usually (but not always) adjacent in the final, folded protein.

– Some of the more common motifs are illustrated in Figure (3).

Protein Secondary Structure


  • Lehninger  Principles of Biochemistry / David L. Nelson, Michael M. Cox/ 7th ed, 2017.
  • Lippincott’s Illustrated Reviews: Biochemistry / Richard A. Harvey, Denise R. Ferrier/ 5th ed, 2011 / Lippincott Williams & Wilkins, USA.
  • Harper’s Illustrated Biochemistry /Robert K. Murray, David A. Bender , Kathleen M. Botham / 28th, 2009/ McGraw-Hill Companies, Inc. USA.

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