Secondary Protein Structure

Submitted by ChemPRIME Staff on Thu, 12/16/2010 - 16:24

One might expect a long-chain proteinA biological polymer of amino acids joined by peptide bonds. moleculeA set of atoms joined by covalent bonds and having no net charge. to be rather floppy, adopting a variety of molecular shapes and changing rapidly from one conformationIn an ion or molecule, one of many spatial arrangements of atoms that differ by rotation about single bonds, but that do not differ in which atoms are attached to each other. to another. In practice this seldom happens. Instead the protein chain stays more or less in the same conformation all the time. It is held in this shape by the cooperative effect of a large number of hydrogen bonds between different segments of the chain.

Figure 1 Ball-and-stick model of the α helix. Hydrogen bonds are shown as dotted bonds. Note that R groups extend almost perpendicular from the axis.

A particularly important conformation of the polypeptideA polymer of many amino acids joined by amide linkages or "peptide bonds." chain is the spiral structure shown in Fig. 1. This is called an α helix. Many fibrous proteins like hair, skin, and nails consist almost entirely of α helices. In globular proteins too, although the overall structure is more complexA central metal and the ligands surrounding it; also called coordination complex., short lengths of the chain often have this configurationThe 3-D arrangement of atoms about a chiral center in a molecule.. In an a helix the polypeptide chain is twisted into a right-hand spiral—the chain turns around clockwise as one moves along it. The spiral is held together by hydrogen bonds from the amido (Image:Chapter 20 page 21text.jpg) group of one peptide bondThe amide linkage that joins the carboxylic acid end of one amino acid with the amine end of another amino acid to form a peptide or protein. to the carbonylThe functional group consisting of a carbon atom doubly bonded to an oxygen atom; found in aldehydes and ketones. group Image:Chapter 20 page 22text1.jpg of a peptide bond three residues farther along the chain. Two factors contribute toward making this a particularly stable structure. One is the involvement of all the Image:Chapter 20 page 22text2.jpg and Image:Chapter 20 page 22text1.jpg groups in the chain in the hydrogen bonding. Spirals with slightly more or slightly less twist do not permit this. The second factor is the way in which the side chains project outward from an α helix. Bulky side chains therefore do not interfere with the hydrogen bonding, enabling a fairly rigid cylinder to be formed.

Figure 2 The β keratin, pleated-sheet structure. (a) Edge view; rotating by 90° gives (b) the top view. (Hydrogen bonds are shown as dotted bonds.)

A second regular arrangement of the polypeptide chain is the β sheet, the β-keratin structure found in silk and shown in Fig. 2. As in the α helix, this structure allows all the amido and carbonyl groups to participate in hydrogen bonds. This hydrogen bonding structure can be accomplished in two manners, either a parallel or antiparallel β sheet, which are compared in Fig. 3. Unlike the α helix, though, the side chains are squeezed rather close together in a pleated-sheet arrangement. In consequence very bulky side chains make the structure unstable. This explains why silk is composed almost entirely of glycine, alanine, and serine, the three amino acids with the smallest side chains. Most other proteins contain a much more haphazard collection of amino acid residues.

Figure 3 The parallel and antiparallel β sheet structures. In the parallel β sheet, the chains are oriented in the same direction, in terms of amino and carboxyl terminals. The aniparallel β sheet has adjacent chains oriented in opposite directions in terms of amino and carboxyl terminals. R groups are not included in this diagram, but would be coming out and into the screen if present.