The primary and secondary structures of protein show the structure of a protein, whether it is alpha helical or beta staggered conformation, showing that it draws its strength from inter-poly peptide hydrogen bonding. In an aqueous solution, water can easily compete for these hydrogen bonding sites on an Î±-helical backbone. This ruptures the internal bonds of a protein, and protein assumes a completely random configuration with this disruption of its bonds. Experimentally, though, it is seen that protein still maintains the helical shape even in an aqueous solution. This proves that apart from the normal secondary structure, there are certain factors, which maintains the definite geometrical shape of a protein.
The characteristic three-dimensional shape resulting from the precise folding and bending of the helical coil, is termed as the tertiary structure of a protein.
Various linkages are responsible for the tertiary structure of protein. These depend on the nature of the amino acid side chain in the protein molecule.a. Salt linkages or ionic bonds between positively and negatively charged groups present in the side chains-
Example: -CO2 - and -NH3 + groups.
b. Hydrogen bonding.
c. Disulphide linkage, example - as in -CH2-S-S-CH2-
d. Hydrophobic Interactions: Non -covalent hydrophobic forces are important not only because they are very strong but because there are so many of them.
- The protein or peptide tertiary structure is in respect with the folding of the respective chain. The manner in which the chain is folded is responsible for both the protein physical properties and also its biological function.
- The structural proteins, namely as those which are present in hair, tendons, wool, and silk, might have either the helical secondary or secondary pleated sheet structures. These are typically shaoed elongated with a chain length more than many times of the helical chain's diameter. These are classified as fibrous proteins and due to their structural form are insoluble in water.
- Most of other proteins, like enzymes, are active in the aqueous medium; while some of these are soluble, the rest get dispersed as colloids. This type of proteins are called the globular proteins which are spherical in shape.
- A typical protein such as carboxy peptidase A , incorporates elements of a number of secondary structures, some segments are helical, others, pleated sheet, and still others correspond to no simple description.
- The shape of a large protein is influenced by many factors, including its primary and secondary structure. Carboxy peptidase A has Zn2+ ion, which is very much required to the enzymes catalytic, and the presence of this enzyme effects the tertiary structure.
- The Zn2+ ion lies near the center of the enzyme, and from there this is coordinated to the imidazole 'N' nitrogen of the 02 histidine residues along with the carboxylate side chain of Glutamine-72.
The Protein tertiary structure also gets affected by factors of the environment. A globular protein within water goes for a shape that has hydrophobic groups towards the interior side, and the polar groups right on the surface. The globular protein gets solvated by the water molecules. Around 65% of the mass of most of the cells is water, while the proteins present in these cells are found to be in native state or the tertiary structure in which they express their biological activity.The protein tertiary structure are usually disrupted by the addition of substances that causes the unfolding of the protein chain, leading to the denaturation of protein and the protein loses most of its activity.
Determination of Tertiary Structure of Protein
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Tertiary structure may be determined by X- ray analysis, light-scattering, diffusion, viscosity determination, ultra centrifuge method and electron microscopy. Most protein tertiary structures are determined by X-ray crystallography. The structure of Myoglobin was the first tertiary structure to be determined using this technique.
Determination of structure of Myoglobin
Myoglobin is a small, oxygen binding heme protein present in the muscles. The structure of myoglobin was elucidated by X-ray diffraction method. Myoglobin molecule has a total of 153 amino acid residues in one single strand and a single prosthetic iron-porphyrin (or heme) group, identical with that of hemoglobin. Mammals like whale, seal and porpoise have muscles rich in protein and contains abundant amount of myoglobin. The heme group is responsible for the deep brown color of myoglobin.
The function of myoglobin is to bind oxygen in the muscles and to enhance its transport to the mitochondria, which consume oxygen during respiration. The features of Myoglobin, as per the X-ray studies were as follows.
- Myoglobin is very compact in nature and it can accommodate only 4 water molecules because of its closely packed structure.
- All the polar R groups of the molecule, except two, are located on its outer surface and all of them are hydrated.
- Myoglobin has a backbone made up of eight almost straight alpha helical segments, designated from the N-terminus as A through H.
- The peptide bonds of myoglobin is planar, with the carbonyl and amide groups being trans to each other.
The three levels of protein structure can be disrupted by the application of an external force, such as heating, coming in contact with solvents like alcohol, chloroform, etc. This disruption is termed as denaturation.
Denaturation of a protein molecule within the body of an organism can stop all the protein activity, thereby causing problems to the normal functioning of it. Examples of denaturation is the boiling of an egg. The egg albumin becomes hardened, and loses its structure, on heating.
There are some proteins , whose structure is a mere aggregate of polypeptide sub-units. Thus, the Quaternary structure of a protein is the manner in which various separate polypeptide chains fit together in these proteins containing more than one chain. A fourth degree of complexity in protein structure, the quaternary structure, is of great importance in many proteins. Each peptide chain in such a protein is called a sub unit.
Quaternary structure can be referred to as the spatial arrangement of these sub-units and the nature of bonding between them.
In globular proteins e.g, hemoglobin the polypeptide chains consist
partly of helical sections which are folded about the random cuts to
give it a spherical shape. The primary, secondary and tertiary and
quaternary levels of hemoglobin structure are given in figure below.