This is the term given to the overall three dimensional structure of the polypeptide, also written 3^o structure. This describes how the peptide chain folds so that sidechains are packed and organised. This may bring two sidechains which are distant, in terms of primary structure, close together. It also creates binding sites and other functional regions on the surface of the protein.

If we know the 3D structure of the protein, we can begin to understand how the protein works. If the protein comes from a bacterium or a virus, we can start to design drugs which affect the bacterial or viral form of the protein, and not the host (eukaryotic) form. If an animal is making a defective protein (as is the case in cystic fibrosis patients) then by using protein engineering and gene therapy, it may be possible to get the animal to start making the functional protein. All this leads to a new area of science called "Structural Biology".

There are 5 forces affecting the 3D shape of proteins. All of them build upon the framework started by the secondary structures.

Hydrophobic Interactions

Non-Polar/Hydrophobic/Aliphatic sidechains cannot hydrogen bond with water, hence the network of water is disrupted by them. This is avoided if the non-polar sidechains are removed or shielded from the water and buried in the interior of the protein. In this coiled coil structure note that the interior of the structure is occupied solely by hydrophobic residues (green sidechains).
Turn on rotation to get a better idea of the complete structure.

Hydrophobic interaction are a major driving force in protein folding. Hydrophobic interactions are also important in the formation of secondary structure elements such as a-helices and b-sheets. The peptide backbone is relatively hydrophillic because of the C=O and N-H groups of each peptide bond. However in the centre of the protein these tend to be in a hydrophobic environment. One way to reduce the hydrophilicity of the peptide backbone is to for hydrogen bonds between the peptide atoms. The a-helix and b-sheet are two structures which maximise the hydrogen bonding between the peptide bonds of the backbone and reduce its hydrophilicity.

Hydrogen Bonds

When unfolded, all polar/hydrophillic sidechains can interact via H-bonds with water. When the protein folds, they must H-bond to each other and exclude much of the water. All groups capable of forming a hydrogen bond MUST, hence H-bonding in the backbone (C=O to N-H) by way of helices and sheets is an efficient way of ensuring maximum H-bonding.

Sidechains can either accept (as in C=O) or donate (as in N-H, or O-H) an H-bond.

The capacity of proteins to form hydrogen bonds is an important determinant of protein stability. Hydrogen bonds can be between backbone groups, as in helices and sheets; between side chains, such as serine or threonine O-H groups and carbonyl carbons of side chains (-C=O); and between backbone groups and side chain groups.

Ion Pairs

When amino acid sidechains of opposite carge are in close proximity, they can form an ion pair (also called a salt bridge). But they are also capable of hydrogen bonding and hence, are usually found on the surface of the protein. If they can form a salt bridge, they will usually be buried. Since charge is affected by pH, so is the formation and the breakage of these ion pairs.

Salt bridges also increase the stability of the tertiary structure.

Hydrophobic interactions, hydrogen bonds and salt bridges are all non-covalent interactions

These are all relatively weak interactions but the large number in a protein combine to give the overall stability of the structure.

Disulphide Bonds

If two cysteine sidechains are close to one another and the local environment is conducive to oxidation,then they can form a disulphide bond/bridge as shown. The residues can either be in the same peptide chain (forming a loop) or in different chains.

As Disulphide bonds are covalent linkages they add considerably to the stability of proteins in which they occur. However they mainly occur in secreted proteins and in the parts of membrane proteins which face the outside.

Note that disuphide bridges only form after the protein has folded into its tertiary structure. This folding is driven by the combined energy of all of the weak interactions described in the previous section above.

Cysteine side chains in cytosolic proteins are usually found as -SH groups as the cytosolic environmemt is sufficiently reducing to prevent disulphides from forming.

NON-COVALENT BONDS

The tertiary structure of proteins is maintained by a host of weak, non-covalent interactions e.g.:

Hydrophobic Interactions
Hydrogen Bonds
Salt Bridges

Protein stability is a function of many weak interactions. If these interactions are maintained the protein keeps its tertiary ("native") stucture. However once the bonds maintaining the structure begin to be disrupted the tertiary structure is destroyed and the protein is said to be "denatured"

Proteins can be denatured easily via one or more methods outlined below.

Factors Which Can Denature A Protein
Heat: increase atomic vibrations, ruins interactions, need heat of >50^oC to denature most proteins.
pH: breaks the salt bridges.
Organic Solvents: disrupt hydrophobic interactions
Detergents: hydrophobic part pushes into protein core

Factors Which Can Denature A Protein
	Heat: increase atomic vibrations, ruins interactions, need heat of >50^oC to denature most proteins. pH: breaks the salt bridges. Organic Solvents: disrupt hydrophobic interactions Detergents: hydrophobic part pushes into protein core

When a protein is denatured, it loses it's 3D shape. When a protein is denatured, it loses it's biological activity. Therefore...

A PROTEINS TERTIARY STRUCTURE IS ESSENTIAL TO IT'S BIOLOGICAL ACTIVITY

EXAMPLES

These examples show how 2^o structure is used as a framework, and show the importance of hydrophobic interactions.

Myoglobin

This protein binds and stores oxygen in muscle. It consists of 153 amino acids, which fold into 8 a-helices of differing lengths.

The helices have non-polar sidechains on one side (green=Valine) and polar sidechains on the other (red = glutamate, lilac = histidine). They are described as "amphipathic" helices. It may be easier to see this if you look down the axis of the helix - the first one has been done for you but you will need to rotate the image to see the rest. All these helices arrange themselves so that all the hydrophobic sidechains are buried in the interior of the protein, while the polar ones contact the aqueous solution.

Ribonuclease

This protein hydrolyses RNA. It is made from 124 amino acids and folds into a b-sheet (3 b-strands) and 3 a-helices. Ribonuclease has several disulphide bonds stabilising its tertiary structure. Use the pop up menu in the structure frame to turn disulphide bridges on (in the "Options" SubMenu).

The helices are packed against the sheet so that non-polar sidechains are sandwiched between the two secondary structures.

You now have a pretty good idea about the way in which a protein folds. You should remember the driving forces and the other factors which influence a proteins secondary and tertiary shape, as well as how agents which disrupt the weak forces maintaining this structure can denature the protein.

However we still have one further level of protein structure to examine. This involves the way in which two or more protein chains interact in proteins which have several subunits.