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Tertiary Structure

Tertiary structure refers to the three-dimensional structure of the entire polypeptide chain.

Primary structure Secondary structure Quaternary structure

The images (courtesy of Dr. D. R. Davies) represent the tertiary structure of the antigen-binding portion of an antibody molecule. Each circle represents an alpha carbon in one of the two polypeptide chains that make up this protein. (The filled circles at the top are amino acids that bind to the antigen.) Most of the secondary structure of this protein consists of beta conformation, which is particularly easy to see on the right side of the image.

Do try to fuse these two images into a stereoscopic (3D) view. I find that it works best when my eyes are about 18" from the screen and I try to relax so that my eyes are directed at a point behind the screen.

Where the entire protein or parts of a protein are exposed to water (e.g., in blood or the cytosol), hydrophilic R groups — including R groups with sugars attached [Link] — are found at the surface; hydrophobic R groups are buried in the interior.

Tertiary structure is important!

The function of a protein (except as food) depends on its tertiary structure. If this is disrupted, the protein is said to be denatured [Discussion], and it loses its activity. Examples: A mutation in the gene encoding a protein is a frequent cause of altered tertiary structure. The many hydrogen bonds that can form between the polypeptide backbones in the beta conformation suggests that this is a stable secondary structure potentially available to many proteins and so a tendency to form insoluble aggregates is as well. Avoidance of amyloid formation may account for the large investment in the cell in as well as the crucial importance of particular amino acid side chains in maintaining a globular, and hence soluble, tertiary structure.

Protein Domains

The tertiary structure of many proteins is built from several domains.

Often each domain has a separate function to perform for the protein, such as:

In some (but not all) cases, each domain in a protein is encoded by a separate exon in the gene encoding that protein.

In the histocompatibility molecule shown here ,

This image (courtesy of P. J. Bjorkman from Nature 329:506, 1987) is a schematic representation of the extracellular portion of HLA-A2, a human class I histocompatibility molecule. It also illustrates two common examples of secondary structure: the stretches of beta conformation are represented by the broad green arrows (pointing N -> C terminal); regions of alpha helix are shown as helical ribbons. The pairs of purple spheres represent the disulfide bridges.

A correspondence between exons and domains is more likely to be seen in recently-evolved proteins. Presumably, "exon shuffling" during evolution has enabled organisms to manufacture new proteins, with new functions, by adding exons from other parts of the genome to encode new domains (rather like Lego® pieces). [Link to gene duplication]

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31 August 2013