Structural Organisation of Proteins
Proteins are organised into primary structure, secondary structure, tertiary structure and quaternary structure. Linear sequence of covalently linked amino acids is called primary structure
(A) Different part of amino acids undergo conformational changes (such as alpha helices, beta- sheets) forming secondary structure
(B) These structural elements are packed into domains i.e. several compact globular units called tertiary structure
(C) Two or more independent polypeptides interact and linked by non- covalent bonds to form a multisteric protein. This association of protein gives rise to quaternary structure
(D) The mechanism of protein folding of linear chain or polypeptide to give special shape is caused by forces present on amino acids. On this basis amino acids have been put into three categories: (i) hydrophobic (leucin, tryptophan), (ii) charged (aspartate, lysine) and (iii) polar (glutamate, serine) amino acids. Some of these interactions are discussed below:
(a) Non-covalent Interaction:
A chemical bond which involves sharing of electron pairs is called covalent bond. On the other hand the bond formed between two charged groups is called non-covalent bond.
In aqueous solution the non-covalent interaction among biomolecules are weak. Proteins are organised into specific structures due to non-covalent interaction. Interactions between antigen and antibody depend on these four types of non-covalent forces. There are four types of non-covalent interactions.
(i) Hydrogen Bonds:
The two electronegative atoms e.g. O and N share their one of the hydrogen atoms. Thus they form hydrogen bond. The O and N nucleus attracts electrons more strongly than H nucleus (proton).
Therefore, sharing of electrons between H and O or N is unequal. The O atom bears partial negative charge (28") and H atom a partial positive charge (8+). This results in electrostatic attraction between
H atoms of one molecules and O or N atom of the other, and formation of hydrogen bond. The hydrogen bonds are strongest when the nuclei of H atom and the two other atoms sharing this bond are in a straight line i.e. linearly arranged.
(ii) Ionic Interactions:
The oppositely charged groups of a molecule form ionic bond. For example, the positively charged amino (-NH3 +) side groups of lysine and arginine, and the negatively charged carboxyl group (-COO) of aspartate and glutamate form ionic bonds.
The strength of ionic bondsis similar to covalent bonds. When treated with water the strength of ionic bonds is drastically reduced. This is caused due to dielectric strength (insulating property) of water.
(iii) Hydrophobic Interactions:
The best examples to study hydrophobic interaction are the mixing of water with benzene, hexane or oil. Two phases are formed. No liquid is soluble in water. They are unable to undergo favourable interactions with water molecules, and interfere with the hydrogen bonding among water molecules.
In aqueous solution all molecules or ions interfere with hydrogen bonding of some water molecules in their immediate vicinity. But polar or charged solutes (e.g. NaCl)
Compensate for lost water-water hydrogen bonds by forming new solute-water interactions. The net charge in enthalpy (AH) for dissolving these solutes is generally small. The hydrophobic solutes offer no such compensation.
When hydrophobic compounds are dissolved in water entropy decreases slightly. Water molecules in the immediate vicinity of non-polar (uncharged) solutes are constrained in their possible orientations.
They form a highly ordered cage like shell around each molecule of solute. The ordering of water molecules reduces entropy which in turn is proportional to the surface area of the hydrophobic solute enclosed within the cage of water molecules.
On the other hand, amphipathic compounds contain polar (charged) and non-polar (uncharged) regions. When the amphipathic compound is mixed with water, the polar region interacts with solvent and tends to dissolve.
But the non-polar regions avoid to contact with the water. These structures are stable in water and are called micelles. The forces that hold the non-polar regions of the molecules together are called hydrophobic interactions.
(iv) Van der Waals Interactions:
When two uncharged atoms are placed together, their surrounding electron clouds influence each other resulting in attraction of molecules.
This weak interatomic interaction is called the 'Van der Waals interactions' or radius i.e. the region of electron clouds. As the two nuclei come closer their electron clouds begin to repel each other.
All the points when the Van der Waals attraction balances these repulsive forces, the nuclei are said to be in Van der Waals contact.