Note: It is assumed that students will be already familiar with basic concepts of protein and nucleic acid structure, as well as enzyme kinetics and mechanisms, before using the Biochemistry of Metabolism educational web. A review of some elementary concepts relating to protein structure is provided here. For a more complete discussion see, e.g., Biochemistry by D. Voet & J. G. Voet, 3rd Ed, chapters 4, 7 & 8.
Key-words on this page:
primary structure,
secondary structure,
tertiary structure,
quaternary structure,
a-helix,
b-pleated
sheet,
amino acids,
peptide bond
Proteins are polymers of amino acids. Each amino acid has the same fundamental structure, differing only in the side-chain, designated the R-group. The carbon atom to which the amino group, carboxyl group, and side chain (R-group) are attached is the alpha carbon (Ca). |
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Structures of amino acids, with their R-groups in blue, are shown below with their three-letter and one-letter abbreviated names. Glycine has just a hydrogen atom in place of an R-group. At physiological pH, some amino acid R-groups are charged, because of dissociation or association of a proton by, e.g., a carboxyl or amino group. Note that histidine is shown charged, but its pK is close to the physiological range. Some side-chain groups that are uncharged at the near-neutral pH of the cytosol or extracellular space, may dissociate or gain a proton in the microenvironment of an enzyme active site.
| Peptide bonds link amino acid
residues within proteins. The sequence of covalently linked amino acids is
known as the primary structure of a
protein. The reaction by which two amino acids are joined in a peptide bond, with elimination of H2O, is represented at right. For detail on the mechanism of peptide bond formation, see the section on protein synthesis. |
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| A protein is a
polypeptide, a linear polymer of many amino acids, linked by peptide bonds.
The peptide linkages, along with the a-carbon atoms to which R-groups are attached, form the protein backbone, with sequence NCCNCCNCCNCC... |
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| Protein Secondary Structure. Segments of polypeptides often fold locally into stable structures that
include a-helices and b-pleated
sheets. a-Helix. In an a-helix (alpha helix), the polypeptide backbone follows a helical path. There are 3.6 amino acid residues per turn of the helix. Some protein domains assume other helical structures, but the a-helix is most common. |
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An a-helix is stabilized by hydrogen bonds between backbone amino and carbonyl groups and those in the next turn of the helix, represented as N-H····O=C. The hydrogen and oxygen atoms are attracted to one another because the H atom carries a partial positive charge and the O atom carries a partial negative charge, due to unequal sharing of electrons in N-H and O=C bonds. Diagram p. 224 of Voet & Voet text. |
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In an a-helix, the amino acid R-groups protrude out from the helically coiled polypeptide backbone. The surface of an a-helix largely consists of the R-groups of amino acid residues. At right, an a-helix is shown end-on and from the side. In this image, H atoms are not visible. Colors: C N O R-group |
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| Some amino acids have a greater tendency to be found within an a-helix. The amino acid proline tends to interrupt an a-helix. Its fused ring, which includes the a-carbon and the peptide-forming amino N, prevents the polypeptide backbone from assuming a conformation compatible with an a-helix in the vicinity of a proline. |  |
Explore below the structure of an a-helix, using MDL's software plug-in Chime. Note that with this data file hydrogen atoms will not be visible. For a tutorial on the Chime software, see Chime: How to use it , a website maintained by Eric Martz.
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Using the right mouse button, choose display backbone.
Identify atoms of the protein
backbone with sequence NCCNCCNCCNCC...
Question: Structures of individual
amino acids are given above. Based on the R-group structures,
identify each amino acid residue and
specify the sequence of amino acids in this peptide. Select protein - protein. Try other display options including spacefill-Van der Waals, and ribbons.
Questions: |
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Because of the tetrahedral nature of carbon bonds, a b-sheet is puckered, leading to the designation pleated sheet.
R groups of amino acids in a b-strand alternately point to one side or the other of a b-strand. Hence every other amino acid is exposed on one side or the other of a b-sheet.
| Explore at right two strands of a
b-sheet (Data file derived from
PDB 1ICM). Recommended displays: Display as
cartoon. Now change the display to ball & stick,
with color CPK. View the 2-stranded
b-sheet from the side. These two b-strands are actually part of a larger protein that you will explore below. |
| A common structural motif, the b-barrel,
is equivalent to a b-sheet that is rolled up to
form a cylinder. An example of a protein that consists mainly of a b-barrel is the bacterial channel
porin.
In some cases, a b-barrel may be partly flattened, to form what is called a b-clam structure (see below). |
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| Other common folding motifs involve combinations of a-helices and b-strands. One example is the a,b-barrel, explored elsewhere in an exercise on Triose Phosphate Isomerase (TIM). |  |
| Explore at right an intestinal fatty acid
binding protein (Data file PDB 1ICM, structure solved by J. C. Eads, J. C. Sacchettini, A. Kromminga,
& J. I Gordon in 1993.) Recommended displays: Display as cartoon, and color structure. Different colors distinguish the b-strands, a-helices and sharp turns called hairpin loops. Question: Would you describe the predominant structure as a b-sheet, b-barrel, or b-clam? To view the fatty acid, select
hetero-ligand and display as spacefill |
Tertiary protein structure refers to the complete three dimensional folding of a protein. Stabilization of a protein's tertiary structure may involve interactions between amino acids located far apart along the primary sequence. These may include:
Interactions with the aqueous solvent, known as the hydrophobic effect results in residues with non-polar side-chains typically being buried in the interior of a protein. Conversely, polar amino acid side-chains tend to on the surface of a protein where they are exposed to the aqueous milieu. There are, however, many exceptions in which polar residues are buried or non-polar residues exposed on the surface of a protein. Such atypical locations might be stabilized, e.g., by interaction of amino acid side-chains with enzyme prosthetic groups or other ligands, by interactions between amino acid side-chains, or by association of proteins with lipid membranes, etc.
| Many proteins have a modular design with multiple distinct domains resulting from gene fusion events during evolution. A domain with a particular structure and function may be part of the structure of several otherwise distinct proteins. For example, an enzyme's primary structure may include a segment that folds to produce an active site with particular catalytic activity, plus other segments that may mediate regulation of the enzyme or binding of the enzyme to a membrane. |  |
| Quaternary protein structure
refers to the regular association of two or more polypeptide chains to form a
complex. A multi-subunit protein may be composed of two or more identical
polypeptides, or it may include different polypeptides. Quaternary structure
tends to be stabilized mainly by weak interactions between residues exposed on surfaces
polypeptides within a complex.
A multimeric complex may be important to enzyme activity, e.g., in cases in which an active site is formed by residues from more than one polypeptide subunit, or when adjacent active sites may be involved sequentially in catalysis of a complex reaction. Regulation of functional activity may involve cooperative interactions among protein subunits in a complex. Examples of these are included throughout this web. |
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Copyright © 2003 by Joyce J. Diwan. All rights reserved.
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