Secondary structure:

The local conformations of the polypeptide chain resulting from intra-chain hydrogen bonding and short range interactions of the -R groups. Hydrogen bonding of amide groups play a major role.

alpha-helix: a structure formed when the polypeptide chain coils along an imaginary central axis and is stabilized by hydrogen bonding between amide groups spaced four residues apart (each amide oxygen hydrogen bonds with the amide -NH- four residues away toward the C-terminus). The R groups stick out of the helix, away from the center. The helix is right-handed for L-amino acids; otherwise the R-groups would be inside and cause steric hindrance. Each residue causes a rise of about 0.15 nm along the central axis. Each turn from one point on the helix to the equivalent point on the next loop involves about 3.6 residues and results in a pitch of about 0.54 nm. Because of differential distribution of residues, the two sides or faces of an alpha helix can be different in polarity, or charge with respect to each other. There are other helical structures, but they are less common than the alpha-helix.

What affects alpha-helix stability?

• Proline residues--proline is the one amino acid without a primary alpha-amine (it is actually an immino acid). Because there is not free rotation about an amide formed with the proline immino group, it puts a kink (called a beta-turn) in the alpha-helix and disrupts it.
• Clustered (+) and (-) R-groups of the same charge will cause electrostatic repulsion and break up the structure. Clustered pairs of opposite charge can stabilize the helix. Examples: poly-Glu versus poly-(Glu-Lys)
• Clustered groups of hydrophobic residues can interact positively with one another and stabilize.
• Neighboring bulky R-groups cause steric hindrance which may not allow helix formation or cause the helix to bend. Adjacent Gly residues will help accommodate bulky groups.
• Gly residues may make the helix too flexible to be stable.

Because the amino acid side-chains stick out from the sides of the alpha-helix, they can greatly affect the surface properties of the helix. It is possible for a helix to have an assymetric distribution of polar and nonpolar residues resulting in a hydrophobic side and a hydrophilic side.

beta sheets:

If two sections of chain run alongside one another, they can hydrogen bond to one another. The resulting 3-D effect is like a ruffled potato chip. If two strands in a beta-sheet are both running N-->C terminal in the same direction, they are parallel to each other. If two strands are running N-->C in opposite directions, they are anti-parallel to each other. Many of the same factors which will stabilize or destabilize an alpha-helix will also affect a beta-sheet. Anti-parallel beta-sheets are more stable when formed from only two or several strands; parallel beta-sheets have a slightly weaker hydrogen bonding of amides and tend to require that more chains participate in the beta-sheet for stability. Also parallel beta-sheets tend to distribute nonpolar residues on both sides and are therefore usually found in internal structures.

Beta-sheets can contain irregularities in hydrogen bonding that cause minor kinks called beta-bulges. Arrays of beta-sheets often form a right-handed twist.

Tertiary structure:

Focus on the 3-D structure of the polypeptide chain in globular proteins. Secondary structures like alpha-helices and beta-sheets are held in place by connecting loops or bends. Much of the interior of globular proteins are helix and sheet because it is a hydrophobic environment and the amide bonds in the polypeptide backbone must be hydrogen bonded to satisfy their polarity. These loops and bends are part of the 3°-structure, but result from information encoded in the 1°-structure. Loops and bends are

1. External (usually) and usually not hydrophobic.

2. Often contain proline (causing beta-turns) and glycine residues.

The structures seen in the book are derived from X-ray crystallography data and represent average structures. Many proteins spontaneously assume these native 3°-structures. Some proteins need other proteins to help them fold into the native 3°-structure. A protein that is not in the native conformation is said to be denatured.

Stabilizing the native conformation. The folding of a polypeptide or protein in 3-D usually involves stabilization of associations between residues not adjacent to one another in the 1°-structure. Stabilization can involve:

Cys-Cys (Cystine) covalent bonds 2 Cysteine

disulfide

R1-S-S-R2 (oxidized)

Two common reductants used in biochem labs are 2-mercaptoethanol and dithiothreitol

Non-covalent associations
     ion pairs     R1-COO-  . . .  +H3N-R2
     salt bridges R1-COO-  . . .  Mg2+ . . .-OOC-R2
     hydrogen bonding     R-OH . . . O=C-R2

The environment outside and inside the protein can be very different. Polar residues tend to be on the outside of the protein. These interact with water and make proteins soluble. If you look at a space filling picture of a protein you can see that there is not really room inside for water. The inside of most proteins contains hydrophobic residues. These hydrophobic residues are shielded from water. This may result in one face of an alpha helix being hydrophobic, whereas the other face may contain polar residues. Parallel beta-sheets tend to have hydrophobic R-groups on both sides and have to be shielded (i.e., require another structure between the sheet and the solvent). Antiparallel beta-sheets tend to have hydrophobic residues on only one side and don't require shielding.

If a protein is denatured, these residues are exposed to water and solubility is decreased. Because of the exposed hydrophobic residues, high concentrations of denatured proteins tend to aggregate (e.g. hard boiled egg) or collect at an air-water interface (froth on cappuccino)

Click on 'Proteins' in the left box and then view the relevant sections covering primary, secondary, tertiary and quaternary structure. Protein structure.

• Protein Structure [local] describing the various levels of protein structure.
• Protein Structure [local]
• Protein Structure [local]

Three lessons on protein structure using the Chime plug-in

• Lesson 1 [local]
• Lesson 2 [local]
• Lesson 3 [local]

Another Chime-based tutorial [local]

A chime view of alpha-helix and beta-sheet [local]

If you can't get the Chime plug-in to work, you can download a program called Mage from this site. In addition to the Mage program, you will want to download a series of files called Protein Tourist which have protein structure files to be viewed with Mage.

You can also download your own protein database files from several sources on the web.

Molecules To Go is a searchable database of protein structures that will let you download the structural files for viewers like RasMol.

The National Institutes of Health has a portal named Entrez where you can access and download protein structure files for viewers like RasMol and Cn3D.

Some major classifications of tertiary structure

antiparallel alpha-helix proteins

parallel or mixed beta-sheet proteins (both faces of sheet have nonpolar residues)

beta-sheet proteins

beta-barrel proteins

doubly-wound parallel beta-sheet

antiparallel beta-sheet proteins (only one face usually has hydrohobic residues)

disulfide-rich/metal rich

Quaternary structure:

The assembly of multiple polypeptide chains into specific and discrete structures. When two or more polypeptide chains form a stable association, the individual polypeptides are called subunits. The whole complex is called a protein, holoprotein, holocomplex or oligomer. A protein with 2 subunits is a dimer. A protein with 3 subunits is called a trimer. A protein with 2 identical subunits (alpha₂) is a homodimer, whereas a protein with 2 different subunits (alpha-beta) is a heterodimer.

In addition to associations of different polypeptides, some proteins bind small organic molecules or metals necessary for function. The organic molecule or metal is called a cofactor. The protein plus cofactor complex is called the holoprotein, whereas the protein without the cofactor is called the apoprotein. A cofactor that is very tightly bound to an apoprotein is sometimes termed a prosthetic group.

The following links are to the Entrez files for the indicated proteins that illustrate particular aspects of secondary, tertiary or quaternary structure.