Tertiary Structure

Tertiary structure is the folding of units of secondary structures, alpha helices and beta sheets, into a more compact form.

Tertiary structure can vary from all helix to all beta sheet, with varying amounts of irregular structure.

Patterns of folding:

1. proteins have a defined inside (predominantly hydrophobic) and an outside (predominantly hydrophilic)

2. beta sheets are usually twisted into what are called barrel structures because they look like staves in barrel

3. beta sheets have turns called beta turns, these consist of three amino acids in a hairpin turn with H-bonding; alpha helices have proline residues at turns

4. proteins have other structures besides alpha helices, beta sheets and turns, these are called irregularly structured regions

5. some protein folding is dominated by prosthetic group, for example, in myoglobin helices act to cage the heme group

Thermodynamics of folding:

Central Dogma of protein chemistry: Amino acid sequence determines the 3-D structure of proteins. Recent studies, however, have indicated that heat shock proteins and chaperonins are required for the successful folding of some proteins.

Evidence for the central dogma: A protein can be denatured to a random coil by heating, pH change, etc. When these conditions are reversed, the native structure of the protein can often reform.

Thermodynamic analysis begins with the consideration of the Gibbs free energy equation:

G = H - TS

For any chemical process to occur, G must be negative. Let us examine the chemical changes that occur during protein folding and the thermodynamic implications of these changes.

Enthalpy (H) contributions:

1. electrostatic interactions can occur between charged amino acid side chains to form what are called salt bridges; their formation is pH-dependent.

2. amino acid can form internal hydrogen bonds as in alpha helices and beta sheets

3. van der Waals interactions

The sum of all of these weak interactions is significant and forms the basis of all polymer physical chemistry.

Entropy (S) and the Hydrophobic Effect:

There are many random arrangements of any given sequence of amino acids; there is only one active configuration. Therefore, for the polypeptide chain, folding results in a large decrease in its entropy.

This change in entropy is partially balanced by the hydrophobic effect. When hydrocarbons are exposed to water, they cause the water around them to organize into cage-like structures.

If hydrocarbon residues (like the side chains of hydrophobic amino acids) are withdrawn from an aqueous environment to the inside of a protein where there are other hydrocarbon side chains, the entropy of the water increases.

Summary:

a. folding is unfavorable in regard to polypeptide entropy
b. it is favorable in interaction energy (the three above)
c. it is favorable in water entropy (hydrophobic effect)

Protein folded structure is fragile due to the small overall energy of stabilization of the native structure over that of a random coil, and, in the laboratory, they must be handled with care.

Disulfide bonds:

After protein folding is complete, disulfide bonds may form if two cysteine side chain residues are near each other; these bonds further stabilize the native structure.

Motion in proteins:

There are several levels of motion in proteins: vibrations, small concerted motions of helices and sheets, and motions of whole domains. These motions are important in binding and catalysis.

Prediction of structure:

Secondary structure:

There are some fairly effective guidelines for predicting secondary structure from an amino acid sequence. These are listed below:

helix stable = Ala, Cys, Leu, Met, Glu, Gln, His, Lys
helix breakers = Pro, HO-Pro (part of collagen)
beta sheet = Val, Ile, Phe, Tyr, Trp, Thr,
favor turns = Gly, Ser, Asp, Asn, Pro

Tertiary structure:

Biochemists (now often called structural biologists) have not had much luck predicting complete protein structures based on amino acid sequences, which depend strongly on tertiary structure. They have, however, studied the problem intensively and have developed sophisticated computer programs that run on super computers. A solution to this problem is quite important because it would allow the large DNA sequence databases to be connected to protein 3-D structure, which would allow more informed guesses as to a biological function of a given sequence of DNA.

Quaternary structure:

Quaternary structure is the aggregation of more than one polypeptide chain to form multi-subunit proteins

This aggregation can take a variety of forms such as a string, as in actin, or a ring as in glutamine synthetase, in addition to more standard types of crystal packing.